diff --git a/docs/Windup-Core-Development-Guide.adoc b/docs/Windup-Core-Development-Guide.adoc
index 7ea4c9abfa..0b8bbedb39 100644
--- a/docs/Windup-Core-Development-Guide.adoc
+++ b/docs/Windup-Core-Development-Guide.adoc
@@ -1,7 +1,10 @@
 = Windup Core Development Guide
 
-:toc:
-:toclevels: 4
+:toc: left
+:toclevels: 5
+:sectnumlevels: 5
+:numbered:
+
 
 == Overview
 
diff --git a/docs/Windup-Rules-Development-Guide.adoc b/docs/Windup-Rules-Development-Guide.adoc
index ada2632d95..b607f2e72d 100644
--- a/docs/Windup-Rules-Development-Guide.adoc
+++ b/docs/Windup-Rules-Development-Guide.adoc
@@ -1,7 +1,9 @@
 = Windup Rules Development Guide
 
-:toc:
-:toclevels: 4
+:toc: left
+:toclevels: 5
+:sectnumlevels: 5
+:numbered:
 
 
 == Overview
diff --git a/docs/Windup-User-Guide.adoc b/docs/Windup-User-Guide.adoc
index 950471e2ec..9b4d3983d1 100644
--- a/docs/Windup-User-Guide.adoc
+++ b/docs/Windup-User-Guide.adoc
@@ -1,7 +1,9 @@
 = Windup User Guide
 
-:toc:
-:toclevels: 4
+:toc: left
+:toclevels: 5
+:sectnumlevels: 5
+:numbered:
 
 
 == Overview
diff --git a/html/WindupCoreDevelopmentGuide.html b/html/WindupCoreDevelopmentGuide.html
index 421aeeb44b..92a3f51680 100644
--- a/html/WindupCoreDevelopmentGuide.html
+++ b/html/WindupCoreDevelopmentGuide.html
@@ -415,99 +415,99 @@ <h1>Windup Core Development Guide</h1>
 <div id="toc" class="toc">
 <div id="toctitle">Table of Contents</div>
 <ul class="sectlevel1">
-<li><a href="#_overview">Overview</a>
+<li><a href="#_overview">1. Overview</a>
 <ul class="sectlevel2">
-<li><a href="#What-is-Windup">What is Windup?</a></li>
-<li><a href="#Features-of-Windup-2.0">Features of Windup 2.0</a></li>
-<li><a href="#Get-Involved">Get Involved</a></li>
-<li><a href="#Report-Issues-with-Windup">Report Issues with Windup</a></li>
+<li><a href="#What-is-Windup">1.1. What is Windup?</a></li>
+<li><a href="#Features-of-Windup-2.0">1.2. Features of Windup 2.0</a></li>
+<li><a href="#Get-Involved">1.3. Get Involved</a></li>
+<li><a href="#Report-Issues-with-Windup">1.4. Report Issues with Windup</a></li>
 </ul>
 </li>
-<li><a href="#_developer_contributing_information">Developer Contributing Information</a>
+<li><a href="#_developer_contributing_information">2. Developer Contributing Information</a>
 <ul class="sectlevel2">
-<li><a href="#Dev-Development-Guidelines">Development Guidelines</a></li>
-<li><a href="#Dev-Submit-Code-Updates-to-the-Windup-Project">Submit Code Updates to the Windup Project</a></li>
+<li><a href="#Dev-Development-Guidelines">2.1. Development Guidelines</a></li>
+<li><a href="#Dev-Submit-Code-Updates-to-the-Windup-Project">2.2. Submit Code Updates to the Windup Project</a></li>
 </ul>
 </li>
-<li><a href="#_understand_the_windup_architecture_and_structure">Understand the Windup Architecture and Structure</a>
+<li><a href="#_understand_the_windup_architecture_and_structure">3. Understand the Windup Architecture and Structure</a>
 <ul class="sectlevel2">
-<li><a href="#Windup-Architectural-Components">Windup Architectural Components</a></li>
-<li><a href="#Dev-Windup-Project-Structure">Windup Project Structure</a></li>
+<li><a href="#Windup-Architectural-Components">3.1. Windup Architectural Components</a></li>
+<li><a href="#Dev-Windup-Project-Structure">3.2. Windup Project Structure</a></li>
 </ul>
 </li>
-<li><a href="#_get_started">Get Started</a>
+<li><a href="#_get_started">4. Get Started</a>
 <ul class="sectlevel2">
-<li><a href="#Install-and-Configure-Maven">Install and Configure Maven</a></li>
-<li><a href="#Dev-Build-Windup-from-Source">Build Windup from Source</a></li>
-<li><a href="#Dev-Execute-Windup-Built-from-Source">Execute Windup (Built from Windup Source)</a></li>
-<li><a href="#Execute-Windup">Execute Windup</a></li>
-<li><a href="#Review-the-Report">Review the Report</a></li>
+<li><a href="#Install-and-Configure-Maven">4.1. Install and Configure Maven</a></li>
+<li><a href="#Dev-Build-Windup-from-Source">4.2. Build Windup from Source</a></li>
+<li><a href="#Dev-Execute-Windup-Built-from-Source">4.3. Execute Windup (Built from Windup Source)</a></li>
+<li><a href="#Execute-Windup">4.4. Execute Windup</a></li>
+<li><a href="#Review-the-Report">4.5. Review the Report</a></li>
 </ul>
 </li>
-<li><a href="#_rules_and_rulesets">Rules and Rulesets</a>
+<li><a href="#_rules_and_rulesets">5. Rules and Rulesets</a>
 <ul class="sectlevel2">
-<li><a href="#Windup-Processing-Overview">Windup Processing Overview</a></li>
-<li><a href="#Rules-Rule-Execution-Lifecycle">Rule Execution Lifecycle</a></li>
-<li><a href="#Rules-Rule-Story-Points">Rule Story Points</a></li>
+<li><a href="#Windup-Processing-Overview">5.1. Windup Processing Overview</a></li>
+<li><a href="#Rules-Rule-Execution-Lifecycle">5.2. Rule Execution Lifecycle</a></li>
+<li><a href="#Rules-Rule-Story-Points">5.3. Rule Story Points</a></li>
 </ul>
 </li>
-<li><a href="#_create_and_test_java_rule_add_ons">Create and Test Java Rule Add-ons</a>
+<li><a href="#_create_and_test_java_rule_add_ons">6. Create and Test Java Rule Add-ons</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Java-based-Rule-Structure">Java-based Rule Structure</a></li>
-<li><a href="#Rules-Basic-Rule-Execution-Flow-Patterns">Basic Rule Execution Flow Patterns</a></li>
-<li><a href="#Rules-Create-a-Basic-Java-based-Rule-Add-on">Create a Basic Java-based Rule Add-on</a></li>
+<li><a href="#Rules-Java-based-Rule-Structure">6.1. Java-based Rule Structure</a></li>
+<li><a href="#Rules-Basic-Rule-Execution-Flow-Patterns">6.2. Basic Rule Execution Flow Patterns</a></li>
+<li><a href="#Rules-Create-a-Basic-Java-based-Rule-Add-on">6.3. Create a Basic Java-based Rule Add-on</a></li>
 </ul>
 </li>
-<li><a href="#_create_and_test_xml_rules">Create and Test XML Rules</a>
+<li><a href="#_create_and_test_xml_rules">7. Create and Test XML Rules</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Create-a-Basic-XML-Rule">Create a Basic XML Rule</a></li>
+<li><a href="#Rules-Create-a-Basic-XML-Rule">7.1. Create a Basic XML Rule</a></li>
 </ul>
 </li>
-<li><a href="#_core_developer_topics">Core Developer topics</a>
+<li><a href="#_core_developer_topics">8. Core Developer topics</a>
 <ul class="sectlevel2">
-<li><a href="#Dev-Windup-Bootstrap">Windup Bootstrap</a></li>
-<li><a href="#Dev-Classloading-Notes">Classloading Notes</a></li>
-<li><a href="#Dev-Connect-to-the-Graph-via-Rexster">Connect to the Graph via Rexster</a></li>
-<li><a href="#Dev-Decompiling">Decompiling</a></li>
-<li><a href="#Dev-Dependencies">Dependencies (Forge add-ons)</a></li>
-<li><a href="#Dev-Frames-Extensions">Frames Extensions</a></li>
-<li><a href="#Dev-Internal-API-Features">Internal API Features</a></li>
-<li><a href="#Dev-Logging">Logging</a></li>
-<li><a href="#Dev-Variables-Stack">Variables Stack</a></li>
-<li><a href="#Dev-Port-WindRide-Functionality-to-Windup">Port WindRide Functionality to Windup</a></li>
-<li><a href="#some-classes-mapping">Some classes mapping</a></li>
-<li><a href="#server-side-code-to-be-moved">Server-side code to be moved</a></li>
+<li><a href="#Dev-Windup-Bootstrap">8.1. Windup Bootstrap</a></li>
+<li><a href="#Dev-Classloading-Notes">8.2. Classloading Notes</a></li>
+<li><a href="#Dev-Connect-to-the-Graph-via-Rexster">8.3. Connect to the Graph via Rexster</a></li>
+<li><a href="#Dev-Decompiling">8.4. Decompiling</a></li>
+<li><a href="#Dev-Dependencies">8.5. Dependencies (Forge add-ons)</a></li>
+<li><a href="#Dev-Frames-Extensions">8.6. Frames Extensions</a></li>
+<li><a href="#Dev-Internal-API-Features">8.7. Internal API Features</a></li>
+<li><a href="#Dev-Logging">8.8. Logging</a></li>
+<li><a href="#Dev-Variables-Stack">8.9. Variables Stack</a></li>
+<li><a href="#Dev-Port-WindRide-Functionality-to-Windup">8.10. Port WindRide Functionality to Windup</a></li>
+<li><a href="#some-classes-mapping">8.11. Some classes mapping</a></li>
+<li><a href="#server-side-code-to-be-moved">8.12. Server-side code to be moved</a></li>
 </ul>
 </li>
-<li><a href="#_rules_topics">Rules topics</a>
+<li><a href="#_rules_topics">9. Rules topics</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Available-Rules-Utilities">Available Rule Utilities</a></li>
-<li><a href="#Dev-Concepts-and-Philosophy">Concepts &amp; Philosophy</a></li>
-<li><a href="#_rulesets">Rulesets</a></li>
-<li><a href="#_ruleset_java_classifications_and_inline_hints">Ruleset Java Classifications and Inline Hints</a></li>
-<li><a href="#Ruleset-Java-EE-Apps">Ruleset Java EE Apps</a></li>
-<li><a href="#Ruleset-Reporting">Ruleset Reporting</a></li>
-<li><a href="#Rules-Windup-Models">Windup Models</a></li>
-<li><a href="#Rules-Create-Java-Queries">Create Java Queries</a></li>
-<li><a href="#Rules-Rules-Metadata">Rules Metadata</a></li>
-<li><a href="#Rules-Rules-Operations">Rules Operations</a></li>
+<li><a href="#Rules-Available-Rules-Utilities">9.1. Available Rule Utilities</a></li>
+<li><a href="#Dev-Concepts-and-Philosophy">9.2. Concepts &amp; Philosophy</a></li>
+<li><a href="#_rulesets">9.3. Rulesets</a></li>
+<li><a href="#_ruleset_java_classifications_and_inline_hints">9.4. Ruleset Java Classifications and Inline Hints</a></li>
+<li><a href="#Ruleset-Java-EE-Apps">9.5. Ruleset Java EE Apps</a></li>
+<li><a href="#Ruleset-Reporting">9.6. Ruleset Reporting</a></li>
+<li><a href="#Rules-Windup-Models">9.7. Windup Models</a></li>
+<li><a href="#Rules-Create-Java-Queries">9.8. Create Java Queries</a></li>
+<li><a href="#Rules-Rules-Metadata">9.9. Rules Metadata</a></li>
+<li><a href="#Rules-Rules-Operations">9.10. Rules Operations</a></li>
 </ul>
 </li>
-<li><a href="#_debugging_and_troubleshooting">Debugging and Troubleshooting</a>
+<li><a href="#_debugging_and_troubleshooting">10. Debugging and Troubleshooting</a>
 <ul class="sectlevel2">
-<li><a href="#Dev-Debugging-and-Profiling">Debugging and Profiling</a></li>
-<li><a href="#_troubleshoot_windup_issues">Troubleshoot Windup Issues</a></li>
-<li><a href="#About-the-Windup-Wiki">About the Windup Wiki</a></li>
-<li><a href="#Dev-Add-Images-to-the-Windup-Wiki">Add Images to the Windup Wiki</a></li>
-<li><a href="#Dev-Create-Windup-JavaDoc">Create Windup JavaDoc</a></li>
-<li><a href="#Dev-Windup-Documentation-Process">Windup Documentation Process</a></li>
+<li><a href="#Dev-Debugging-and-Profiling">10.1. Debugging and Profiling</a></li>
+<li><a href="#_troubleshoot_windup_issues">10.2. Troubleshoot Windup Issues</a></li>
+<li><a href="#About-the-Windup-Wiki">10.3. About the Windup Wiki</a></li>
+<li><a href="#Dev-Add-Images-to-the-Windup-Wiki">10.4. Add Images to the Windup Wiki</a></li>
+<li><a href="#Dev-Create-Windup-JavaDoc">10.5. Create Windup JavaDoc</a></li>
+<li><a href="#Dev-Windup-Documentation-Process">10.6. Windup Documentation Process</a></li>
 </ul>
 </li>
-<li><a href="#_additional_resources">Additional Resources</a>
+<li><a href="#_additional_resources">11. Additional Resources</a>
 <ul class="sectlevel2">
-<li><a href="#Review-the-Windup-Quickstarts">Review the Windup Quickstarts</a></li>
-<li><a href="#Known-Issues">Known Windup Issues</a></li>
-<li><a href="#Glossary">Glossary of Terms Used in Windup</a></li>
+<li><a href="#Review-the-Windup-Quickstarts">11.1. Review the Windup Quickstarts</a></li>
+<li><a href="#Known-Issues">11.2. Known Windup Issues</a></li>
+<li><a href="#Glossary">11.3. Glossary of Terms Used in Windup</a></li>
 </ul>
 </li>
 </ul>
@@ -515,14 +515,14 @@ <h1>Windup Core Development Guide</h1>
 </div>
 <div id="content">
 <div class="sect1">
-<h2 id="_overview">Overview</h2>
+<h2 id="_overview">1. Overview</h2>
 <div class="sectionbody">
 <div class="paragraph">
 <p>This guide is for developers who plan to contribute source code updates
 or core rule add-ons to the Windup 2.0 project.</p>
 </div>
 <div class="sect2">
-<h3 id="What-is-Windup">What is Windup?</h3>
+<h3 id="What-is-Windup">1.1. What is Windup?</h3>
 <div class="paragraph">
 <p><span class="image"><img src="images/windup-logo-wiki-header.jpg" alt="Windup Logo"></span></p>
 </div>
@@ -537,13 +537,13 @@ <h3 id="What-is-Windup">What is Windup?</h3>
 migrating from other containers to JBoss EAP a piece of cake.</p>
 </div>
 <div class="sect3">
-<h4 id="_windup_2_0_vs_windup_0_7_x">Windup 2.0 vs. Windup 0.7.x</h4>
+<h4 id="_windup_2_0_vs_windup_0_7_x">1.1.1. Windup 2.0 vs. Windup 0.7.x</h4>
 <div class="paragraph">
 <p>Windup 2.0 aims to deliver the same functionality as legacy Windup, however, the internal architecture and rule structure is very different and allows for the creation of much more complex rules.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?</h4>
+<h4 id="_how_does_windup_simplify_migration">1.1.2. How Does Windup Simplify Migration?</h4>
 <div class="paragraph">
 <p>Windup looks for common resources and highlight technologies and known “trouble
 spots” in migrating applications. The goal of Windup is to provide a
@@ -583,14 +583,14 @@ <h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?
 </table>
 </div>
 <div class="sect3">
-<h4 id="_follow_windup_on_twitter">Follow Windup on Twitter!</h4>
+<h4 id="_follow_windup_on_twitter">1.1.3. Follow Windup on Twitter!</h4>
 <div class="paragraph">
 <p>Follow Windup on Twitter <a href="https://twitter.com/jbosswindup">@JBossWindup</a> for updates and more!</p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
+<h3 id="Features-of-Windup-2.0">1.2. Features of Windup 2.0</h3>
 <div class="hdlist">
 <table>
 <tr>
@@ -724,9 +724,9 @@ <h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Get-Involved">Get Involved</h3>
+<h3 id="Get-Involved">1.3. Get Involved</h3>
 <div class="sect3">
-<h4 id="_how_can_you_help">How can you help?</h4>
+<h4 id="_how_can_you_help">1.3.1. How can you help?</h4>
 <div class="paragraph">
 <p>To help us make Windup cover most application constructs and server configurations, including yours, you can help with any of the following items. Some items require only a few minutes of your time!</p>
 </div>
@@ -793,7 +793,7 @@ <h4 id="_how_can_you_help">How can you help?</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_helpful_links">Helpful links</h4>
+<h4 id="_helpful_links">1.3.2. Helpful links</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -838,7 +838,7 @@ <h4 id="_helpful_links">Helpful links</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_github_repository">Github Repository</h4>
+<h4 id="_github_repository">1.3.3. Github Repository</h4>
 <div class="paragraph">
 <p>The Windup project github repository is located at <a href="https://github.com/windup/windup/" class="bare">https://github.com/windup/windup/</a>.</p>
 </div>
@@ -847,7 +847,7 @@ <h4 id="_github_repository">Github Repository</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_documentation">Documentation</h4>
+<h4 id="_documentation">1.3.4. Documentation</h4>
 <div class="paragraph">
 <p>The Windup documentation is currently located here in the Windup project <a href="https://github.com/windup/windup/wiki/">Wiki</a>.</p>
 </div>
@@ -856,7 +856,7 @@ <h4 id="_documentation">Documentation</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_website">Website</h4>
+<h4 id="_website">1.3.5. Website</h4>
 <div class="paragraph">
 <p>There is currently no website for Windup 2.0.</p>
 </div>
@@ -866,14 +866,14 @@ <h4 id="_website">Website</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_irc_chat">IRC chat</h4>
+<h4 id="_irc_chat">1.3.6. IRC chat</h4>
 <div class="paragraph">
 <p>Server: irc.freenode.net<br>
 Channel: #windup</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_mailing_lists">Mailing lists</h4>
+<h4 id="_mailing_lists">1.3.7. Mailing lists</h4>
 <div class="paragraph">
 <p>Subscribe to the JBoss mailing lists at
 <a href="https://lists.jboss.org/mailman/listinfo/windup-dev" class="bare">https://lists.jboss.org/mailman/listinfo/windup-dev</a>.</p>
@@ -890,7 +890,7 @@ <h4 id="_mailing_lists">Mailing lists</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_core_development_team_and_irc_nicks">Core development team (and IRC nicks)</h4>
+<h4 id="_core_development_team_and_irc_nicks">1.3.8. Core development team (and IRC nicks)</h4>
 <div class="paragraph">
 <p>Lead: Lincoln Baxter (lincolnthree)<br>
 Members: Jess Sightler (jsightler), Matej Briskar (mbriskar), Ondrej
@@ -898,7 +898,7 @@ <h4 id="_core_development_team_and_irc_nicks">Core development team (and IRC nic
 </div>
 </div>
 <div class="sect3">
-<h4 id="_irc_meeting_bot_commands_hint_for_the_moderator">IRC meeting bot commands (hint for the moderator)</h4>
+<h4 id="_irc_meeting_bot_commands_hint_for_the_moderator">1.3.9. IRC meeting bot commands (hint for the moderator)</h4>
 <div class="listingblock">
 <div class="content">
 <pre>#startmeeting
@@ -914,12 +914,12 @@ <h4 id="_irc_meeting_bot_commands_hint_for_the_moderator">IRC meeting bot comman
 </div>
 </div>
 <div class="sect2">
-<h3 id="Report-Issues-with-Windup">Report Issues with Windup</h3>
+<h3 id="Report-Issues-with-Windup">1.4. Report Issues with Windup</h3>
 <div class="paragraph">
 <p>Windup uses JIRA as its issue tracking system. If you encounter an issue executing Windup, please file a Windup JIRA Issue.</p>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_account">Create a JIRA Account</h4>
+<h4 id="_create_a_jira_account">1.4.1. Create a JIRA Account</h4>
 <div class="paragraph">
 <p>If you do not yet have a JIRA account, create one using the following procedure.</p>
 </div>
@@ -941,7 +941,7 @@ <h4 id="_create_a_jira_account">Create a JIRA Account</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
+<h4 id="_create_a_jira_issue">1.4.2. Create a JIRA Issue</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1016,17 +1016,17 @@ <h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_developer_contributing_information">Developer Contributing Information</h2>
+<h2 id="_developer_contributing_information">2. Developer Contributing Information</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Dev-Development-Guidelines">Development Guidelines</h3>
+<h3 id="Dev-Development-Guidelines">2.1. Development Guidelines</h3>
 <div class="sect3">
-<h4 id="_project_source_code_format">Project Source Code Format</h4>
+<h4 id="_project_source_code_format">2.1.1. Project Source Code Format</h4>
 <div class="paragraph">
 <p>All project source code contributed to Windup should be formatted using the settings defined in the <code>Eclipse_Code_Format_Profile.xml</code> file located in the root directory of the Windup project.</p>
 </div>
 <div class="sect4">
-<h5 id="_eclipse_ide">Eclipse IDE</h5>
+<h5 id="_eclipse_ide">2.1.1.1. Eclipse IDE</h5>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1045,27 +1045,27 @@ <h5 id="_eclipse_ide">Eclipse IDE</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_netbeans_ide">Netbeans IDE</h5>
+<h5 id="_netbeans_ide">2.1.1.2. Netbeans IDE</h5>
 <div class="paragraph">
 <p>Use this file to format Windup source code: <a href="http://plugins.netbeans.org/plugin/50877/eclipse-code-formatter-for-java" class="bare">http://plugins.netbeans.org/plugin/50877/eclipse-code-formatter-for-java</a></p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_intellij_idea">IntelliJ IDEA</h5>
+<h5 id="_intellij_idea">2.1.1.3. IntelliJ IDEA</h5>
 <div class="paragraph">
 <p>Use this file to format Windup source code: <a href="http://plugins.jetbrains.com/plugin/?id=6546" class="bare">http://plugins.jetbrains.com/plugin/?id=6546</a></p>
 </div>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_naming_conventions">Naming conventions</h4>
+<h4 id="_naming_conventions">2.1.2. Naming conventions</h4>
 <div class="sect4">
-<h5 id="_suffixes_and_prefixes">Suffixes and prefixes</h5>
+<h5 id="_suffixes_and_prefixes">2.1.2.1. Suffixes and prefixes</h5>
 <div class="paragraph">
 <p><code>*RuleProvider</code></p>
 </div>
 <div class="sect5">
-<h6 id="_models">Models</h6>
+<h6 id="_models">2.1.2.1.1. Models</h6>
 <div class="paragraph">
 <p><code>*Model</code></p>
 </div>
@@ -1074,7 +1074,7 @@ <h6 id="_models">Models</h6>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_tests">Tests</h6>
+<h6 id="_tests">2.1.2.1.2. Tests</h6>
 <div class="paragraph">
 <p>All test names should be prefixed with 'Test'.</p>
 </div>
@@ -1083,7 +1083,7 @@ <h6 id="_tests">Tests</h6>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Submit-Code-Updates-to-the-Windup-Project">Submit Code Updates to the Windup Project</h3>
+<h3 id="Dev-Submit-Code-Updates-to-the-Windup-Project">2.2. Submit Code Updates to the Windup Project</h3>
 <div class="paragraph">
 <p>To get the Windup Source Code, see <a href="#Dev-Get-the-Windup-Source-Code">Get the Windup Source Code</a> for instructions.</p>
 </div>
@@ -1188,10 +1188,10 @@ <h3 id="Dev-Submit-Code-Updates-to-the-Windup-Project">Submit Code Updates to th
 </div>
 </div>
 <div class="sect1">
-<h2 id="_understand_the_windup_architecture_and_structure">Understand the Windup Architecture and Structure</h2>
+<h2 id="_understand_the_windup_architecture_and_structure">3. Understand the Windup Architecture and Structure</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
+<h3 id="Windup-Architectural-Components">3.1. Windup Architectural Components</h3>
 <div class="paragraph">
 <p>The following open source software, tools, and APIs are used within
 Windup to analyze and provide migration information. If you plan to
@@ -1199,7 +1199,7 @@ <h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
 familiar with them.</p>
 </div>
 <div class="sect3">
-<h4 id="_forge">Forge</h4>
+<h4 id="_forge">3.1.1. Forge</h4>
 <div class="paragraph">
 <p>Forge is an open source, extendable, rapid application development tool
 for creating Java EE applications using Maven. For more information
@@ -1207,7 +1207,7 @@ <h4 id="_forge">Forge</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_forge_furnace">Forge Furnace</h4>
+<h4 id="_forge_furnace">3.1.2. Forge Furnace</h4>
 <div class="paragraph">
 <p>Forge Furnace is a modular runtime container behind Forge that provides
 the ability to run Forge addons in an embedded application. For more
@@ -1216,21 +1216,21 @@ <h4 id="_forge_furnace">Forge Furnace</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_tinkerpop">TinkerPop</h4>
+<h4 id="_tinkerpop">3.1.3. TinkerPop</h4>
 <div class="paragraph">
 <p>TinkerPop is an open source graph computing framework. For more
 information, see: <a href="http://www.tinkerpop.com/">TinkerPop</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_titan">Titan</h4>
+<h4 id="_titan">3.1.4. Titan</h4>
 <div class="paragraph">
 <p>Titan is a scalable graph database optimized for storing and querying graphs.
 For more information, see: <a href="http://thinkaurelius.github.io/titan/">Titan Distributed Graph Database</a> and <a href="https://github.com/thinkaurelius/titan/wiki/Beginner%27s-Guide">Titan Beginner&#8217;s Guide</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_frames">Frames</h4>
+<h4 id="_frames">3.1.5. Frames</h4>
 <div class="paragraph">
 <p>Frames represents graph data in the form of interrelated Java Objects or
 a collection of annotated Java Interfaces. For more information, see:
@@ -1242,7 +1242,7 @@ <h4 id="_frames">Frames</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_gremlin">Gremlin</h4>
+<h4 id="_gremlin">3.1.6. Gremlin</h4>
 <div class="paragraph">
 <p>Gremlin is a graph traversal language that allows you to query, analyze,
 and manipulate property graphs that implement the Blueprints property
@@ -1251,7 +1251,7 @@ <h4 id="_gremlin">Gremlin</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_blueprints">Blueprints</h4>
+<h4 id="_blueprints">3.1.7. Blueprints</h4>
 <div class="paragraph">
 <p>Blueprints is an industry standard API used to access graph databases.
 For more information about Blueprints, see:
@@ -1259,7 +1259,7 @@ <h4 id="_blueprints">Blueprints</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_pipes">Pipes</h4>
+<h4 id="_pipes">3.1.8. Pipes</h4>
 <div class="paragraph">
 <p>Pipes is a dataflow framework used to process graph data. It for the
 transformation of data from input to output. For more information, see:
@@ -1267,14 +1267,14 @@ <h4 id="_pipes">Pipes</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rexster">Rexster</h4>
+<h4 id="_rexster">3.1.9. Rexster</h4>
 <div class="paragraph">
 <p>Rexster is a graph server that exposes any Blueprints graph through HTTP/REST and a binary protocol called RexPro. Rexster makes extensive use of Blueprints, Pipes, and Gremlin. For more information, see:
 <a href="https://github.com/tinkerpop/rexster/wiki">TinkerPop Rexster Wiki</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
+<h4 id="_ocpsoft_rewrite">3.1.10. OCPsoft Rewrite</h4>
 <div class="paragraph">
 <p>OCPsoft Rewrite is an open source routing and URL rewriting solution for
 Servlets, Java Web Frameworks, and Java EE. For more information about
@@ -1283,7 +1283,7 @@ <h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Windup-Project-Structure">Windup Project Structure</h3>
+<h3 id="Dev-Windup-Project-Structure">3.2. Windup Project Structure</h3>
 <div class="paragraph">
 <p>The Windup 2.0 project consists of the following subprojects.</p>
 </div>
@@ -1350,12 +1350,12 @@ <h3 id="Dev-Windup-Project-Structure">Windup Project Structure</h3>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_get_started">Get Started</h2>
+<h2 id="_get_started">4. Get Started</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Install-and-Configure-Maven">Install and Configure Maven</h3>
+<h3 id="Install-and-Configure-Maven">4.1. Install and Configure Maven</h3>
 <div class="sect3">
-<h4 id="_download_and_install_maven">Download and Install Maven</h4>
+<h4 id="_download_and_install_maven">4.1.1. Download and Install Maven</h4>
 <div class="paragraph">
 <p>If you plan to use Eclipse Luna (4.4) to build Windup, you can skip this
 step. This version of Eclipse embeds Maven 3.2.1 so you do not need to
@@ -1381,7 +1381,7 @@ <h4 id="_download_and_install_maven">Download and Install Maven</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_configure_the_maven_installation_in_your_ide">Configure the Maven Installation in Your IDE</h4>
+<h4 id="_configure_the_maven_installation_in_your_ide">4.1.2. Configure the Maven Installation in Your IDE</h4>
 <div class="paragraph">
 <p>JBoss Developer Studio 7.1.1 is built upon Eclipse Kepler (4.3), which
 embeds Maven 3.0.4. If you plan to use JBoss Developer Studio 7.1.1 or
@@ -1415,7 +1415,7 @@ <h4 id="_configure_the_maven_installation_in_your_ide">Configure the Maven Insta
 </div>
 </div>
 <div class="sect3">
-<h4 id="configure-maven-to-build-windup">Configure Maven to Build Windup</h4>
+<h4 id="configure-maven-to-build-windup">4.1.3. Configure Maven to Build Windup</h4>
 <div class="paragraph">
 <p>Windup uses artifacts located in the
 <a href="http://repository.jboss.org/nexus/content/groups/public/">JBoss Nexus</a>
@@ -1481,7 +1481,7 @@ <h4 id="configure-maven-to-build-windup">Configure Maven to Build Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_install_the_git_client">Install the Git Client</h4>
+<h4 id="_install_the_git_client">4.1.4. Install the Git Client</h4>
 <div class="paragraph">
 <p>If you don&#8217;t have the Git client (<code>git</code>), get it from:
 <a href="http://git-scm.com/" class="bare">http://git-scm.com/</a></p>
@@ -1512,7 +1512,7 @@ <h4 id="_install_the_git_client">Install the Git Client</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_fork_and_clone_the_windup_repository">Fork and Clone the Windup Repository</h4>
+<h4 id="_fork_and_clone_the_windup_repository">4.1.5. Fork and Clone the Windup Repository</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1554,7 +1554,7 @@ <h4 id="_fork_and_clone_the_windup_repository">Fork and Clone the Windup Reposit
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Build-Windup-from-Source">Build Windup from Source</h3>
+<h3 id="Dev-Build-Windup-from-Source">4.2. Build Windup from Source</h3>
 <div class="paragraph">
 <p>This information is provided for new developers who plan to contribute code
 to the Windup open source project. This section describes how to build Windup from source and how to extract the Windup distribution that is created during the build process.</p>
@@ -1563,7 +1563,7 @@ <h3 id="Dev-Build-Windup-from-Source">Build Windup from Source</h3>
 <p>If you use Linux and are an experienced Windup developer looking for a quick refresher, jump to: <a href="#quick-build-review-for-experienced-windup-developers">Quick Build Review for Experienced Windup Developers</a>.</p>
 </div>
 <div class="sect3">
-<h4 id="_system_requirements_to_build_windup">System Requirements to Build Windup</h4>
+<h4 id="_system_requirements_to_build_windup">4.2.1. System Requirements to Build Windup</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1619,7 +1619,7 @@ <h4 id="_system_requirements_to_build_windup">System Requirements to Build Windu
 </div>
 </div>
 <div class="sect3">
-<h4 id="_build_windup_using_maven_command_line">Build Windup Using Maven Command Line</h4>
+<h4 id="_build_windup_using_maven_command_line">4.2.2. Build Windup Using Maven Command Line</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1693,7 +1693,7 @@ <h4 id="_build_windup_using_maven_command_line">Build Windup Using Maven Command
 </div>
 </div>
 <div class="sect3">
-<h4 id="_build_windup_using_red_hat_jboss_developer_studio_or_eclipse">Build Windup Using Red Hat JBoss Developer Studio or Eclipse</h4>
+<h4 id="_build_windup_using_red_hat_jboss_developer_studio_or_eclipse">4.2.3. Build Windup Using Red Hat JBoss Developer Studio or Eclipse</h4>
 <div class="paragraph">
 <p>If you prefer, you can use an IDE to build Windup.</p>
 </div>
@@ -1732,7 +1732,7 @@ <h4 id="_build_windup_using_red_hat_jboss_developer_studio_or_eclipse">Build Win
 </div>
 </div>
 <div class="sect3">
-<h4 id="_extract_the_windup_distribution_source_file">Extract the Windup Distribution Source File</h4>
+<h4 id="_extract_the_windup_distribution_source_file">4.2.4. Extract the Windup Distribution Source File</h4>
 <div class="paragraph">
 <p>The build process creates a <code>windup-distribution-2.0.0-SNAPSHOT-offline.zip file</code> in the Windup source <code>dist/target/</code> directory.</p>
 </div>
@@ -1741,7 +1741,7 @@ <h4 id="_extract_the_windup_distribution_source_file">Extract the Windup Distrib
 </div>
 </div>
 <div class="sect3">
-<h4 id="quick-build-review-for-experienced-windup-developers">Quick Build Review for Experienced Windup Developers</h4>
+<h4 id="quick-build-review-for-experienced-windup-developers">4.2.5. Quick Build Review for Experienced Windup Developers</h4>
 <div class="listingblock">
 <div class="content">
 <pre>git clone git@github.com:windup/windup.git Windup
@@ -1755,7 +1755,7 @@ <h4 id="quick-build-review-for-experienced-windup-developers">Quick Build Review
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Execute-Windup-Built-from-Source">Execute Windup (Built from Windup Source)</h3>
+<h3 id="Dev-Execute-Windup-Built-from-Source">4.3. Execute Windup (Built from Windup Source)</h3>
 <div class="paragraph">
 <p>These instructions are for Windup core developers who plan to build Windup from source to test code updates.</p>
 </div>
@@ -1790,9 +1790,9 @@ <h3 id="Dev-Execute-Windup-Built-from-Source">Execute Windup (Built from Windup
 </div>
 </div>
 <div class="sect2">
-<h3 id="Execute-Windup">Execute Windup</h3>
+<h3 id="Execute-Windup">4.4. Execute Windup</h3>
 <div class="sect3">
-<h4 id="_prerequisites">Prerequisites</h4>
+<h4 id="_prerequisites">4.4.1. Prerequisites</h4>
 <div class="paragraph">
 <p>Before you begin, you must gather the following information.</p>
 </div>
@@ -1857,7 +1857,7 @@ <h4 id="_prerequisites">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_start_windup">Start Windup</h4>
+<h4 id="_start_windup">4.4.2. Start Windup</h4>
 <div class="paragraph">
 <p>For information about the use of WINDUP_HOME in the instructions below, see <a href="#About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</a>.</p>
 </div>
@@ -1898,7 +1898,7 @@ <h4 id="_start_windup">Start Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migrate-app</code> Command</h4>
+<h4 id="_run_the_code_windup_migrate_app_code_command">4.4.3. Run the <code>windup-migrate-app</code> Command</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1981,7 +1981,7 @@ <h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migr
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
+<h4 id="_run_windup_in_batch_mode">4.4.4. Run Windup in Batch Mode</h4>
 <div class="paragraph">
 <p>Windup can be also executed in batch mode within a shell or batch script using the <code>--evaluate</code> argument as follows.</p>
 </div>
@@ -2003,7 +2003,7 @@ <h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_windup_help">Windup Help</h4>
+<h4 id="_windup_help">4.4.5. Windup Help</h4>
 <div class="paragraph">
 <p>To see the list of available parameters for the <code>windup-migrate-app</code> command, execute the following command in the Windup prompt:</p>
 </div>
@@ -2014,12 +2014,12 @@ <h4 id="_windup_help">Windup Help</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="windup-command-examples">Windup Command Examples</h4>
+<h4 id="windup-command-examples">4.4.6. Windup Command Examples</h4>
 <div class="paragraph">
 <p>The following Windup command examples report against applications located in the Windup source <a href="https://github.com/windup/windup/tree/master/test-files">test-files</a> directory.</p>
 </div>
 <div class="sect4">
-<h5 id="_source_code_example">Source Code Example</h5>
+<h5 id="_source_code_example">4.4.6.1. Source Code Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/tree/master/test-files/seam-booking-5.2">seam-booking-5.2</a> application source code. It evaluates all <code>org.jboss.seam</code> packages and creates a folder named 'seam-booking-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -2030,7 +2030,7 @@ <h5 id="_source_code_example">Source Code Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_example">Archive Example</h5>
+<h5 id="_archive_example">4.4.6.2. Archive Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -2041,7 +2041,7 @@ <h5 id="_archive_example">Archive Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_batch_example">Windup Batch Example</h5>
+<h5 id="_windup_batch_example">4.4.6.3. Windup Batch Example</h5>
 <div class="paragraph">
 <p>The following Windup batch command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -2053,7 +2053,7 @@ <h5 id="_windup_batch_example">Windup Batch Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
+<h5 id="_windup_quickstart_examples">4.4.6.4. Windup Quickstart Examples</h5>
 <div class="paragraph">
 <p>For more concrete examples, see the Windup quickstarts located on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a>. If you prefer, you can download the <a href="https://github.com/windup/windup-quickstarts/releases/tag/2.0.0.Alpha1">2.0.0.Alpha1 release</a> ZIP or TAR  distribution of the quickstarts.</p>
 </div>
@@ -2064,9 +2064,9 @@ <h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Review-the-Report">Review the Report</h3>
+<h3 id="Review-the-Report">4.5. Review the Report</h3>
 <div class="sect3">
-<h4 id="_about_the_report">About the Report</h4>
+<h4 id="_about_the_report">4.5.1. About the Report</h4>
 <div class="paragraph">
 <p>When you execute Windup, the report is generated in the <code>OUTPUT_REPORT_DIRECTORY</code> you specify for the <code>--output</code> argument in the command line. This output directory contains the following files and subdirectories:</p>
 </div>
@@ -2099,7 +2099,7 @@ <h4 id="_about_the_report">About the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_open_the_report">Open the Report</h4>
+<h4 id="_open_the_report">4.5.2. Open the Report</h4>
 <div class="paragraph">
 <p>Use your favorite browser to open the <code>index.html</code> file located in the output report directory. You should see something like the following:</p>
 </div>
@@ -2111,9 +2111,9 @@ <h4 id="_open_the_report">Open the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_report_sections">Report Sections</h4>
+<h4 id="_report_sections">4.5.3. Report Sections</h4>
 <div class="sect4">
-<h5 id="_application_report_page">Application Report Page</h5>
+<h5 id="_application_report_page">4.5.3.1. Application Report Page</h5>
 <div class="paragraph">
 <p>The first section of the application report page summarizes the migration effort. It provides the total <em>Story Points</em> and a graphically displays the effort by technology. A <em>Story Point</em> is a term commonly used in Scrum Agile software development methodology to estimate the level of effort needed to implement a feature or change. It does not necessarily translate to man-hours, but the value should be consistent across tasks.</p>
 </div>
@@ -2135,7 +2135,7 @@ <h5 id="_application_report_page">Application Report Page</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
+<h5 id="_archive_analysis_sections">4.5.3.2. Archive Analysis Sections</h5>
 <div class="paragraph">
 <p>Each archive summary begins with a total of the story points assigned to its migration, followed by a table detailing the changes required for each file in the archive. The report contains the following columns.</p>
 </div>
@@ -2198,7 +2198,7 @@ <h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_file_analysis_pages">File Analysis Pages</h5>
+<h5 id="_file_analysis_pages">4.5.3.3. File Analysis Pages</h5>
 <div class="paragraph">
 <p>The analysis of the <code>jee-example-services.jar</code> lists the files in the JAR and the warnings and story points assigned to each one. Notice the <code>com.acme.anvil.listener.AnvilWebLifecycleListener</code> file has 5 warnings and is assigned 7 story points. Click on the file to see the detail.</p>
 </div>
@@ -2227,12 +2227,12 @@ <h5 id="_file_analysis_pages">File Analysis Pages</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_additional_reports">Additional Reports</h4>
+<h4 id="_additional_reports">4.5.4. Additional Reports</h4>
 <div class="paragraph">
 <p>Explore the Windup <code>OUTPUT_REPORT_DIRECTORY/reports</code> folder to find additional reporting information.</p>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report">4.5.4.1. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
@@ -2241,13 +2241,13 @@ <h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report_2">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report_2">4.5.4.2. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
+<h5 id="_individual_file_analysis_reports">4.5.4.3. Individual File Analysis Reports</h5>
 <div class="paragraph">
 <p>You can directly access the the file analysis report pages described above by browsing for them by name in the <code>OUTPUT_REPORT_DIRECTORY/reports/</code> directory. Because the same common file names can exist in multiple archives, for example "manifest.mf" or "web.xml", Windup adds a unique numeric suffix to each report file name.</p>
 </div>
@@ -2260,10 +2260,10 @@ <h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_rules_and_rulesets">Rules and Rulesets</h2>
+<h2 id="_rules_and_rulesets">5. Rules and Rulesets</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
+<h3 id="Windup-Processing-Overview">5.1. Windup Processing Overview</h3>
 <div class="paragraph">
 <p>Windup is a rule-based migration tool that allows you to write customized rules to analyze the APIs, technologies, and architectures used by the applications you plan to migrate. The Windup tool also executes its own core rules through all phases of the migration process.</p>
 </div>
@@ -2271,7 +2271,7 @@ <h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
 <p>The following is a high level conceptual overview of what happens within Windup when you execute the tool against your application or archive.</p>
 </div>
 <div class="sect3">
-<h4 id="_discovery_phase">Discovery Phase</h4>
+<h4 id="_discovery_phase">5.1.1. Discovery Phase</h4>
 <div class="paragraph">
 <p>Wnen you run the <code>windup-migrate-app</code> command, Windup executes its own core rules to extract files from archives, decompile classes, and analyze the application. In this phase, Windup builds a datamodel, storing component data and relationships in a graph database, which can then be queried and updated as needed by the migration rules and for reporting purposes.</p>
 </div>
@@ -2280,7 +2280,7 @@ <h4 id="_discovery_phase">Discovery Phase</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_application_migration">Application Migration</h4>
+<h4 id="_application_migration">5.1.2. Application Migration</h4>
 <div class="paragraph">
 <p>The next step in the process is the execution of the migration rules. In this phase, the rules typically do not execute against the application input files. Instead, they execute against the graph database model. Windup rules are independent and decoupled and they communicate with each other using the graph database model. Rules query the graph database to obtain information needed to test the rule condition. They also update the data model with information based on the result of the rule execution. This allows rules to easily interact with other rules and enables the creation of very complex rules.</p>
 </div>
@@ -2289,7 +2289,7 @@ <h4 id="_application_migration">Application Migration</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Findings Based on the Rule Execution Results</h4>
+<h4 id="_generate_findings_based_on_the_rule_execution_results">5.1.3. Generate Findings Based on the Rule Execution Results</h4>
 <div class="paragraph">
 <p>The final step in the process is to pull data from the graph database model to generate of reports and optionally generate scripts. Again, Windup uses rules to generate the final output.</p>
 </div>
@@ -2315,9 +2315,9 @@ <h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Finding
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rule-Execution-Lifecycle">Rule Execution Lifecycle</h3>
+<h3 id="Rules-Rule-Execution-Lifecycle">5.2. Rule Execution Lifecycle</h3>
 <div class="sect3">
-<h4 id="_rule_lifecycle">Rule Lifecycle</h4>
+<h4 id="_rule_lifecycle">5.2.1. Rule Lifecycle</h4>
 <div class="paragraph">
 <p>Windup executes each rule in sequential order. The following
 sections describe the phases of rule execution and how rules may specify
@@ -2331,7 +2331,7 @@ <h4 id="_rule_lifecycle">Rule Lifecycle</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rule_phases">Rule Phases</h4>
+<h4 id="_rule_phases">5.2.2. Rule Phases</h4>
 <div class="listingblock">
 <div class="content">
 <pre>INFO: Loaded [67] org.jboss.windup.config.WindupRuleProvider [
@@ -2431,7 +2431,7 @@ <h4 id="_rule_phases">Rule Phases</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_execute_before_and_execute_after">Execute Before and Execute After</h4>
+<h4 id="_execute_before_and_execute_after">5.2.3. Execute Before and Execute After</h4>
 <div class="paragraph">
 <p>A rule may specify that one or more rules must be executed before it is
 run. In this case, all named rules will be fired in the order specified
@@ -2463,16 +2463,16 @@ <h4 id="_execute_before_and_execute_after">Execute Before and Execute After</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rule-Story-Points">Rule Story Points</h3>
+<h3 id="Rules-Rule-Story-Points">5.3. Rule Story Points</h3>
 <div class="sect3">
-<h4 id="_what_are_story_points">What are Story Points?</h4>
+<h4 id="_what_are_story_points">5.3.1. What are Story Points?</h4>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>Story points are an abstract metric used in Scrum methodology to estimate the level of effort for various tasks. They are based on a <a href="http://scrummethodology.com/scrum-effort-estimation-and-story-points/">modified Fibonacci sequence</a>. In a similar manner, Windup uses story points to express the level of effort needed to migrate particular application constructs, and in a sum, the application as a whole.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_to_estimate_story_points_in_a_rule">How to Estimate Story Points in a Rule</h4>
+<h4 id="_how_to_estimate_story_points_in_a_rule">5.3.2. How to Estimate Story Points in a Rule</h4>
 <div class="paragraph">
 <p>Estimating story points for a rule can be tricky. The following are general guidelines or suggestions to use when estimating the level of effort required for a rule.</p>
 </div>
@@ -2524,17 +2524,17 @@ <h4 id="_how_to_estimate_story_points_in_a_rule">How to Estimate Story Points in
 </div>
 </div>
 <div class="sect1">
-<h2 id="_create_and_test_java_rule_add_ons">Create and Test Java Rule Add-ons</h2>
+<h2 id="_create_and_test_java_rule_add_ons">6. Create and Test Java Rule Add-ons</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Java-based-Rule-Structure">Java-based Rule Structure</h3>
+<h3 id="Rules-Java-based-Rule-Structure">6.1. Java-based Rule Structure</h3>
 <div class="paragraph">
 <p>TODO:
 * Add a how-to for compound rules, nested rules, rules over multiple sources, negative queries (not matched by anything).
 Points] <a href="https://issues.jboss.org/browse/WINDUP-255">WINDUP-255</a></p>
 </div>
 <div class="sect3">
-<h4 id="_windup_rule_provider">Windup Rule Provider</h4>
+<h4 id="_windup_rule_provider">6.1.1. Windup Rule Provider</h4>
 <div class="paragraph">
 <p>Windup rules are based on <a href="http://ocpsoft.org/rewrite/">OCPsoft Rewrite</a>, an open source routing and URL rewriting solution for Servlets, Java Web Frameworks, and Java EE. The <strong>rewrite</strong> framework allows you to create rule providers and rules in an easy to read format.</p>
 </div>
@@ -2586,7 +2586,7 @@ <h4 id="_windup_rule_provider">Windup Rule Provider</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_rule_code_structure">Add Rule Code Structure</h4>
+<h4 id="_add_rule_code_structure">6.1.2. Add Rule Code Structure</h4>
 <div class="paragraph">
 <p>Like most rule-based frameworks, Windup rules consist of the following:</p>
 </div>
@@ -2605,7 +2605,7 @@ <h4 id="_add_rule_code_structure">Add Rule Code Structure</h4>
 and some others, all of which are optional.</p>
 </div>
 <div class="sect4">
-<h5 id="_when">when()</h5>
+<h5 id="_when">6.1.2.1. when()</h5>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.when(Query.fromType(XmlMetaFacetModel.class))</code></pre>
@@ -2628,7 +2628,7 @@ <h5 id="_when">when()</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_perform">perform()</h5>
+<h5 id="_perform">6.1.2.2. perform()</h5>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.perform(
@@ -2655,7 +2655,7 @@ <h5 id="_perform">perform()</h5>
 (<code>Iteration</code>).</p>
 </div>
 <div class="sect5">
-<h6 id="_iteration">Iteration</h6>
+<h6 id="_iteration">6.1.2.2.1. Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.perform(
@@ -2677,13 +2677,13 @@ <h6 id="_iteration">Iteration</h6>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_nested_iterations">Nested iterations</h6>
+<h6 id="_nested_iterations">6.1.2.2.2. Nested iterations</h6>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_otherwise">otherwise</h6>
+<h6 id="_otherwise">6.1.2.2.3. otherwise</h6>
 <div class="paragraph">
 <p>Windup rules inherit the rule constructs from OCP Rewrite. For example,
 <code>.otherwise()</code> Gives you a chance to perform something in case the
@@ -2706,13 +2706,13 @@ <h6 id="_otherwise">otherwise</h6>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_where">Where</h5>
+<h5 id="_where">6.1.2.3. Where</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_metadata">Metadata</h5>
+<h5 id="_metadata">6.1.2.4. Metadata</h5>
 <div class="paragraph">
 <p>Rules can specify metadata. Currently, the only appearing in some rules,
 and not actually used, is <code>RuleMetadata.CATEGORY</code>.</p>
@@ -2729,7 +2729,7 @@ <h5 id="_metadata">Metadata</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_available_utilities">Available utilities</h4>
+<h4 id="_available_utilities">6.1.3. Available utilities</h4>
 <div class="paragraph">
 <p>For a list of what key services and constructs can be used in the rule,
 see <a href="#Rules-Available-Rules-Utilities">Available Rules Utilities</a>.</p>
@@ -2737,12 +2737,12 @@ <h4 id="_available_utilities">Available utilities</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Basic-Rule-Execution-Flow-Patterns">Basic Rule Execution Flow Patterns</h3>
+<h3 id="Rules-Basic-Rule-Execution-Flow-Patterns">6.2. Basic Rule Execution Flow Patterns</h3>
 <div class="paragraph">
 <p>SGILDA: TODO - Need some links to github to the respective example files.</p>
 </div>
 <div class="sect3">
-<h4 id="_operation_single_operation">operation();  - single operation</h4>
+<h4 id="_operation_single_operation">6.2.1. operation();  - single operation</h4>
 <div class="paragraph">
 <p>When no iteration or condition is needed.</p>
 </div>
@@ -2763,7 +2763,7 @@ <h4 id="_operation_single_operation">operation();  - single operation</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_if_operation_single_conditional_operation">if( &#8230;&#8203; ){ operation(); }  - single conditional operation</h4>
+<h4 id="_if_operation_single_conditional_operation">6.2.2. if( &#8230;&#8203; ){ operation(); }  - single conditional operation</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2779,7 +2779,7 @@ <h4 id="_if_operation_single_conditional_operation">if( &#8230;&#8203; ){ operat
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_foomodel_class_single_iteration">for( FooModel.class ){ &#8230;&#8203; } - Single iteration</h4>
+<h4 id="_for_foomodel_class_single_iteration">6.2.3. for( FooModel.class ){ &#8230;&#8203; } - Single iteration</h4>
 <div class="paragraph">
 <p>For simple iterations, <code>IteratingRuleProvider</code> can be used, which makes the <code>perform</code> a bit less verbose:</p>
 </div>
@@ -2810,7 +2810,7 @@ <h4 id="_for_foomodel_class_single_iteration">for( FooModel.class ){ &#8230;&#82
 </div>
 </div>
 <div class="sect3">
-<h4 id="_if_for_conditional_iteration">if( &#8230;&#8203; ){ for( &#8230;&#8203; ) } - conditional iteration</h4>
+<h4 id="_if_for_conditional_iteration">6.2.4. if( &#8230;&#8203; ){ for( &#8230;&#8203; ) } - conditional iteration</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2825,7 +2825,7 @@ <h4 id="_if_for_conditional_iteration">if( &#8230;&#8203; ){ for( &#8230;&#8203;
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_if_iteration_with_a_condition">for( &#8230;&#8203; ){ if( &#8230;&#8203; ){ &#8230;&#8203; } } - iteration with a condition</h4>
+<h4 id="_for_if_iteration_with_a_condition">6.2.5. for( &#8230;&#8203; ){ if( &#8230;&#8203; ){ &#8230;&#8203; } } - iteration with a condition</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2852,7 +2852,7 @@ <h4 id="_for_if_iteration_with_a_condition">for( &#8230;&#8203; ){ if( &#8230;&#
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_for_nested_iterations">for( &#8230;&#8203; ){ for( &#8230;&#8203; ) { &#8230;&#8203; } } - nested iterations</h4>
+<h4 id="_for_for_nested_iterations">6.2.6. for( &#8230;&#8203; ){ for( &#8230;&#8203; ) { &#8230;&#8203; } } - nested iterations</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java"></code></pre>
@@ -2861,12 +2861,12 @@ <h4 id="_for_for_nested_iterations">for( &#8230;&#8203; ){ for( &#8230;&#8203; )
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Create-a-Basic-Java-based-Rule-Add-on">Create a Basic Java-based Rule Add-on</h3>
+<h3 id="Rules-Create-a-Basic-Java-based-Rule-Add-on">6.3. Create a Basic Java-based Rule Add-on</h3>
 <div class="paragraph">
 <p>You can create a rule using Java or XML. This topic describes how to create a rule add-on using Java.</p>
 </div>
 <div class="sect3">
-<h4 id="_prerequisites_2">Prerequisites</h4>
+<h4 id="_prerequisites_2">6.3.1. Prerequisites</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -2904,9 +2904,9 @@ <h4 id="_prerequisites_2">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_rule_add_on">Create a Rule Add-on</h4>
+<h4 id="_create_a_rule_add_on">6.3.2. Create a Rule Add-on</h4>
 <div class="sect4">
-<h5 id="_create_a_maven_project">Create a Maven Project</h5>
+<h5 id="_create_a_maven_project">6.3.2.1. Create a Maven Project</h5>
 <div class="paragraph">
 <p>Create a new Maven Java Project. These instructions will refer to the project folder location with the <strong>replaceable</strong> variable 'RULE_PROJECT_HOME'. Modify the project <code>pom.xml</code> file as follows</p>
 </div>
@@ -3070,7 +3070,7 @@ <h5 id="_create_a_maven_project">Create a Maven Project</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_create_the_java_ruleprovider">Create the Java RuleProvider</h5>
+<h5 id="_create_the_java_ruleprovider">6.3.2.2. Create the Java RuleProvider</h5>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -3182,7 +3182,7 @@ <h5 id="_create_the_java_ruleprovider">Create the Java RuleProvider</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_install_the_java_based_rule_add_on">Install the Java-based Rule Add-on</h4>
+<h4 id="_install_the_java_based_rule_add_on">6.3.3. Install the Java-based Rule Add-on</h4>
 <div class="paragraph">
 <p>The easiest and fastest way to build the rule add-on, install it into the local Maven repository, and install it into Windup as a rule add-on is to use the Windup <code>addon-build-and-install</code> command.</p>
 </div>
@@ -3211,7 +3211,7 @@ <h4 id="_install_the_java_based_rule_add_on">Install the Java-based Rule Add-on<
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_the_java_based_rule_add_on">Test the Java-based Rule Add-on</h4>
+<h4 id="_test_the_java_based_rule_add_on">6.3.4. Test the Java-based Rule Add-on</h4>
 <div class="paragraph">
 <p>Test the Java-based rule add-on against your application file by running the <code>windup-migrate-app</code> command in the Windup console prompt.</p>
 </div>
@@ -3236,7 +3236,7 @@ <h4 id="_test_the_java_based_rule_add_on">Test the Java-based Rule Add-on</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_review_the_output_report">Review the Output Report</h4>
+<h4 id="_review_the_output_report">6.3.5. Review the Output Report</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -3338,15 +3338,15 @@ <h4 id="_review_the_output_report">Review the Output Report</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_create_and_test_xml_rules">Create and Test XML Rules</h2>
+<h2 id="_create_and_test_xml_rules">7. Create and Test XML Rules</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Create-a-Basic-XML-Rule">Create a Basic XML Rule</h3>
+<h3 id="Rules-Create-a-Basic-XML-Rule">7.1. Create a Basic XML Rule</h3>
 <div class="paragraph">
 <p>You can create a rule addon using Java or a rule using XML or Groovy. This topic describes how to create a rule using XML.</p>
 </div>
 <div class="sect3">
-<h4 id="_prerequisites_3">Prerequisites</h4>
+<h4 id="_prerequisites_3">7.1.1. Prerequisites</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -3381,7 +3381,7 @@ <h4 id="_prerequisites_3">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_rule">Create a Rule</h4>
+<h4 id="_create_a_rule">7.1.2. Create a Rule</h4>
 <div class="paragraph">
 <p>The following is an example of an XML rule.</p>
 </div>
@@ -3435,7 +3435,7 @@ <h4 id="_create_a_rule">Create a Rule</h4>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_create_the_xml_rule">Create the XML Rule</h5>
+<h5 id="_create_the_xml_rule">7.1.2.1. Create the XML Rule</h5>
 <div class="paragraph">
 <p><strong>Note:</strong> Windup only analyzes XML files with names ending in <code>.windup.xml</code>. Be sure to name XML-based rules using this naming convention!</p>
 </div>
@@ -3515,7 +3515,7 @@ <h5 id="_create_the_xml_rule">Create the XML Rule</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_the_rule_to_windup">Add the Rule to Windup</h4>
+<h4 id="_add_the_rule_to_windup">7.1.3. Add the Rule to Windup</h4>
 <div class="paragraph">
 <p>A Windup rule is installed simply by copying the rule to the appropriate Windup folder. Windup scans for rules in the following locations:</p>
 </div>
@@ -3539,7 +3539,7 @@ <h4 id="_add_the_rule_to_windup">Add the Rule to Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_the_xml_rule">Test the XML Rule</h4>
+<h4 id="_test_the_xml_rule">7.1.4. Test the XML Rule</h4>
 <div class="admonitionblock note">
 <table>
 <tr>
@@ -3579,16 +3579,16 @@ <h4 id="_test_the_xml_rule">Test the XML Rule</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_core_developer_topics">Core Developer topics</h2>
+<h2 id="_core_developer_topics">8. Core Developer topics</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Dev-Windup-Bootstrap">Windup Bootstrap</h3>
+<h3 id="Dev-Windup-Bootstrap">8.1. Windup Bootstrap</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>This section describes how Windup starts up, finds the resources, loads the rules, and executes them.</p>
 </div>
 <div class="sect3">
-<h4 id="_boot">Boot</h4>
+<h4 id="_boot">8.1.1. Boot</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -3624,15 +3624,15 @@ <h4 id="_boot">Boot</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_graphcontext">GraphContext</h4>
+<h4 id="_graphcontext">8.1.2. GraphContext</h4>
 
 </div>
 <div class="sect3">
-<h4 id="_rulesubset">RuleSubset</h4>
+<h4 id="_rulesubset">8.1.3. RuleSubset</h4>
 
 </div>
 <div class="sect3">
-<h4 id="_frames_creation">Frames creation</h4>
+<h4 id="_frames_creation">8.1.4. Frames creation</h4>
 <div class="paragraph">
 <p>In the <code>GraphContextImpl</code> constructor. For additonal method Handlers,
 see</p>
@@ -3657,7 +3657,7 @@ <h4 id="_frames_creation">Frames creation</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Classloading-Notes">Classloading Notes</h3>
+<h3 id="Dev-Classloading-Notes">8.2. Classloading Notes</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p><em>Page contains temporary notes, to be edited.</em></p>
@@ -3666,7 +3666,7 @@ <h3 id="Dev-Classloading-Notes">Classloading Notes</h3>
 <p>This covers the specific situations when the Windup core developer needs to look up certain runtime classes. Does not relate to rules authoring.</p>
 </div>
 <div class="sect3">
-<h4 id="_finding_classes">Finding classes</h4>
+<h4 id="_finding_classes">8.2.1. Finding classes</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">AddonRegistry.getServices(MyServiceInterface.class)</code></pre>
@@ -3682,20 +3682,20 @@ <h4 id="_finding_classes">Finding classes</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_instantiating">Instantiating</h4>
+<h4 id="_instantiating">8.2.2. Instantiating</h4>
 <div class="paragraph">
 <p>If you want something from the current addon, you need to @Inject its ServiceRegistry and get services from that.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_which_classloader_is_used_always_the_one_of_the_current_code">Which classloader is used? Always the one of the current code?</h4>
+<h4 id="_which_classloader_is_used_always_the_one_of_the_current_code">8.2.3. Which classloader is used? Always the one of the current code?</h4>
 <div class="paragraph">
 <p>Depends, if you are in a Furnace Service, then yes, it will use the
 current code&#8217;s addon&#8217;s classloader.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_do_i_know_if_i_am_in_a_furnace_service">How do I know if I am in a Furnace service?</h4>
+<h4 id="_how_do_i_know_if_i_am_in_a_furnace_service">8.2.4. How do I know if I am in a Furnace service?</h4>
 <div class="paragraph">
 <p>Every furnace service is wrapped in a proxy. If it came from another
 addon (not your current addon) and was not instantiated with new Blah(),
@@ -3745,7 +3745,7 @@ <h4 id="_how_do_i_know_if_i_am_in_a_furnace_service">How do I know if I am in a
 </div>
 </div>
 <div class="sect3">
-<h4 id="_resources_loading">Resources loading</h4>
+<h4 id="_resources_loading">8.2.5. Resources loading</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code>(16:48:30) ozizka-FN: lincolnthree:  Just a note - the potential collisions caused  by addon's CL span is not considered as a risk?
@@ -3773,27 +3773,27 @@ <h4 id="_resources_loading">Resources loading</h4>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_furnace_proxies">Furnace Proxies:</h5>
+<h5 id="_furnace_proxies">8.2.5.1. Furnace Proxies:</h5>
 <div class="paragraph">
 <p><a href="https://github.com/forge/furnace/blob/master/proxy/src/main/java/org/jboss/forge/furnace/proxy/Proxies.java#L15" class="bare">https://github.com/forge/furnace/blob/master/proxy/src/main/java/org/jboss/forge/furnace/proxy/Proxies.java#L15</a></p>
 </div>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_what_classloader_is_used_by_freemarker_to_load_resources">What classloader is used by Freemarker to load resources?</h4>
+<h4 id="_what_classloader_is_used_by_freemarker_to_load_resources">8.2.6. What classloader is used by Freemarker to load resources?</h4>
 <div class="paragraph">
 <p><code>org.jboss.windup.reporting.freemarker.FurnaceFreeMarkerTemplateLoader</code></p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Connect-to-the-Graph-via-Rexster">Connect to the Graph via Rexster</h3>
+<h3 id="Dev-Connect-to-the-Graph-via-Rexster">8.3. Connect to the Graph via Rexster</h3>
 <div class="paragraph">
 <p>There is a specific addon for running Rexster along your graph with
 groupId <strong>org.jboss.windup.rexster</strong> and <strong>artifactId</strong> Rexster.</p>
 </div>
 <div class="sect3">
-<h4 id="_running_rexster_within_your_test">Running Rexster Within Your Test</h4>
+<h4 id="_running_rexster_within_your_test">8.3.1. Running Rexster Within Your Test</h4>
 <div class="paragraph">
 <p>Deploy the Rexster add-on by adding the Rexster add-on to the dependencies.</p>
 </div>
@@ -3812,7 +3812,7 @@ <h4 id="_running_rexster_within_your_test">Running Rexster Within Your Test</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_rexster_within_windup">Run Rexster within Windup</h4>
+<h4 id="_run_rexster_within_windup">8.3.2. Run Rexster within Windup</h4>
 <div class="paragraph">
 <p>Make sure the Rexster add-on is deployed in Furnace and is accessible on <a href="http://localhost:8182/" class="bare">http://localhost:8182/</a>.</p>
 </div>
@@ -3825,9 +3825,9 @@ <h4 id="_run_rexster_within_windup">Run Rexster within Windup</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Decompiling">Decompiling</h3>
+<h3 id="Dev-Decompiling">8.4. Decompiling</h3>
 <div class="sect3">
-<h4 id="_the_strong_decompiler_strong_api">The <strong>Decompiler</strong> API</h4>
+<h4 id="_the_strong_decompiler_strong_api">8.4.1. The <strong>Decompiler</strong> API</h4>
 <div class="ulist">
 <div class="title">DRAFT</div>
 <ul>
@@ -3857,9 +3857,9 @@ <h4 id="_the_strong_decompiler_strong_api">The <strong>Decompiler</strong> API</
 </div>
 </div>
 <div class="sect3">
-<h4 id="_procyon">Procyon</h4>
+<h4 id="_procyon">8.4.2. Procyon</h4>
 <div class="sect4">
-<h5 id="_config">Config</h5>
+<h5 id="_config">8.4.2.1. Config</h5>
 <div class="ulist">
 <ul>
 <li>
@@ -3873,13 +3873,13 @@ <h5 id="_config">Config</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_typereference">TypeReference</h5>
+<h5 id="_typereference">8.4.2.2. TypeReference</h5>
 <div class="paragraph">
 <p>TODO: Check how we get info about Java files; perhaps cache the <code>TypeReference</code> results - if worth it?</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_itypeloader">ITypeLoader</h5>
+<h5 id="_itypeloader">8.4.2.3. ITypeLoader</h5>
 <div class="ulist">
 <ul>
 <li>
@@ -3909,7 +3909,7 @@ <h5 id="_itypeloader">ITypeLoader</h5>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Dependencies">Dependencies (Forge add-ons)</h3>
+<h3 id="Dev-Dependencies">8.5. Dependencies (Forge add-ons)</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p><em>Based on
@@ -3917,7 +3917,7 @@ <h3 id="Dev-Dependencies">Dependencies (Forge add-ons)</h3>
 discussion.</em></p>
 </div>
 <div class="sect3">
-<h4 id="_maven_add_on_structure">Maven Add-on Structure</h4>
+<h4 id="_maven_add_on_structure">8.5.1. Maven Add-on Structure</h4>
 <div class="paragraph">
 <p>The following is the typical structure of Maven <code>add-on</code> modules.</p>
 </div>
@@ -3967,7 +3967,7 @@ <h4 id="_maven_add_on_structure">Maven Add-on Structure</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_on_sub_parts">Add-on sub-parts</h4>
+<h4 id="_add_on_sub_parts">8.5.2. Add-on sub-parts</h4>
 <div class="paragraph">
 <p>Add-on sub-parts declare dependency preferably on forge add-on APIs, not
 on the add-ons themselves, wherever possible (wherever an add-on has an
@@ -4025,7 +4025,7 @@ <h4 id="_add_on_sub_parts">Add-on sub-parts</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_dependencies">Test dependencies</h4>
+<h4 id="_test_dependencies">8.5.3. Test dependencies</h4>
 <div class="paragraph">
 <p>For test dependencies on add-ons: Any addon/sub-part requiring an addon
 for testing purposes should use <code>&lt;scope&gt;test&lt;/scope&gt;</code>.</p>
@@ -4043,7 +4043,7 @@ <h4 id="_test_dependencies">Test dependencies</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_dependencies_between_sub_parts_within_the_same_add_on">Dependencies between sub-parts within the same add-on</h4>
+<h4 id="_dependencies_between_sub_parts_within_the_same_add_on">8.5.4. Dependencies between sub-parts within the same add-on</h4>
 <div class="paragraph">
 <p>Subpart may declare dependency on other subpart. E.g. <code>impl</code> typically
 depends on <code>api</code>. In that case, the scope should be set appropriately
@@ -4061,18 +4061,18 @@ <h4 id="_dependencies_between_sub_parts_within_the_same_add_on">Dependencies bet
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Frames-Extensions">Frames Extensions</h3>
+<h3 id="Dev-Frames-Extensions">8.6. Frames Extensions</h3>
 <div class="paragraph">
 <p>Windup has several Frames extensions to satisfy its needs.</p>
 </div>
 <div class="sect3">
-<h4 id="_multiple_types_in_a_vertex">Multiple Types in a Vertex</h4>
+<h4 id="_multiple_types_in_a_vertex">8.6.1. Multiple Types in a Vertex</h4>
 <div class="paragraph">
 <p>Frames stores only one type in the <em>type</em> property. To specify multiple types, use the '|' separator. All sub-parts are indexed.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_map_handler">Map Handler</h4>
+<h4 id="_map_handler">8.6.2. Map Handler</h4>
 <div class="paragraph">
 <p>TBD</p>
 </div>
@@ -4081,7 +4081,7 @@ <h4 id="_map_handler">Map Handler</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_map">Map</h4>
+<h4 id="_map">8.6.3. Map</h4>
 <div class="paragraph">
 <p>To store a map in as adjacent vertices.</p>
 </div>
@@ -4100,7 +4100,7 @@ <h4 id="_map">Map</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_list_handler">List handler.</h4>
+<h4 id="_list_handler">8.6.4. List handler.</h4>
 <div class="paragraph">
 <p>TBD.</p>
 </div>
@@ -4110,7 +4110,7 @@ <h4 id="_list_handler">List handler.</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_list">List</h4>
+<h4 id="_list">8.6.5. List</h4>
 <div class="paragraph">
 <p><code>WindupVertexListModel</code> offers a generic model for lists of other
 models, which are stored as adjacent vertices.</p>
@@ -4118,9 +4118,9 @@ <h4 id="_list">List</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Internal-API-Features">Internal API Features</h3>
+<h3 id="Dev-Internal-API-Features">8.7. Internal API Features</h3>
 <div class="sect3">
-<h4 id="_find_the_ruleprovider_that_provided_a_rule">Find the RuleProvider that provided a Rule</h4>
+<h4 id="_find_the_ruleprovider_that_provided_a_rule">8.7.1. Find the RuleProvider that provided a Rule</h4>
 <div class="paragraph">
 <p>A <code>Rule</code> implements <code>Context</code>, which stores metadata. The following example gets the RuleProvider from the Rule context.</p>
 </div>
@@ -4135,7 +4135,7 @@ <h4 id="_find_the_ruleprovider_that_provided_a_rule">Find the RuleProvider that
 </div>
 </div>
 <div class="sect3">
-<h4 id="_in_memory_frames">In-memory Frames</h4>
+<h4 id="_in_memory_frames">8.7.2. In-memory Frames</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">GraphService&lt;FooModel&gt; fooModelService = context.getService(FooModel.class);
@@ -4144,7 +4144,7 @@ <h4 id="_in_memory_frames">In-memory Frames</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_performance_measurement">Performance measurement</h4>
+<h4 id="_performance_measurement">8.7.3. Performance measurement</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">ExecutionStatistics.get().begin("Process-01");
@@ -4158,13 +4158,13 @@ <h4 id="_performance_measurement">Performance measurement</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Logging">Logging</h3>
+<h3 id="Dev-Logging">8.8. Logging</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p><em>This page describes how to log from the Java-based rules.</em></p>
 </div>
 <div class="sect3">
-<h4 id="_textual_logging">Textual logging</h4>
+<h4 id="_textual_logging">8.8.1. Textual logging</h4>
 <div class="paragraph">
 <p>Windup uses <code>java.util.logging</code>. Convenient way to get the logger is:</p>
 </div>
@@ -4175,7 +4175,7 @@ <h4 id="_textual_logging">Textual logging</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_displaying_progress">Displaying Progress</h4>
+<h4 id="_displaying_progress">8.8.2. Displaying Progress</h4>
 <div class="paragraph">
 <p>IterationProgress</p>
 </div>
@@ -4192,59 +4192,59 @@ <h4 id="_displaying_progress">Displaying Progress</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Variables-Stack">Variables Stack</h3>
+<h3 id="Dev-Variables-Stack">8.9. Variables Stack</h3>
 <div class="paragraph">
 <p>The <code>Variables</code> class stores the variables which are available in rules, EL expressions, and FreeMarker and XSLT templates.</p>
 </div>
 <div class="sect3">
-<h4 id="_accessing_variables">Accessing variables</h4>
+<h4 id="_accessing_variables">8.9.1. Accessing variables</h4>
 <div class="sect4">
-<h5 id="_from_a_java_based_rule">From a Java-based rule</h5>
+<h5 id="_from_a_java_based_rule">8.9.1.1. From a Java-based rule</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_from_a_groovy_based_rule">From a Groovy-based rule</h5>
+<h5 id="_from_a_groovy_based_rule">8.9.1.2. From a Groovy-based rule</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_from_an_el_expression">From an EL expression</h5>
+<h5 id="_from_an_el_expression">8.9.1.3. From an EL expression</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_from_a_freemarker">From a FreeMarker</h5>
+<h5 id="_from_a_freemarker">8.9.1.4. From a FreeMarker</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_from_xslt_template">From XSLT template</h5>
+<h5 id="_from_xslt_template">8.9.1.5. From XSLT template</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_accessing_variables_as_a_flat_code_map_code">Accessing variables as a flat <code>Map</code></h4>
+<h4 id="_accessing_variables_as_a_flat_code_map_code">8.9.2. Accessing variables as a flat <code>Map</code></h4>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Port-WindRide-Functionality-to-Windup">Port WindRide Functionality to Windup</h3>
+<h3 id="Dev-Port-WindRide-Functionality-to-Windup">8.10. Port WindRide Functionality to Windup</h3>
 <div class="paragraph">
 <p><em>For the purposes of tracking the porting WindRide functionality to Windup. Will be
 removed when done.</em></p>
 </div>
 </div>
 <div class="sect2">
-<h3 id="some-classes-mapping">Some classes mapping</h3>
+<h3 id="some-classes-mapping">8.11. Some classes mapping</h3>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">@ConfigPartDescriptor = @ReportItem
@@ -4254,7 +4254,7 @@ <h3 id="some-classes-mapping">Some classes mapping</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="server-side-code-to-be-moved">Server-side code to be moved</h3>
+<h3 id="server-side-code-to-be-moved">8.12. Server-side code to be moved</h3>
 <div class="ulist">
 <ul>
 <li>
@@ -4315,7 +4315,7 @@ <h3 id="server-side-code-to-be-moved">Server-side code to be moved</h3>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_alternate_approach">Alternate Approach</h4>
+<h4 id="_alternate_approach">8.12.1. Alternate Approach</h4>
 <div class="paragraph">
 <p>This is the approach GitHub suggests.</p>
 </div>
@@ -4355,12 +4355,12 @@ <h4 id="_alternate_approach">Alternate Approach</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_rules_topics">Rules topics</h2>
+<h2 id="_rules_topics">9. Rules topics</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Available-Rules-Utilities">Available Rule Utilities</h3>
+<h3 id="Rules-Available-Rules-Utilities">9.1. Available Rule Utilities</h3>
 <div class="sect3">
-<h4 id="_programmatically_access_the_graph">Programmatically Access the Graph</h4>
+<h4 id="_programmatically_access_the_graph">9.1.1. Programmatically Access the Graph</h4>
 <div class="paragraph">
 <p><em>Note: Needs update. This is out of date!</em></p>
 </div>
@@ -4371,13 +4371,13 @@ <h4 id="_programmatically_access_the_graph">Programmatically Access the Graph</h
 <p>This topic describes how to to programmatically access or update graph data when you create a Java-based rule addon.</p>
 </div>
 <div class="sect4">
-<h5 id="_query_the_graph">Query the graph</h5>
+<h5 id="_query_the_graph">9.1.1.1. Query the graph</h5>
 <div class="paragraph">
 <p>There are several ways - including Query API, Gremlin support, or
 GraphService methods.</p>
 </div>
 <div class="sect5">
-<h6 id="_query_the_graph_within_the_when_method">Query the Graph Within the .when() method</h6>
+<h6 id="_query_the_graph_within_the_when_method">9.1.1.1.1. Query the Graph Within the .when() method</h6>
 <div class="paragraph">
 <p>Building a rule contains the method when(), which is used to create a
 <strong>condition</strong>. Vertices that fulfill the condition, are passed to the
@@ -4411,7 +4411,7 @@ <h6 id="_query_the_graph_within_the_when_method">Query the Graph Within the .whe
 </div>
 </div>
 <div class="sect5">
-<h6 id="_iteration_2">Iteration</h6>
+<h6 id="_iteration_2">9.1.1.1.2. Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">ConfigurationBuilder.begin().addRule()
@@ -4426,7 +4426,7 @@ <h6 id="_iteration_2">Iteration</h6>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_nested_iteration">Nested Iteration</h6>
+<h6 id="_nested_iteration">9.1.1.1.3. Nested Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">code,java
@@ -4454,7 +4454,7 @@ <h6 id="_nested_iteration">Nested Iteration</h6>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_modify_graph_data">Modify Graph Data</h4>
+<h4 id="_modify_graph_data">9.1.2. Modify Graph Data</h4>
 <div class="paragraph">
 <p>For more custom operations dealing with Graph data that are not covered by the <code>Query</code> mechanism, use the GraphService.</p>
 </div>
@@ -4484,7 +4484,7 @@ <h4 id="_modify_graph_data">Modify Graph Data</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Concepts-and-Philosophy">Concepts &amp; Philosophy</h3>
+<h3 id="Dev-Concepts-and-Philosophy">9.2. Concepts &amp; Philosophy</h3>
 <div class="paragraph">
 <p><em>TODO - OZIZKA: Can this topic be marked obsolete and be replaced by this one: <a href="#Windup-Processing-Overview">Windup Processing Overview</a> ?</em></p>
 </div>
@@ -4500,7 +4500,7 @@ <h3 id="Dev-Concepts-and-Philosophy">Concepts &amp; Philosophy</h3>
 database.</p>
 </div>
 <div class="sect3">
-<h4 id="_graph_database_and_models_frames">Graph database and Models (Frames)</h4>
+<h4 id="_graph_database_and_models_frames">9.2.1. Graph database and Models (Frames)</h4>
 <div class="paragraph">
 <p>As a graph db implementation, we use <a href="http://tinkerpop.com/">TinkerPop</a>
 backed by <a href="http://thinkaurelius.github.io/titan/">Titan</a> backed by
@@ -4522,7 +4522,7 @@ <h4 id="_graph_database_and_models_frames">Graph database and Models (Frames)</h
 </div>
 </div>
 <div class="sect3">
-<h4 id="_examples_of_breaking_non_trivial_workflows_into_rules">Examples of breaking non-trivial workflows into rules</h4>
+<h4 id="_examples_of_breaking_non_trivial_workflows_into_rules">9.2.2. Examples of breaking non-trivial workflows into rules</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -4568,7 +4568,7 @@ <h4 id="_examples_of_breaking_non_trivial_workflows_into_rules">Examples of brea
 </div>
 </div>
 <div class="sect2">
-<h3 id="_rulesets">Rulesets</h3>
+<h3 id="_rulesets">9.3. Rulesets</h3>
 <div class="paragraph">
 <p>DRAFT</p>
 </div>
@@ -4576,7 +4576,7 @@ <h3 id="_rulesets">Rulesets</h3>
 <p>Example page for design decisions. Could be generated automatically in the future.</p>
 </div>
 <div class="sect3">
-<h4 id="_what_is_a_ruleset">What is a Ruleset?</h4>
+<h4 id="_what_is_a_ruleset">9.3.1. What is a Ruleset?</h4>
 <div class="paragraph">
 <p>A ruleset is a Windup "plug-in" targetting a specific area of migration (e.g. Spring to Java EE 6 migration). Underhood, it is a set of rules, and everything they might need: Operations and Conditions, Report templates (if needed), and  static files (e.g. images, XML or CSV files, etc.).
 A ruleset may also declare metadata, like ruleset ID, dependencies on other rulesets, etc.</p>
@@ -4593,7 +4593,7 @@ <h4 id="_what_is_a_ruleset">What is a Ruleset?</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_basic_tags">Basic tags</h4>
+<h4 id="_basic_tags">9.3.2. Basic tags</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -4616,9 +4616,9 @@ <h4 id="_basic_tags">Basic tags</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rulesets_2">Rulesets</h4>
+<h4 id="_rulesets_2">9.3.3. Rulesets</h4>
 <div class="sect4">
-<h5 id="_core_rulesets">Core rulesets</h5>
+<h5 id="_core_rulesets">9.3.3.1. Core rulesets</h5>
 <div class="paragraph">
 <p>Rulesets distributed with Windup and maintained by the Windup team.</p>
 </div>
@@ -4662,7 +4662,7 @@ <h5 id="_core_rulesets">Core rulesets</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_community_rulesets">Community rulesets</h5>
+<h5 id="_community_rulesets">9.3.3.2. Community rulesets</h5>
 <div class="paragraph">
 <p>Rulesets contributed by Windup users.
 === Java Basic Ruleset</p>
@@ -4677,14 +4677,14 @@ <h5 id="_community_rulesets">Community rulesets</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_metadata_2">Metadata</h4>
+<h4 id="_metadata_2">9.3.4. Metadata</h4>
 <div class="paragraph">
 <p><strong>ID:</strong> myRuleset
 <strong>Graph prefix:</strong> myRuleset</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rule_providers">Rule providers</h4>
+<h4 id="_rule_providers">9.3.5. Rule providers</h4>
 <div class="paragraph">
 <p><em>A definition list (dl/dt/dd) of RuleProviders of given Ruleset.</em></p>
 </div>
@@ -4709,7 +4709,7 @@ <h4 id="_rule_providers">Rule providers</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_models_2">Models</h4>
+<h4 id="_models_2">9.3.6. Models</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -4812,7 +4812,7 @@ <h4 id="_models_2">Models</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_configuration">Configuration</h4>
+<h4 id="_configuration">9.3.7. Configuration</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -4822,18 +4822,18 @@ <h4 id="_configuration">Configuration</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reports">Reports</h4>
+<h4 id="_reports">9.3.8. Reports</h4>
 
 </div>
 </div>
 <div class="sect2">
-<h3 id="_ruleset_java_classifications_and_inline_hints">Ruleset Java Classifications and Inline Hints</h3>
+<h3 id="_ruleset_java_classifications_and_inline_hints">9.4. Ruleset Java Classifications and Inline Hints</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>Some of the most important rules are <strong>classifications</strong> and <strong>inline hints</strong>.</p>
 </div>
 <div class="sect3">
-<h4 id="_classifications">Classifications</h4>
+<h4 id="_classifications">9.4.1. Classifications</h4>
 <div class="paragraph">
 <p>Classifications are important because they tell developers very quickly
 <strong><em>what</em></strong> the resource is, so that they can quickly identify resources of
@@ -4859,7 +4859,7 @@ <h4 id="_classifications">Classifications</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_inline_hints">Inline Hints</h4>
+<h4 id="_inline_hints">9.4.2. Inline Hints</h4>
 <div class="paragraph">
 <p>Windup takes the approach of profiling resources and providing
 syntactically highlighted resource reports. The resource report will
@@ -4873,7 +4873,7 @@ <h4 id="_inline_hints">Inline Hints</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Ruleset-Java-EE-Apps">Ruleset Java EE Apps</h3>
+<h3 id="Ruleset-Java-EE-Apps">9.5. Ruleset Java EE Apps</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>TBD?
@@ -4884,7 +4884,7 @@ <h3 id="Ruleset-Java-EE-Apps">Ruleset Java EE Apps</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Ruleset-Reporting">Ruleset Reporting</h3>
+<h3 id="Ruleset-Reporting">9.6. Ruleset Reporting</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>TBD?
@@ -4905,14 +4905,14 @@ <h3 id="Ruleset-Reporting">Ruleset Reporting</h3>
 <p>A core ruleset to provide support for XML files.</p>
 </div>
 <div class="sect3">
-<h4 id="_metadata_3">Metadata</h4>
+<h4 id="_metadata_3">9.6.1. Metadata</h4>
 <div class="paragraph">
 <p><strong>ID:</strong> xml
 <strong>Graph prefix:</strong> xml</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rule_providers_2">Rule providers</h4>
+<h4 id="_rule_providers_2">9.6.2. Rule providers</h4>
 <div class="paragraph">
 <p><em>A definition list (dl/dt/dd) of RuleProviders of given Ruleset with brief descriptions.</em></p>
 </div>
@@ -4979,7 +4979,7 @@ <h4 id="_rule_providers_2">Rule providers</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_models_3">Models</h4>
+<h4 id="_models_3">9.6.3. Models</h4>
 <div class="paragraph">
 <p>_Subclasses of <code>WindupVertexFrame</code>.</p>
 </div>
@@ -5001,20 +5001,20 @@ <h4 id="_models_3">Models</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_configuration_2">Configuration</h4>
+<h4 id="_configuration_2">9.6.4. Configuration</h4>
 <div class="paragraph">
 <p>_Subclasses of <code>TODO</code></p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reports_2">Reports</h4>
+<h4 id="_reports_2">9.6.5. Reports</h4>
 <div class="paragraph">
 <p><em>Report files or report parts created by this ruleset.</em></p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Windup-Models">Windup Models</h3>
+<h3 id="Rules-Windup-Models">9.7. Windup Models</h3>
 <div class="paragraph">
 <p>Windup models are the classes extending WindupVertexFrame.
 They are used to model the data in the graph database to Java objects.</p>
@@ -5027,7 +5027,7 @@ <h3 id="Rules-Windup-Models">Windup Models</h3>
 <p><span class="image"><img src="images/WindupModels-NbScreenshot.png" alt="Windup Models Graphic"></span></p>
 </div>
 <div class="sect3">
-<h4 id="_meta_models">Meta Models</h4>
+<h4 id="_meta_models">9.7.1. Meta Models</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -5040,26 +5040,26 @@ <h4 id="_meta_models">Meta Models</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_core_models">Core Models</h4>
+<h4 id="_core_models">9.7.2. Core Models</h4>
 <div class="paragraph">
 <p>FileModel ArchiveModel</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reporting_models">Reporting Models</h4>
+<h4 id="_reporting_models">9.7.3. Reporting Models</h4>
 
 </div>
 <div class="sect3">
-<h4 id="_custom_models_coming_from_addons">Custom Models (coming from Addons)</h4>
+<h4 id="_custom_models_coming_from_addons">9.7.4. Custom Models (coming from Addons)</h4>
 <div class="paragraph">
 <p>See respective ruleset&#8217;s documentation.</p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Create-Java-Queries">Create Java Queries</h3>
+<h3 id="Rules-Create-Java-Queries">9.8. Create Java Queries</h3>
 <div class="sect3">
-<h4 id="_query_for_all_frames_of_some_model">Query for all frames of some Model</h4>
+<h4 id="_query_for_all_frames_of_some_model">9.8.1. Query for all frames of some Model</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">Query.find(FileModel.class).as("result")</code></pre>
@@ -5067,7 +5067,7 @@ <h4 id="_query_for_all_frames_of_some_model">Query for all frames of some Model<
 </div>
 </div>
 <div class="sect3">
-<h4 id="_query_by_property">Query by property</h4>
+<h4 id="_query_by_property">9.8.2. Query by property</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">Query.find(FileModel.class)
@@ -5077,7 +5077,7 @@ <h4 id="_query_by_property">Query by property</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_gremlin_query">Gremlin query</h4>
+<h4 id="_gremlin_query">9.8.3. Gremlin query</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">code,java
@@ -5092,7 +5092,7 @@ <h4 id="_gremlin_query">Gremlin query</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_custom_query">Custom query</h4>
+<h4 id="_custom_query">9.8.4. Custom query</h4>
 <div class="paragraph">
 <p>The <code>Query</code> API is just a convenience implementation. For a custom
 query, implement your own <code>GraphCondition</code>:</p>
@@ -5111,16 +5111,16 @@ <h4 id="_custom_query">Custom query</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rules-Metadata">Rules Metadata</h3>
+<h3 id="Rules-Rules-Metadata">9.9. Rules Metadata</h3>
 <div class="sect3">
-<h4 id="_overview_2">Overview</h4>
+<h4 id="_overview_2">9.9.1. Overview</h4>
 <div class="paragraph">
 <div class="title">Draft</div>
 <p>Rules metadata are used for ordering, filtering, debugging and performance reasons.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_metadata_used_by_windup">Metadata used by Windup</h4>
+<h4 id="_metadata_used_by_windup">9.9.2. Metadata used by Windup</h4>
 <div class="paragraph">
 <p>To control ordering, override <code>getExecuteAfter()</code> and <code>getExecuteBefore()</code>.</p>
 </div>
@@ -5174,7 +5174,7 @@ <h4 id="_metadata_used_by_windup">Metadata used by Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_to_define_rule_metadata">How to define rule metadata</h4>
+<h4 id="_how_to_define_rule_metadata">9.9.3. How to define rule metadata</h4>
 <div class="paragraph">
 <p>The <code>RuleMetadata</code> is defined using the <code>.withMetadata(Object key, Object value)</code>.</p>
 </div>
@@ -5205,7 +5205,7 @@ <h4 id="_how_to_define_rule_metadata">How to define rule metadata</h4>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_why_a_map">Why a Map?</h5>
+<h5 id="_why_a_map">9.9.3.1. Why a Map?</h5>
 <div class="paragraph">
 <p>For the rules definition, Windup uses the OCPsoft Rewrite library. Whenever there is something Windup specific which can&#8217;t be pulled to the upstream implementation, Windup resorts to putting data into a metadata map.</p>
 </div>
@@ -5215,7 +5215,7 @@ <h5 id="_why_a_map">Why a Map?</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_ruleset_metadata">Ruleset metadata</h4>
+<h4 id="_ruleset_metadata">9.9.4. Ruleset metadata</h4>
 <div class="paragraph">
 <p>Ruleset metadata cover the whole Ruleset, not individual rules.
 For ruleset metadata, unlike rules, Windup uses a type-safe interface <code>WindupRulesetMetadata</code>
@@ -5227,7 +5227,7 @@ <h4 id="_ruleset_metadata">Ruleset metadata</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rules-Operations">Rules Operations</h3>
+<h3 id="Rules-Rules-Operations">9.10. Rules Operations</h3>
 <div class="paragraph">
 <p><em>A list of high-level operations across rulesets.</em></p>
 </div>
@@ -5279,12 +5279,12 @@ <h3 id="Rules-Rules-Operations">Rules Operations</h3>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_debugging_and_troubleshooting">Debugging and Troubleshooting</h2>
+<h2 id="_debugging_and_troubleshooting">10. Debugging and Troubleshooting</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Dev-Debugging-and-Profiling">Debugging and Profiling</h3>
+<h3 id="Dev-Debugging-and-Profiling">10.1. Debugging and Profiling</h3>
 <div class="sect3">
-<h4 id="_debug_the_windup_distribution_runtime">Debug the Windup Distribution Runtime</h4>
+<h4 id="_debug_the_windup_distribution_runtime">10.1.1. Debug the Windup Distribution Runtime</h4>
 <div class="paragraph">
 <p>You can debug the Windup distribution using one of the following approaches.</p>
 </div>
@@ -5311,13 +5311,13 @@ <h4 id="_debug_the_windup_distribution_runtime">Debug the Windup Distribution Ru
 </div>
 </div>
 <div class="sect3">
-<h4 id="_debug_a_test_using_netbeans">Debug a Test Using NetBeans</h4>
+<h4 id="_debug_a_test_using_netbeans">10.1.2. Debug a Test Using NetBeans</h4>
 <div class="paragraph">
 <p>Click the <code>Debug Test File</code> button, or choose <code>Menu</code> → <code>Debug</code> → <code>Debug Test File</code>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_profile_a_test_using_netbeans">Profile a Test Using NetBeans</h4>
+<h4 id="_profile_a_test_using_netbeans">10.1.3. Profile a Test Using NetBeans</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -5359,7 +5359,7 @@ <h4 id="_profile_a_test_using_netbeans">Profile a Test Using NetBeans</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_profile_forge_runtime_using_yourkit">Profile Forge Runtime Using YourKit</h4>
+<h4 id="_profile_forge_runtime_using_yourkit">10.1.4. Profile Forge Runtime Using YourKit</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -5391,9 +5391,9 @@ <h4 id="_profile_forge_runtime_using_yourkit">Profile Forge Runtime Using YourKi
 </div>
 </div>
 <div class="sect2">
-<h3 id="_troubleshoot_windup_issues">Troubleshoot Windup Issues</h3>
+<h3 id="_troubleshoot_windup_issues">10.2. Troubleshoot Windup Issues</h3>
 <div class="sect3">
-<h4 id="_logging">Logging</h4>
+<h4 id="_logging">10.2.1. Logging</h4>
 <div class="paragraph">
 <p>Logging is currently broken and will not be fixed any time soon.</p>
 </div>
@@ -5402,7 +5402,7 @@ <h4 id="_logging">Logging</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_debugging_exceptions">Debugging Exceptions</h4>
+<h4 id="_debugging_exceptions">10.2.2. Debugging Exceptions</h4>
 <div class="paragraph">
 <p>Exceptions in Surefire reports are broken due to the way Forge wraps
 exceptions and the way Surefire handles them. You need to
@@ -5413,27 +5413,27 @@ <h4 id="_debugging_exceptions">Debugging Exceptions</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_classloading_problems">Classloading Problems</h4>
+<h4 id="_classloading_problems">10.2.3. Classloading Problems</h4>
 <div class="paragraph">
 <p>Configuring dependencies in a Forge-based project can be a little tricky.
 See <a href="#Dev-Dependencies">Dependencies</a> for some hints.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_wiki_and_product_documentation">Wiki and Product Documentation</h4>
+<h4 id="_wiki_and_product_documentation">10.2.4. Wiki and Product Documentation</h4>
 
 </div>
 </div>
 <div class="sect2">
-<h3 id="About-the-Windup-Wiki">About the Windup Wiki</h3>
+<h3 id="About-the-Windup-Wiki">10.3. About the Windup Wiki</h3>
 <div class="sect3">
-<h4 id="_purpose">Purpose</h4>
+<h4 id="_purpose">10.3.1. Purpose</h4>
 <div class="paragraph">
 <p>This wiki is a place to create Windup documentation in a collaborative manner, a bit wildly, and on the fly. It is intended to reflect the state of the Windup source code master branch, however pages may become obsolete as the master changes quickly.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_areas_of_interest">Areas of Interest</h4>
+<h4 id="_areas_of_interest">10.3.2. Areas of Interest</h4>
 <div class="paragraph">
 <p>The Wiki pages are divided into the following main areas of interest, which may often overlap. The page names use these prefixes:</p>
 </div>
@@ -5455,13 +5455,13 @@ <h4 id="_areas_of_interest">Areas of Interest</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_markdown_asciidoc_or">Markdown, AsciiDoc, or&#8230;&#8203;?</h4>
+<h4 id="_markdown_asciidoc_or">10.3.3. Markdown, AsciiDoc, or&#8230;&#8203;?</h4>
 <div class="paragraph">
 <p>This Wiki uses AsciiDoc because it is capable of handling the publishing requirements and structural elements needed to create technical books. If you would like to contribute to the documentation, feel free to use your favorite Wiki language, however, it will ultimately be converted to AsciiDoc.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_contributor_guidelines">Contributor Guidelines</h4>
+<h4 id="_contributor_guidelines">10.3.4. Contributor Guidelines</h4>
 <div class="paragraph">
 <p>Please see the <a href="https://github.com/windup/windup-documentation/blob/master/CONTRIBUTING.adoc">Contributing Guidelines</a> for details about how to name pages and use the correct AsciiDoc syntax to make the transition to the final documentation go more smoothly.</p>
 </div>
@@ -5519,7 +5519,7 @@ <h4 id="_contributor_guidelines">Contributor Guidelines</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Add-Images-to-the-Windup-Wiki">Add Images to the Windup Wiki</h3>
+<h3 id="Dev-Add-Images-to-the-Windup-Wiki">10.4. Add Images to the Windup Wiki</h3>
 <div class="ulist">
 <ul>
 <li>
@@ -5610,7 +5610,7 @@ <h3 id="Dev-Add-Images-to-the-Windup-Wiki">Add Images to the Windup Wiki</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Create-Windup-JavaDoc">Create Windup JavaDoc</h3>
+<h3 id="Dev-Create-Windup-JavaDoc">10.5. Create Windup JavaDoc</h3>
 <div class="paragraph">
 <p>The most recent Windup JavaDoc build is located here: <a href="http://windup.github.io/windup/docs/javadoc/latest/index.html" class="bare">http://windup.github.io/windup/docs/javadoc/latest/index.html</a></p>
 </div>
@@ -5646,9 +5646,9 @@ <h3 id="Dev-Create-Windup-JavaDoc">Create Windup JavaDoc</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Windup-Documentation-Process">Windup Documentation Process</h3>
+<h3 id="Dev-Windup-Documentation-Process">10.6. Windup Documentation Process</h3>
 <div class="sect3">
-<h4 id="_wiki_documentation">Wiki Documentation</h4>
+<h4 id="_wiki_documentation">10.6.1. Wiki Documentation</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -5661,7 +5661,7 @@ <h4 id="_wiki_documentation">Wiki Documentation</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_product_documentation">Product Documentation</h4>
+<h4 id="_product_documentation">10.6.2. Product Documentation</h4>
 <div class="paragraph">
 <p>Windup product documentation is stored here: <a href="https://github.com/windup/windup-documentation" class="bare">https://github.com/windup/windup-documentation</a></p>
 </div>
@@ -5673,7 +5673,7 @@ <h4 id="_product_documentation">Product Documentation</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_publish_the_html_docs_to_online_docs_at_github_io">Publish the HTML docs to online docs (at GitHub IO)</h4>
+<h4 id="_publish_the_html_docs_to_online_docs_at_github_io">10.6.3. Publish the HTML docs to online docs (at GitHub IO)</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -5760,10 +5760,10 @@ <h4 id="_publish_the_html_docs_to_online_docs_at_github_io">Publish the HTML doc
 </div>
 </div>
 <div class="sect1">
-<h2 id="_additional_resources">Additional Resources</h2>
+<h2 id="_additional_resources">11. Additional Resources</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
+<h3 id="Review-the-Windup-Quickstarts">11.1. Review the Windup Quickstarts</h3>
 <div class="paragraph">
 <p>The Windup quickstarts provide working examples of how to create custom Java-based rule addons and XML rules. You can use them as a starting point for creating your own custom rules. The quickstarts are available on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a></p>
 </div>
@@ -5771,7 +5771,7 @@ <h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
 <p>You can fork and clone the project to have access to regular updates or you can download a ZIP file of the latest version.</p>
 </div>
 <div class="sect3">
-<h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
+<h4 id="_download_the_latest_zip">11.1.1. Download the Latest ZIP</h4>
 <div class="paragraph">
 <p>To download the latest quickstart ZIP file, browse to: <a href="https://github.com/windup/windup-quickstarts/releases" class="bare">https://github.com/windup/windup-quickstarts/releases</a></p>
 </div>
@@ -5780,7 +5780,7 @@ <h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h4>
+<h4 id="_fork_and_clone_the_github_project">11.1.2. Fork and Clone the GitHub Project</h4>
 <div class="paragraph">
 <p>If you don&#8217;t have the GitHub client (<code>git</code>), download it from: <a href="http://git-scm.com/" class="bare">http://git-scm.com/</a></p>
 </div>
@@ -5826,15 +5826,15 @@ <h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h
 </div>
 </div>
 <div class="sect2">
-<h3 id="Known-Issues">Known Windup Issues</h3>
+<h3 id="Known-Issues">11.2. Known Windup Issues</h3>
 <div class="paragraph">
 <p>Windup known issues are tracked here: <a href="https://issues.jboss.org/browse/WINDUP-496?jql=project%20%3D%20WINDUP%20AND%20issuetype%20%3D%20Bug%20AND%20status%20in%20%28Open%2C%20%22Coding%20In%20Progress%22%2C%20Reopened%2C%20%22Pull%20Request%20Sent%22%29">Open Windup issues</a></p>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Glossary">Glossary of Terms Used in Windup</h3>
+<h3 id="Glossary">11.3. Glossary of Terms Used in Windup</h3>
 <div class="sect3">
-<h4 id="_rules_terms">Rules Terms</h4>
+<h4 id="_rules_terms">11.3.1. Rules Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Rule</dt>
@@ -5897,7 +5897,7 @@ <h4 id="_rules_terms">Rules Terms</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reporting_terms">Reporting Terms</h4>
+<h4 id="_reporting_terms">11.3.2. Reporting Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Lift and Shift (Level of effort)</dt>
@@ -5925,7 +5925,7 @@ <h4 id="_reporting_terms">Reporting Terms</h4>
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2015-02-04 16:09:16 EST
+Last updated 2015-02-09 14:16:26 EST
 </div>
 </div>
 </body>
diff --git a/html/WindupRulesDevelopmentGuide.html b/html/WindupRulesDevelopmentGuide.html
index 0fa2bb90ae..f759e9cfa0 100644
--- a/html/WindupRulesDevelopmentGuide.html
+++ b/html/WindupRulesDevelopmentGuide.html
@@ -415,76 +415,76 @@ <h1>Windup Rules Development Guide</h1>
 <div id="toc" class="toc">
 <div id="toctitle">Table of Contents</div>
 <ul class="sectlevel1">
-<li><a href="#_overview">Overview</a>
+<li><a href="#_overview">1. Overview</a>
 <ul class="sectlevel2">
-<li><a href="#What-is-Windup">What is Windup?</a></li>
-<li><a href="#Features-of-Windup-2.0">Features of Windup 2.0</a></li>
-<li><a href="#Windup-Processing-Overview">Windup Processing Overview</a></li>
-<li><a href="#Get-Involved">Get Involved</a></li>
-<li><a href="#Report-Issues-with-Windup">Report Issues with Windup</a></li>
-<li><a href="#About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</a></li>
+<li><a href="#What-is-Windup">1.1. What is Windup?</a></li>
+<li><a href="#Features-of-Windup-2.0">1.2. Features of Windup 2.0</a></li>
+<li><a href="#Windup-Processing-Overview">1.3. Windup Processing Overview</a></li>
+<li><a href="#Get-Involved">1.4. Get Involved</a></li>
+<li><a href="#Report-Issues-with-Windup">1.5. Report Issues with Windup</a></li>
+<li><a href="#About-the-WINDUP_HOME-Variable">1.6. About the WINDUP_HOME Variable</a></li>
 </ul>
 </li>
-<li><a href="#_get_started">Get Started</a>
+<li><a href="#_get_started">2. Get Started</a>
 <ul class="sectlevel2">
-<li><a href="#Install-Windup">Install Windup</a></li>
-<li><a href="#Execute-Windup">Execute Windup</a></li>
-<li><a href="#Review-the-Report">Review the Report</a></li>
+<li><a href="#Install-Windup">2.1. Install Windup</a></li>
+<li><a href="#Execute-Windup">2.2. Execute Windup</a></li>
+<li><a href="#Review-the-Report">2.3. Review the Report</a></li>
 </ul>
 </li>
-<li><a href="#_configure_your_system_for_java_based_rules">Configure Your System for Java-based Rules</a>
+<li><a href="#_configure_your_system_for_java_based_rules">3. Configure Your System for Java-based Rules</a>
 <ul class="sectlevel2">
-<li><a href="#Install-and-Configure-Maven">Install and Configure Maven</a></li>
+<li><a href="#Install-and-Configure-Maven">3.1. Install and Configure Maven</a></li>
 </ul>
 </li>
-<li><a href="#_understand_the_rule_processing">Understand the Rule Processing</a>
+<li><a href="#_understand_the_rule_processing">4. Understand the Rule Processing</a>
 <ul class="sectlevel2">
-<li><a href="#Windup-Processing-Overview">Windup Processing Overview</a></li>
-<li><a href="#Rules-Rule-Execution-Lifecycle">Rule Execution Lifecycle</a></li>
-<li><a href="#Rules-Rule-Story-Points">Rule Story Points</a></li>
+<li><a href="#Windup-Processing-Overview">4.1. Windup Processing Overview</a></li>
+<li><a href="#Rules-Rule-Execution-Lifecycle">4.2. Rule Execution Lifecycle</a></li>
+<li><a href="#Rules-Rule-Story-Points">4.3. Rule Story Points</a></li>
 </ul>
 </li>
-<li><a href="#_create_and_test_java_rule_addons">Create and Test Java Rule Addons</a>
+<li><a href="#_create_and_test_java_rule_addons">5. Create and Test Java Rule Addons</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Java-based-Rule-Structure">Java-based Rule Structure</a></li>
-<li><a href="#Rules-Basic-Rule-Execution-Flow-Patterns">Basic Rule Execution Flow Patterns</a></li>
-<li><a href="#Rules-Create-a-Basic-Java-based-Rule-Add-on">Create a Basic Java-based Rule Add-on</a></li>
+<li><a href="#Rules-Java-based-Rule-Structure">5.1. Java-based Rule Structure</a></li>
+<li><a href="#Rules-Basic-Rule-Execution-Flow-Patterns">5.2. Basic Rule Execution Flow Patterns</a></li>
+<li><a href="#Rules-Create-a-Basic-Java-based-Rule-Add-on">5.3. Create a Basic Java-based Rule Add-on</a></li>
 </ul>
 </li>
-<li><a href="#_create_and_test_xml_rules">Create and Test XML Rules</a>
+<li><a href="#_create_and_test_xml_rules">6. Create and Test XML Rules</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Create-a-Basic-XML-Rule">Create a Basic XML Rule</a></li>
+<li><a href="#Rules-Create-a-Basic-XML-Rule">6.1. Create a Basic XML Rule</a></li>
 </ul>
 </li>
-<li><a href="#_review_the_report">Review the Report</a>
+<li><a href="#_review_the_report">7. Review the Report</a>
 <ul class="sectlevel2">
-<li><a href="#Review-the-Report">Review the Report</a></li>
+<li><a href="#Review-the-Report">7.1. Review the Report</a></li>
 </ul>
 </li>
-<li><a href="#_external_rule_examples">External Rule Examples</a>
+<li><a href="#_external_rule_examples">8. External Rule Examples</a>
 <ul class="sectlevel2">
-<li><a href="#Review-the-Windup-Quickstarts">Review the Windup Quickstarts</a></li>
+<li><a href="#Review-the-Windup-Quickstarts">8.1. Review the Windup Quickstarts</a></li>
 </ul>
 </li>
-<li><a href="#_debugging_and_troubleshooting">Debugging and Troubleshooting</a>
+<li><a href="#_debugging_and_troubleshooting">9. Debugging and Troubleshooting</a>
 <ul class="sectlevel2">
-<li><a href="#Dev-Debugging-and-Profiling">Debugging and Profiling</a></li>
-<li><a href="#_troubleshoot_windup_issues">Troubleshoot Windup Issues</a></li>
+<li><a href="#Dev-Debugging-and-Profiling">9.1. Debugging and Profiling</a></li>
+<li><a href="#_troubleshoot_windup_issues">9.2. Troubleshoot Windup Issues</a></li>
 </ul>
 </li>
-<li><a href="#_additional_resources">Additional Resources</a>
+<li><a href="#_additional_resources">10. Additional Resources</a>
 <ul class="sectlevel2">
-<li><a href="#Rules-Available-Rules-Utilities">Available Rule Utilities</a></li>
-<li><a href="#Review-the-Windup-Quickstarts">Review the Windup Quickstarts</a></li>
-<li><a href="#Known-Issues">Known Windup Issues</a></li>
-<li><a href="#Glossary">Glossary of Terms Used in Windup</a></li>
+<li><a href="#Rules-Available-Rules-Utilities">10.1. Available Rule Utilities</a></li>
+<li><a href="#Review-the-Windup-Quickstarts">10.2. Review the Windup Quickstarts</a></li>
+<li><a href="#Known-Issues">10.3. Known Windup Issues</a></li>
+<li><a href="#Glossary">10.4. Glossary of Terms Used in Windup</a></li>
 </ul>
 </li>
-<li><a href="#_appendix">Appendix</a>
+<li><a href="#_appendix">11. Appendix</a>
 <ul class="sectlevel2">
-<li><a href="#Windup-Architectural-Components">Windup Architectural Components</a></li>
-<li><a href="#Dev-Dependencies">Dependencies (Forge add-ons)</a></li>
-<li><a href="#Rules-Windup-Models">Windup Models</a></li>
+<li><a href="#Windup-Architectural-Components">11.1. Windup Architectural Components</a></li>
+<li><a href="#Dev-Dependencies">11.2. Dependencies (Forge add-ons)</a></li>
+<li><a href="#Rules-Windup-Models">11.3. Windup Models</a></li>
 </ul>
 </li>
 </ul>
@@ -492,14 +492,14 @@ <h1>Windup Rules Development Guide</h1>
 </div>
 <div id="content">
 <div class="sect1">
-<h2 id="_overview">Overview</h2>
+<h2 id="_overview">1. Overview</h2>
 <div class="sectionbody">
 <div class="paragraph">
 <p>This guide is for engineers, consultants, and others who plan to create
 custom rules for Windup 2.0.</p>
 </div>
 <div class="sect2">
-<h3 id="What-is-Windup">What is Windup?</h3>
+<h3 id="What-is-Windup">1.1. What is Windup?</h3>
 <div class="paragraph">
 <p><span class="image"><img src="images/windup-logo-wiki-header.jpg" alt="Windup Logo"></span></p>
 </div>
@@ -514,13 +514,13 @@ <h3 id="What-is-Windup">What is Windup?</h3>
 migrating from other containers to JBoss EAP a piece of cake.</p>
 </div>
 <div class="sect3">
-<h4 id="_windup_2_0_vs_windup_0_7_x">Windup 2.0 vs. Windup 0.7.x</h4>
+<h4 id="_windup_2_0_vs_windup_0_7_x">1.1.1. Windup 2.0 vs. Windup 0.7.x</h4>
 <div class="paragraph">
 <p>Windup 2.0 aims to deliver the same functionality as legacy Windup, however, the internal architecture and rule structure is very different and allows for the creation of much more complex rules.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?</h4>
+<h4 id="_how_does_windup_simplify_migration">1.1.2. How Does Windup Simplify Migration?</h4>
 <div class="paragraph">
 <p>Windup looks for common resources and highlight technologies and known “trouble
 spots” in migrating applications. The goal of Windup is to provide a
@@ -560,14 +560,14 @@ <h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?
 </table>
 </div>
 <div class="sect3">
-<h4 id="_follow_windup_on_twitter">Follow Windup on Twitter!</h4>
+<h4 id="_follow_windup_on_twitter">1.1.3. Follow Windup on Twitter!</h4>
 <div class="paragraph">
 <p>Follow Windup on Twitter <a href="https://twitter.com/jbosswindup">@JBossWindup</a> for updates and more!</p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
+<h3 id="Features-of-Windup-2.0">1.2. Features of Windup 2.0</h3>
 <div class="hdlist">
 <table>
 <tr>
@@ -701,7 +701,7 @@ <h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
+<h3 id="Windup-Processing-Overview">1.3. Windup Processing Overview</h3>
 <div class="paragraph">
 <p>Windup is a rule-based migration tool that allows you to write customized rules to analyze the APIs, technologies, and architectures used by the applications you plan to migrate. The Windup tool also executes its own core rules through all phases of the migration process.</p>
 </div>
@@ -709,7 +709,7 @@ <h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
 <p>The following is a high level conceptual overview of what happens within Windup when you execute the tool against your application or archive.</p>
 </div>
 <div class="sect3">
-<h4 id="_discovery_phase">Discovery Phase</h4>
+<h4 id="_discovery_phase">1.3.1. Discovery Phase</h4>
 <div class="paragraph">
 <p>Wnen you run the <code>windup-migrate-app</code> command, Windup executes its own core rules to extract files from archives, decompile classes, and analyze the application. In this phase, Windup builds a datamodel, storing component data and relationships in a graph database, which can then be queried and updated as needed by the migration rules and for reporting purposes.</p>
 </div>
@@ -718,7 +718,7 @@ <h4 id="_discovery_phase">Discovery Phase</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_application_migration">Application Migration</h4>
+<h4 id="_application_migration">1.3.2. Application Migration</h4>
 <div class="paragraph">
 <p>The next step in the process is the execution of the migration rules. In this phase, the rules typically do not execute against the application input files. Instead, they execute against the graph database model. Windup rules are independent and decoupled and they communicate with each other using the graph database model. Rules query the graph database to obtain information needed to test the rule condition. They also update the data model with information based on the result of the rule execution. This allows rules to easily interact with other rules and enables the creation of very complex rules.</p>
 </div>
@@ -727,7 +727,7 @@ <h4 id="_application_migration">Application Migration</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Findings Based on the Rule Execution Results</h4>
+<h4 id="_generate_findings_based_on_the_rule_execution_results">1.3.3. Generate Findings Based on the Rule Execution Results</h4>
 <div class="paragraph">
 <p>The final step in the process is to pull data from the graph database model to generate of reports and optionally generate scripts. Again, Windup uses rules to generate the final output.</p>
 </div>
@@ -753,9 +753,9 @@ <h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Finding
 </div>
 </div>
 <div class="sect2">
-<h3 id="Get-Involved">Get Involved</h3>
+<h3 id="Get-Involved">1.4. Get Involved</h3>
 <div class="sect3">
-<h4 id="_how_can_you_help">How can you help?</h4>
+<h4 id="_how_can_you_help">1.4.1. How can you help?</h4>
 <div class="paragraph">
 <p>To help us make Windup cover most application constructs and server configurations, including yours, you can help with any of the following items. Some items require only a few minutes of your time!</p>
 </div>
@@ -822,7 +822,7 @@ <h4 id="_how_can_you_help">How can you help?</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_helpful_links">Helpful links</h4>
+<h4 id="_helpful_links">1.4.2. Helpful links</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -867,12 +867,12 @@ <h4 id="_helpful_links">Helpful links</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Report-Issues-with-Windup">Report Issues with Windup</h3>
+<h3 id="Report-Issues-with-Windup">1.5. Report Issues with Windup</h3>
 <div class="paragraph">
 <p>Windup uses JIRA as its issue tracking system. If you encounter an issue executing Windup, please file a Windup JIRA Issue.</p>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_account">Create a JIRA Account</h4>
+<h4 id="_create_a_jira_account">1.5.1. Create a JIRA Account</h4>
 <div class="paragraph">
 <p>If you do not yet have a JIRA account, create one using the following procedure.</p>
 </div>
@@ -894,7 +894,7 @@ <h4 id="_create_a_jira_account">Create a JIRA Account</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
+<h4 id="_create_a_jira_issue">1.5.2. Create a JIRA Issue</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -953,7 +953,7 @@ <h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</h3>
+<h3 id="About-the-WINDUP_HOME-Variable">1.6. About the WINDUP_HOME Variable</h3>
 <div class="paragraph">
 <p>This documentation uses the <code>WINDUP_HOME</code> <strong>replaceable</strong> value to denote the path to the Windup distribution. When you encounter this value in the documentation, be sure to replace it with the actual path to your Windup installation.</p>
 </div>
@@ -971,10 +971,10 @@ <h3 id="About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</h3>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_get_started">Get Started</h2>
+<h2 id="_get_started">2. Get Started</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Install-Windup">Install Windup</h3>
+<h3 id="Install-Windup">2.1. Install Windup</h3>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1000,9 +1000,9 @@ <h3 id="Install-Windup">Install Windup</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Execute-Windup">Execute Windup</h3>
+<h3 id="Execute-Windup">2.2. Execute Windup</h3>
 <div class="sect3">
-<h4 id="_prerequisites">Prerequisites</h4>
+<h4 id="_prerequisites">2.2.1. Prerequisites</h4>
 <div class="paragraph">
 <p>Before you begin, you must gather the following information.</p>
 </div>
@@ -1067,7 +1067,7 @@ <h4 id="_prerequisites">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_start_windup">Start Windup</h4>
+<h4 id="_start_windup">2.2.2. Start Windup</h4>
 <div class="paragraph">
 <p>For information about the use of WINDUP_HOME in the instructions below, see <a href="#About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</a>.</p>
 </div>
@@ -1108,7 +1108,7 @@ <h4 id="_start_windup">Start Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migrate-app</code> Command</h4>
+<h4 id="_run_the_code_windup_migrate_app_code_command">2.2.3. Run the <code>windup-migrate-app</code> Command</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1191,7 +1191,7 @@ <h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migr
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
+<h4 id="_run_windup_in_batch_mode">2.2.4. Run Windup in Batch Mode</h4>
 <div class="paragraph">
 <p>Windup can be also executed in batch mode within a shell or batch script using the <code>--evaluate</code> argument as follows.</p>
 </div>
@@ -1213,7 +1213,7 @@ <h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_windup_help">Windup Help</h4>
+<h4 id="_windup_help">2.2.5. Windup Help</h4>
 <div class="paragraph">
 <p>To see the list of available parameters for the <code>windup-migrate-app</code> command, execute the following command in the Windup prompt:</p>
 </div>
@@ -1224,12 +1224,12 @@ <h4 id="_windup_help">Windup Help</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="windup-command-examples">Windup Command Examples</h4>
+<h4 id="windup-command-examples">2.2.6. Windup Command Examples</h4>
 <div class="paragraph">
 <p>The following Windup command examples report against applications located in the Windup source <a href="https://github.com/windup/windup/tree/master/test-files">test-files</a> directory.</p>
 </div>
 <div class="sect4">
-<h5 id="_source_code_example">Source Code Example</h5>
+<h5 id="_source_code_example">2.2.6.1. Source Code Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/tree/master/test-files/seam-booking-5.2">seam-booking-5.2</a> application source code. It evaluates all <code>org.jboss.seam</code> packages and creates a folder named 'seam-booking-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1240,7 +1240,7 @@ <h5 id="_source_code_example">Source Code Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_example">Archive Example</h5>
+<h5 id="_archive_example">2.2.6.2. Archive Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1251,7 +1251,7 @@ <h5 id="_archive_example">Archive Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_batch_example">Windup Batch Example</h5>
+<h5 id="_windup_batch_example">2.2.6.3. Windup Batch Example</h5>
 <div class="paragraph">
 <p>The following Windup batch command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1263,7 +1263,7 @@ <h5 id="_windup_batch_example">Windup Batch Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
+<h5 id="_windup_quickstart_examples">2.2.6.4. Windup Quickstart Examples</h5>
 <div class="paragraph">
 <p>For more concrete examples, see the Windup quickstarts located on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a>. If you prefer, you can download the <a href="https://github.com/windup/windup-quickstarts/releases/tag/2.0.0.Alpha1">2.0.0.Alpha1 release</a> ZIP or TAR  distribution of the quickstarts.</p>
 </div>
@@ -1274,9 +1274,9 @@ <h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Review-the-Report">Review the Report</h3>
+<h3 id="Review-the-Report">2.3. Review the Report</h3>
 <div class="sect3">
-<h4 id="_about_the_report">About the Report</h4>
+<h4 id="_about_the_report">2.3.1. About the Report</h4>
 <div class="paragraph">
 <p>When you execute Windup, the report is generated in the <code>OUTPUT_REPORT_DIRECTORY</code> you specify for the <code>--output</code> argument in the command line. This output directory contains the following files and subdirectories:</p>
 </div>
@@ -1309,7 +1309,7 @@ <h4 id="_about_the_report">About the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_open_the_report">Open the Report</h4>
+<h4 id="_open_the_report">2.3.2. Open the Report</h4>
 <div class="paragraph">
 <p>Use your favorite browser to open the <code>index.html</code> file located in the output report directory. You should see something like the following:</p>
 </div>
@@ -1321,9 +1321,9 @@ <h4 id="_open_the_report">Open the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_report_sections">Report Sections</h4>
+<h4 id="_report_sections">2.3.3. Report Sections</h4>
 <div class="sect4">
-<h5 id="_application_report_page">Application Report Page</h5>
+<h5 id="_application_report_page">2.3.3.1. Application Report Page</h5>
 <div class="paragraph">
 <p>The first section of the application report page summarizes the migration effort. It provides the total <em>Story Points</em> and a graphically displays the effort by technology. A <em>Story Point</em> is a term commonly used in Scrum Agile software development methodology to estimate the level of effort needed to implement a feature or change. It does not necessarily translate to man-hours, but the value should be consistent across tasks.</p>
 </div>
@@ -1345,7 +1345,7 @@ <h5 id="_application_report_page">Application Report Page</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
+<h5 id="_archive_analysis_sections">2.3.3.2. Archive Analysis Sections</h5>
 <div class="paragraph">
 <p>Each archive summary begins with a total of the story points assigned to its migration, followed by a table detailing the changes required for each file in the archive. The report contains the following columns.</p>
 </div>
@@ -1408,7 +1408,7 @@ <h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_file_analysis_pages">File Analysis Pages</h5>
+<h5 id="_file_analysis_pages">2.3.3.3. File Analysis Pages</h5>
 <div class="paragraph">
 <p>The analysis of the <code>jee-example-services.jar</code> lists the files in the JAR and the warnings and story points assigned to each one. Notice the <code>com.acme.anvil.listener.AnvilWebLifecycleListener</code> file has 5 warnings and is assigned 7 story points. Click on the file to see the detail.</p>
 </div>
@@ -1437,12 +1437,12 @@ <h5 id="_file_analysis_pages">File Analysis Pages</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_additional_reports">Additional Reports</h4>
+<h4 id="_additional_reports">2.3.4. Additional Reports</h4>
 <div class="paragraph">
 <p>Explore the Windup <code>OUTPUT_REPORT_DIRECTORY/reports</code> folder to find additional reporting information.</p>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report">2.3.4.1. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
@@ -1451,13 +1451,13 @@ <h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report_2">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report_2">2.3.4.2. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
+<h5 id="_individual_file_analysis_reports">2.3.4.3. Individual File Analysis Reports</h5>
 <div class="paragraph">
 <p>You can directly access the the file analysis report pages described above by browsing for them by name in the <code>OUTPUT_REPORT_DIRECTORY/reports/</code> directory. Because the same common file names can exist in multiple archives, for example "manifest.mf" or "web.xml", Windup adds a unique numeric suffix to each report file name.</p>
 </div>
@@ -1470,15 +1470,15 @@ <h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_configure_your_system_for_java_based_rules">Configure Your System for Java-based Rules</h2>
+<h2 id="_configure_your_system_for_java_based_rules">3. Configure Your System for Java-based Rules</h2>
 <div class="sectionbody">
 <div class="paragraph">
 <p>If you plan to create Java-based rule addons, you must also do the following.</p>
 </div>
 <div class="sect2">
-<h3 id="Install-and-Configure-Maven">Install and Configure Maven</h3>
+<h3 id="Install-and-Configure-Maven">3.1. Install and Configure Maven</h3>
 <div class="sect3">
-<h4 id="_download_and_install_maven">Download and Install Maven</h4>
+<h4 id="_download_and_install_maven">3.1.1. Download and Install Maven</h4>
 <div class="paragraph">
 <p>If you plan to use Eclipse Luna (4.4) to build Windup, you can skip this
 step. This version of Eclipse embeds Maven 3.2.1 so you do not need to
@@ -1504,7 +1504,7 @@ <h4 id="_download_and_install_maven">Download and Install Maven</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_configure_the_maven_installation_in_your_ide">Configure the Maven Installation in Your IDE</h4>
+<h4 id="_configure_the_maven_installation_in_your_ide">3.1.2. Configure the Maven Installation in Your IDE</h4>
 <div class="paragraph">
 <p>JBoss Developer Studio 7.1.1 is built upon Eclipse Kepler (4.3), which
 embeds Maven 3.0.4. If you plan to use JBoss Developer Studio 7.1.1 or
@@ -1538,7 +1538,7 @@ <h4 id="_configure_the_maven_installation_in_your_ide">Configure the Maven Insta
 </div>
 </div>
 <div class="sect3">
-<h4 id="configure-maven-to-build-windup">Configure Maven to Build Windup</h4>
+<h4 id="configure-maven-to-build-windup">3.1.3. Configure Maven to Build Windup</h4>
 <div class="paragraph">
 <p>Windup uses artifacts located in the
 <a href="http://repository.jboss.org/nexus/content/groups/public/">JBoss Nexus</a>
@@ -1604,10 +1604,10 @@ <h4 id="configure-maven-to-build-windup">Configure Maven to Build Windup</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_understand_the_rule_processing">Understand the Rule Processing</h2>
+<h2 id="_understand_the_rule_processing">4. Understand the Rule Processing</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
+<h3 id="Windup-Processing-Overview">4.1. Windup Processing Overview</h3>
 <div class="paragraph">
 <p>Windup is a rule-based migration tool that allows you to write customized rules to analyze the APIs, technologies, and architectures used by the applications you plan to migrate. The Windup tool also executes its own core rules through all phases of the migration process.</p>
 </div>
@@ -1615,7 +1615,7 @@ <h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
 <p>The following is a high level conceptual overview of what happens within Windup when you execute the tool against your application or archive.</p>
 </div>
 <div class="sect3">
-<h4 id="_discovery_phase_2">Discovery Phase</h4>
+<h4 id="_discovery_phase_2">4.1.1. Discovery Phase</h4>
 <div class="paragraph">
 <p>Wnen you run the <code>windup-migrate-app</code> command, Windup executes its own core rules to extract files from archives, decompile classes, and analyze the application. In this phase, Windup builds a datamodel, storing component data and relationships in a graph database, which can then be queried and updated as needed by the migration rules and for reporting purposes.</p>
 </div>
@@ -1624,7 +1624,7 @@ <h4 id="_discovery_phase_2">Discovery Phase</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_application_migration_2">Application Migration</h4>
+<h4 id="_application_migration_2">4.1.2. Application Migration</h4>
 <div class="paragraph">
 <p>The next step in the process is the execution of the migration rules. In this phase, the rules typically do not execute against the application input files. Instead, they execute against the graph database model. Windup rules are independent and decoupled and they communicate with each other using the graph database model. Rules query the graph database to obtain information needed to test the rule condition. They also update the data model with information based on the result of the rule execution. This allows rules to easily interact with other rules and enables the creation of very complex rules.</p>
 </div>
@@ -1633,7 +1633,7 @@ <h4 id="_application_migration_2">Application Migration</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_generate_findings_based_on_the_rule_execution_results_2">Generate Findings Based on the Rule Execution Results</h4>
+<h4 id="_generate_findings_based_on_the_rule_execution_results_2">4.1.3. Generate Findings Based on the Rule Execution Results</h4>
 <div class="paragraph">
 <p>The final step in the process is to pull data from the graph database model to generate of reports and optionally generate scripts. Again, Windup uses rules to generate the final output.</p>
 </div>
@@ -1659,9 +1659,9 @@ <h4 id="_generate_findings_based_on_the_rule_execution_results_2">Generate Findi
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rule-Execution-Lifecycle">Rule Execution Lifecycle</h3>
+<h3 id="Rules-Rule-Execution-Lifecycle">4.2. Rule Execution Lifecycle</h3>
 <div class="sect3">
-<h4 id="_rule_lifecycle">Rule Lifecycle</h4>
+<h4 id="_rule_lifecycle">4.2.1. Rule Lifecycle</h4>
 <div class="paragraph">
 <p>Windup executes each rule in sequential order. The following
 sections describe the phases of rule execution and how rules may specify
@@ -1675,7 +1675,7 @@ <h4 id="_rule_lifecycle">Rule Lifecycle</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rule_phases">Rule Phases</h4>
+<h4 id="_rule_phases">4.2.2. Rule Phases</h4>
 <div class="listingblock">
 <div class="content">
 <pre>INFO: Loaded [67] org.jboss.windup.config.WindupRuleProvider [
@@ -1775,7 +1775,7 @@ <h4 id="_rule_phases">Rule Phases</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_execute_before_and_execute_after">Execute Before and Execute After</h4>
+<h4 id="_execute_before_and_execute_after">4.2.3. Execute Before and Execute After</h4>
 <div class="paragraph">
 <p>A rule may specify that one or more rules must be executed before it is
 run. In this case, all named rules will be fired in the order specified
@@ -1807,16 +1807,16 @@ <h4 id="_execute_before_and_execute_after">Execute Before and Execute After</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Rule-Story-Points">Rule Story Points</h3>
+<h3 id="Rules-Rule-Story-Points">4.3. Rule Story Points</h3>
 <div class="sect3">
-<h4 id="_what_are_story_points">What are Story Points?</h4>
+<h4 id="_what_are_story_points">4.3.1. What are Story Points?</h4>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p>Story points are an abstract metric used in Scrum methodology to estimate the level of effort for various tasks. They are based on a <a href="http://scrummethodology.com/scrum-effort-estimation-and-story-points/">modified Fibonacci sequence</a>. In a similar manner, Windup uses story points to express the level of effort needed to migrate particular application constructs, and in a sum, the application as a whole.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_to_estimate_story_points_in_a_rule">How to Estimate Story Points in a Rule</h4>
+<h4 id="_how_to_estimate_story_points_in_a_rule">4.3.2. How to Estimate Story Points in a Rule</h4>
 <div class="paragraph">
 <p>Estimating story points for a rule can be tricky. The following are general guidelines or suggestions to use when estimating the level of effort required for a rule.</p>
 </div>
@@ -1868,17 +1868,17 @@ <h4 id="_how_to_estimate_story_points_in_a_rule">How to Estimate Story Points in
 </div>
 </div>
 <div class="sect1">
-<h2 id="_create_and_test_java_rule_addons">Create and Test Java Rule Addons</h2>
+<h2 id="_create_and_test_java_rule_addons">5. Create and Test Java Rule Addons</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Java-based-Rule-Structure">Java-based Rule Structure</h3>
+<h3 id="Rules-Java-based-Rule-Structure">5.1. Java-based Rule Structure</h3>
 <div class="paragraph">
 <p>TODO:
 * Add a how-to for compound rules, nested rules, rules over multiple sources, negative queries (not matched by anything).
 Points] <a href="https://issues.jboss.org/browse/WINDUP-255">WINDUP-255</a></p>
 </div>
 <div class="sect3">
-<h4 id="_windup_rule_provider">Windup Rule Provider</h4>
+<h4 id="_windup_rule_provider">5.1.1. Windup Rule Provider</h4>
 <div class="paragraph">
 <p>Windup rules are based on <a href="http://ocpsoft.org/rewrite/">OCPsoft Rewrite</a>, an open source routing and URL rewriting solution for Servlets, Java Web Frameworks, and Java EE. The <strong>rewrite</strong> framework allows you to create rule providers and rules in an easy to read format.</p>
 </div>
@@ -1930,7 +1930,7 @@ <h4 id="_windup_rule_provider">Windup Rule Provider</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_rule_code_structure">Add Rule Code Structure</h4>
+<h4 id="_add_rule_code_structure">5.1.2. Add Rule Code Structure</h4>
 <div class="paragraph">
 <p>Like most rule-based frameworks, Windup rules consist of the following:</p>
 </div>
@@ -1949,7 +1949,7 @@ <h4 id="_add_rule_code_structure">Add Rule Code Structure</h4>
 and some others, all of which are optional.</p>
 </div>
 <div class="sect4">
-<h5 id="_when">when()</h5>
+<h5 id="_when">5.1.2.1. when()</h5>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.when(Query.fromType(XmlMetaFacetModel.class))</code></pre>
@@ -1972,7 +1972,7 @@ <h5 id="_when">when()</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_perform">perform()</h5>
+<h5 id="_perform">5.1.2.2. perform()</h5>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.perform(
@@ -1999,7 +1999,7 @@ <h5 id="_perform">perform()</h5>
 (<code>Iteration</code>).</p>
 </div>
 <div class="sect5">
-<h6 id="_iteration">Iteration</h6>
+<h6 id="_iteration">5.1.2.2.1. Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">.perform(
@@ -2021,13 +2021,13 @@ <h6 id="_iteration">Iteration</h6>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_nested_iterations">Nested iterations</h6>
+<h6 id="_nested_iterations">5.1.2.2.2. Nested iterations</h6>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_otherwise">otherwise</h6>
+<h6 id="_otherwise">5.1.2.2.3. otherwise</h6>
 <div class="paragraph">
 <p>Windup rules inherit the rule constructs from OCP Rewrite. For example,
 <code>.otherwise()</code> Gives you a chance to perform something in case the
@@ -2050,13 +2050,13 @@ <h6 id="_otherwise">otherwise</h6>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_where">Where</h5>
+<h5 id="_where">5.1.2.3. Where</h5>
 <div class="paragraph">
 <p>TODO</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_metadata">Metadata</h5>
+<h5 id="_metadata">5.1.2.4. Metadata</h5>
 <div class="paragraph">
 <p>Rules can specify metadata. Currently, the only appearing in some rules,
 and not actually used, is <code>RuleMetadata.CATEGORY</code>.</p>
@@ -2073,7 +2073,7 @@ <h5 id="_metadata">Metadata</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_available_utilities">Available utilities</h4>
+<h4 id="_available_utilities">5.1.3. Available utilities</h4>
 <div class="paragraph">
 <p>For a list of what key services and constructs can be used in the rule,
 see <a href="#Rules-Available-Rules-Utilities">Available Rules Utilities</a>.</p>
@@ -2081,12 +2081,12 @@ <h4 id="_available_utilities">Available utilities</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Basic-Rule-Execution-Flow-Patterns">Basic Rule Execution Flow Patterns</h3>
+<h3 id="Rules-Basic-Rule-Execution-Flow-Patterns">5.2. Basic Rule Execution Flow Patterns</h3>
 <div class="paragraph">
 <p>SGILDA: TODO - Need some links to github to the respective example files.</p>
 </div>
 <div class="sect3">
-<h4 id="_operation_single_operation">operation();  - single operation</h4>
+<h4 id="_operation_single_operation">5.2.1. operation();  - single operation</h4>
 <div class="paragraph">
 <p>When no iteration or condition is needed.</p>
 </div>
@@ -2107,7 +2107,7 @@ <h4 id="_operation_single_operation">operation();  - single operation</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_if_operation_single_conditional_operation">if( &#8230;&#8203; ){ operation(); }  - single conditional operation</h4>
+<h4 id="_if_operation_single_conditional_operation">5.2.2. if( &#8230;&#8203; ){ operation(); }  - single conditional operation</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2123,7 +2123,7 @@ <h4 id="_if_operation_single_conditional_operation">if( &#8230;&#8203; ){ operat
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_foomodel_class_single_iteration">for( FooModel.class ){ &#8230;&#8203; } - Single iteration</h4>
+<h4 id="_for_foomodel_class_single_iteration">5.2.3. for( FooModel.class ){ &#8230;&#8203; } - Single iteration</h4>
 <div class="paragraph">
 <p>For simple iterations, <code>IteratingRuleProvider</code> can be used, which makes the <code>perform</code> a bit less verbose:</p>
 </div>
@@ -2154,7 +2154,7 @@ <h4 id="_for_foomodel_class_single_iteration">for( FooModel.class ){ &#8230;&#82
 </div>
 </div>
 <div class="sect3">
-<h4 id="_if_for_conditional_iteration">if( &#8230;&#8203; ){ for( &#8230;&#8203; ) } - conditional iteration</h4>
+<h4 id="_if_for_conditional_iteration">5.2.4. if( &#8230;&#8203; ){ for( &#8230;&#8203; ) } - conditional iteration</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2169,7 +2169,7 @@ <h4 id="_if_for_conditional_iteration">if( &#8230;&#8203; ){ for( &#8230;&#8203;
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_if_iteration_with_a_condition">for( &#8230;&#8203; ){ if( &#8230;&#8203; ){ &#8230;&#8203; } } - iteration with a condition</h4>
+<h4 id="_for_if_iteration_with_a_condition">5.2.5. for( &#8230;&#8203; ){ if( &#8230;&#8203; ){ &#8230;&#8203; } } - iteration with a condition</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">return ConfigurationBuilder.begin()
@@ -2196,7 +2196,7 @@ <h4 id="_for_if_iteration_with_a_condition">for( &#8230;&#8203; ){ if( &#8230;&#
 </div>
 </div>
 <div class="sect3">
-<h4 id="_for_for_nested_iterations">for( &#8230;&#8203; ){ for( &#8230;&#8203; ) { &#8230;&#8203; } } - nested iterations</h4>
+<h4 id="_for_for_nested_iterations">5.2.6. for( &#8230;&#8203; ){ for( &#8230;&#8203; ) { &#8230;&#8203; } } - nested iterations</h4>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java"></code></pre>
@@ -2205,12 +2205,12 @@ <h4 id="_for_for_nested_iterations">for( &#8230;&#8203; ){ for( &#8230;&#8203; )
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Create-a-Basic-Java-based-Rule-Add-on">Create a Basic Java-based Rule Add-on</h3>
+<h3 id="Rules-Create-a-Basic-Java-based-Rule-Add-on">5.3. Create a Basic Java-based Rule Add-on</h3>
 <div class="paragraph">
 <p>You can create a rule using Java or XML. This topic describes how to create a rule add-on using Java.</p>
 </div>
 <div class="sect3">
-<h4 id="_prerequisites_2">Prerequisites</h4>
+<h4 id="_prerequisites_2">5.3.1. Prerequisites</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -2248,9 +2248,9 @@ <h4 id="_prerequisites_2">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_rule_add_on">Create a Rule Add-on</h4>
+<h4 id="_create_a_rule_add_on">5.3.2. Create a Rule Add-on</h4>
 <div class="sect4">
-<h5 id="_create_a_maven_project">Create a Maven Project</h5>
+<h5 id="_create_a_maven_project">5.3.2.1. Create a Maven Project</h5>
 <div class="paragraph">
 <p>Create a new Maven Java Project. These instructions will refer to the project folder location with the <strong>replaceable</strong> variable 'RULE_PROJECT_HOME'. Modify the project <code>pom.xml</code> file as follows</p>
 </div>
@@ -2414,7 +2414,7 @@ <h5 id="_create_a_maven_project">Create a Maven Project</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_create_the_java_ruleprovider">Create the Java RuleProvider</h5>
+<h5 id="_create_the_java_ruleprovider">5.3.2.2. Create the Java RuleProvider</h5>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -2526,7 +2526,7 @@ <h5 id="_create_the_java_ruleprovider">Create the Java RuleProvider</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_install_the_java_based_rule_add_on">Install the Java-based Rule Add-on</h4>
+<h4 id="_install_the_java_based_rule_add_on">5.3.3. Install the Java-based Rule Add-on</h4>
 <div class="paragraph">
 <p>The easiest and fastest way to build the rule add-on, install it into the local Maven repository, and install it into Windup as a rule add-on is to use the Windup <code>addon-build-and-install</code> command.</p>
 </div>
@@ -2555,7 +2555,7 @@ <h4 id="_install_the_java_based_rule_add_on">Install the Java-based Rule Add-on<
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_the_java_based_rule_add_on">Test the Java-based Rule Add-on</h4>
+<h4 id="_test_the_java_based_rule_add_on">5.3.4. Test the Java-based Rule Add-on</h4>
 <div class="paragraph">
 <p>Test the Java-based rule add-on against your application file by running the <code>windup-migrate-app</code> command in the Windup console prompt.</p>
 </div>
@@ -2580,7 +2580,7 @@ <h4 id="_test_the_java_based_rule_add_on">Test the Java-based Rule Add-on</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_review_the_output_report">Review the Output Report</h4>
+<h4 id="_review_the_output_report">5.3.5. Review the Output Report</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -2682,15 +2682,15 @@ <h4 id="_review_the_output_report">Review the Output Report</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_create_and_test_xml_rules">Create and Test XML Rules</h2>
+<h2 id="_create_and_test_xml_rules">6. Create and Test XML Rules</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Create-a-Basic-XML-Rule">Create a Basic XML Rule</h3>
+<h3 id="Rules-Create-a-Basic-XML-Rule">6.1. Create a Basic XML Rule</h3>
 <div class="paragraph">
 <p>You can create a rule addon using Java or a rule using XML or Groovy. This topic describes how to create a rule using XML.</p>
 </div>
 <div class="sect3">
-<h4 id="_prerequisites_3">Prerequisites</h4>
+<h4 id="_prerequisites_3">6.1.1. Prerequisites</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -2725,7 +2725,7 @@ <h4 id="_prerequisites_3">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_rule">Create a Rule</h4>
+<h4 id="_create_a_rule">6.1.2. Create a Rule</h4>
 <div class="paragraph">
 <p>The following is an example of an XML rule.</p>
 </div>
@@ -2779,7 +2779,7 @@ <h4 id="_create_a_rule">Create a Rule</h4>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_create_the_xml_rule">Create the XML Rule</h5>
+<h5 id="_create_the_xml_rule">6.1.2.1. Create the XML Rule</h5>
 <div class="paragraph">
 <p><strong>Note:</strong> Windup only analyzes XML files with names ending in <code>.windup.xml</code>. Be sure to name XML-based rules using this naming convention!</p>
 </div>
@@ -2859,7 +2859,7 @@ <h5 id="_create_the_xml_rule">Create the XML Rule</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_the_rule_to_windup">Add the Rule to Windup</h4>
+<h4 id="_add_the_rule_to_windup">6.1.3. Add the Rule to Windup</h4>
 <div class="paragraph">
 <p>A Windup rule is installed simply by copying the rule to the appropriate Windup folder. Windup scans for rules in the following locations:</p>
 </div>
@@ -2883,7 +2883,7 @@ <h4 id="_add_the_rule_to_windup">Add the Rule to Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_the_xml_rule">Test the XML Rule</h4>
+<h4 id="_test_the_xml_rule">6.1.4. Test the XML Rule</h4>
 <div class="admonitionblock note">
 <table>
 <tr>
@@ -2923,12 +2923,12 @@ <h4 id="_test_the_xml_rule">Test the XML Rule</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_review_the_report">Review the Report</h2>
+<h2 id="_review_the_report">7. Review the Report</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Review-the-Report">Review the Report</h3>
+<h3 id="Review-the-Report">7.1. Review the Report</h3>
 <div class="sect3">
-<h4 id="_about_the_report_2">About the Report</h4>
+<h4 id="_about_the_report_2">7.1.1. About the Report</h4>
 <div class="paragraph">
 <p>When you execute Windup, the report is generated in the <code>OUTPUT_REPORT_DIRECTORY</code> you specify for the <code>--output</code> argument in the command line. This output directory contains the following files and subdirectories:</p>
 </div>
@@ -2961,7 +2961,7 @@ <h4 id="_about_the_report_2">About the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_open_the_report_2">Open the Report</h4>
+<h4 id="_open_the_report_2">7.1.2. Open the Report</h4>
 <div class="paragraph">
 <p>Use your favorite browser to open the <code>index.html</code> file located in the output report directory. You should see something like the following:</p>
 </div>
@@ -2973,9 +2973,9 @@ <h4 id="_open_the_report_2">Open the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_report_sections_2">Report Sections</h4>
+<h4 id="_report_sections_2">7.1.3. Report Sections</h4>
 <div class="sect4">
-<h5 id="_application_report_page_2">Application Report Page</h5>
+<h5 id="_application_report_page_2">7.1.3.1. Application Report Page</h5>
 <div class="paragraph">
 <p>The first section of the application report page summarizes the migration effort. It provides the total <em>Story Points</em> and a graphically displays the effort by technology. A <em>Story Point</em> is a term commonly used in Scrum Agile software development methodology to estimate the level of effort needed to implement a feature or change. It does not necessarily translate to man-hours, but the value should be consistent across tasks.</p>
 </div>
@@ -2997,7 +2997,7 @@ <h5 id="_application_report_page_2">Application Report Page</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_analysis_sections_2">Archive Analysis Sections</h5>
+<h5 id="_archive_analysis_sections_2">7.1.3.2. Archive Analysis Sections</h5>
 <div class="paragraph">
 <p>Each archive summary begins with a total of the story points assigned to its migration, followed by a table detailing the changes required for each file in the archive. The report contains the following columns.</p>
 </div>
@@ -3060,7 +3060,7 @@ <h5 id="_archive_analysis_sections_2">Archive Analysis Sections</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_file_analysis_pages_2">File Analysis Pages</h5>
+<h5 id="_file_analysis_pages_2">7.1.3.3. File Analysis Pages</h5>
 <div class="paragraph">
 <p>The analysis of the <code>jee-example-services.jar</code> lists the files in the JAR and the warnings and story points assigned to each one. Notice the <code>com.acme.anvil.listener.AnvilWebLifecycleListener</code> file has 5 warnings and is assigned 7 story points. Click on the file to see the detail.</p>
 </div>
@@ -3089,12 +3089,12 @@ <h5 id="_file_analysis_pages_2">File Analysis Pages</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_additional_reports_2">Additional Reports</h4>
+<h4 id="_additional_reports_2">7.1.4. Additional Reports</h4>
 <div class="paragraph">
 <p>Explore the Windup <code>OUTPUT_REPORT_DIRECTORY/reports</code> folder to find additional reporting information.</p>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report_3">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report_3">7.1.4.1. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
@@ -3103,13 +3103,13 @@ <h5 id="_rule_provider_execution_report_3">Rule Provider Execution Report</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report_4">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report_4">7.1.4.2. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_individual_file_analysis_reports_2">Individual File Analysis Reports</h5>
+<h5 id="_individual_file_analysis_reports_2">7.1.4.3. Individual File Analysis Reports</h5>
 <div class="paragraph">
 <p>You can directly access the the file analysis report pages described above by browsing for them by name in the <code>OUTPUT_REPORT_DIRECTORY/reports/</code> directory. Because the same common file names can exist in multiple archives, for example "manifest.mf" or "web.xml", Windup adds a unique numeric suffix to each report file name.</p>
 </div>
@@ -3122,10 +3122,10 @@ <h5 id="_individual_file_analysis_reports_2">Individual File Analysis Reports</h
 </div>
 </div>
 <div class="sect1">
-<h2 id="_external_rule_examples">External Rule Examples</h2>
+<h2 id="_external_rule_examples">8. External Rule Examples</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
+<h3 id="Review-the-Windup-Quickstarts">8.1. Review the Windup Quickstarts</h3>
 <div class="paragraph">
 <p>The Windup quickstarts provide working examples of how to create custom Java-based rule addons and XML rules. You can use them as a starting point for creating your own custom rules. The quickstarts are available on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a></p>
 </div>
@@ -3133,7 +3133,7 @@ <h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
 <p>You can fork and clone the project to have access to regular updates or you can download a ZIP file of the latest version.</p>
 </div>
 <div class="sect3">
-<h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
+<h4 id="_download_the_latest_zip">8.1.1. Download the Latest ZIP</h4>
 <div class="paragraph">
 <p>To download the latest quickstart ZIP file, browse to: <a href="https://github.com/windup/windup-quickstarts/releases" class="bare">https://github.com/windup/windup-quickstarts/releases</a></p>
 </div>
@@ -3142,7 +3142,7 @@ <h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h4>
+<h4 id="_fork_and_clone_the_github_project">8.1.2. Fork and Clone the GitHub Project</h4>
 <div class="paragraph">
 <p>If you don&#8217;t have the GitHub client (<code>git</code>), download it from: <a href="http://git-scm.com/" class="bare">http://git-scm.com/</a></p>
 </div>
@@ -3190,12 +3190,12 @@ <h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h
 </div>
 </div>
 <div class="sect1">
-<h2 id="_debugging_and_troubleshooting">Debugging and Troubleshooting</h2>
+<h2 id="_debugging_and_troubleshooting">9. Debugging and Troubleshooting</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Dev-Debugging-and-Profiling">Debugging and Profiling</h3>
+<h3 id="Dev-Debugging-and-Profiling">9.1. Debugging and Profiling</h3>
 <div class="sect3">
-<h4 id="_debug_the_windup_distribution_runtime">Debug the Windup Distribution Runtime</h4>
+<h4 id="_debug_the_windup_distribution_runtime">9.1.1. Debug the Windup Distribution Runtime</h4>
 <div class="paragraph">
 <p>You can debug the Windup distribution using one of the following approaches.</p>
 </div>
@@ -3222,13 +3222,13 @@ <h4 id="_debug_the_windup_distribution_runtime">Debug the Windup Distribution Ru
 </div>
 </div>
 <div class="sect3">
-<h4 id="_debug_a_test_using_netbeans">Debug a Test Using NetBeans</h4>
+<h4 id="_debug_a_test_using_netbeans">9.1.2. Debug a Test Using NetBeans</h4>
 <div class="paragraph">
 <p>Click the <code>Debug Test File</code> button, or choose <code>Menu</code> → <code>Debug</code> → <code>Debug Test File</code>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_profile_a_test_using_netbeans">Profile a Test Using NetBeans</h4>
+<h4 id="_profile_a_test_using_netbeans">9.1.3. Profile a Test Using NetBeans</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -3270,7 +3270,7 @@ <h4 id="_profile_a_test_using_netbeans">Profile a Test Using NetBeans</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_profile_forge_runtime_using_yourkit">Profile Forge Runtime Using YourKit</h4>
+<h4 id="_profile_forge_runtime_using_yourkit">9.1.4. Profile Forge Runtime Using YourKit</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -3302,9 +3302,9 @@ <h4 id="_profile_forge_runtime_using_yourkit">Profile Forge Runtime Using YourKi
 </div>
 </div>
 <div class="sect2">
-<h3 id="_troubleshoot_windup_issues">Troubleshoot Windup Issues</h3>
+<h3 id="_troubleshoot_windup_issues">9.2. Troubleshoot Windup Issues</h3>
 <div class="sect3">
-<h4 id="_logging">Logging</h4>
+<h4 id="_logging">9.2.1. Logging</h4>
 <div class="paragraph">
 <p>Logging is currently broken and will not be fixed any time soon.</p>
 </div>
@@ -3313,7 +3313,7 @@ <h4 id="_logging">Logging</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_debugging_exceptions">Debugging Exceptions</h4>
+<h4 id="_debugging_exceptions">9.2.2. Debugging Exceptions</h4>
 <div class="paragraph">
 <p>Exceptions in Surefire reports are broken due to the way Forge wraps
 exceptions and the way Surefire handles them. You need to
@@ -3324,7 +3324,7 @@ <h4 id="_debugging_exceptions">Debugging Exceptions</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_classloading_problems">Classloading Problems</h4>
+<h4 id="_classloading_problems">9.2.3. Classloading Problems</h4>
 <div class="paragraph">
 <p>Configuring dependencies in a Forge-based project can be a little tricky.
 See <a href="#Dev-Dependencies">Dependencies</a> for some hints.</p>
@@ -3334,12 +3334,12 @@ <h4 id="_classloading_problems">Classloading Problems</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_additional_resources">Additional Resources</h2>
+<h2 id="_additional_resources">10. Additional Resources</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Rules-Available-Rules-Utilities">Available Rule Utilities</h3>
+<h3 id="Rules-Available-Rules-Utilities">10.1. Available Rule Utilities</h3>
 <div class="sect3">
-<h4 id="_programmatically_access_the_graph">Programmatically Access the Graph</h4>
+<h4 id="_programmatically_access_the_graph">10.1.1. Programmatically Access the Graph</h4>
 <div class="paragraph">
 <p><em>Note: Needs update. This is out of date!</em></p>
 </div>
@@ -3350,13 +3350,13 @@ <h4 id="_programmatically_access_the_graph">Programmatically Access the Graph</h
 <p>This topic describes how to to programmatically access or update graph data when you create a Java-based rule addon.</p>
 </div>
 <div class="sect4">
-<h5 id="_query_the_graph">Query the graph</h5>
+<h5 id="_query_the_graph">10.1.1.1. Query the graph</h5>
 <div class="paragraph">
 <p>There are several ways - including Query API, Gremlin support, or
 GraphService methods.</p>
 </div>
 <div class="sect5">
-<h6 id="_query_the_graph_within_the_when_method">Query the Graph Within the .when() method</h6>
+<h6 id="_query_the_graph_within_the_when_method">10.1.1.1.1. Query the Graph Within the .when() method</h6>
 <div class="paragraph">
 <p>Building a rule contains the method when(), which is used to create a
 <strong>condition</strong>. Vertices that fulfill the condition, are passed to the
@@ -3390,7 +3390,7 @@ <h6 id="_query_the_graph_within_the_when_method">Query the Graph Within the .whe
 </div>
 </div>
 <div class="sect5">
-<h6 id="_iteration_2">Iteration</h6>
+<h6 id="_iteration_2">10.1.1.1.2. Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">ConfigurationBuilder.begin().addRule()
@@ -3405,7 +3405,7 @@ <h6 id="_iteration_2">Iteration</h6>
 </div>
 </div>
 <div class="sect5">
-<h6 id="_nested_iteration">Nested Iteration</h6>
+<h6 id="_nested_iteration">10.1.1.1.3. Nested Iteration</h6>
 <div class="listingblock">
 <div class="content">
 <pre class="highlight"><code class="language-java" data-lang="java">code,java
@@ -3433,7 +3433,7 @@ <h6 id="_nested_iteration">Nested Iteration</h6>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_modify_graph_data">Modify Graph Data</h4>
+<h4 id="_modify_graph_data">10.1.2. Modify Graph Data</h4>
 <div class="paragraph">
 <p>For more custom operations dealing with Graph data that are not covered by the <code>Query</code> mechanism, use the GraphService.</p>
 </div>
@@ -3463,7 +3463,7 @@ <h4 id="_modify_graph_data">Modify Graph Data</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
+<h3 id="Review-the-Windup-Quickstarts">10.2. Review the Windup Quickstarts</h3>
 <div class="paragraph">
 <p>The Windup quickstarts provide working examples of how to create custom Java-based rule addons and XML rules. You can use them as a starting point for creating your own custom rules. The quickstarts are available on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a></p>
 </div>
@@ -3471,7 +3471,7 @@ <h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
 <p>You can fork and clone the project to have access to regular updates or you can download a ZIP file of the latest version.</p>
 </div>
 <div class="sect3">
-<h4 id="_download_the_latest_zip_2">Download the Latest ZIP</h4>
+<h4 id="_download_the_latest_zip_2">10.2.1. Download the Latest ZIP</h4>
 <div class="paragraph">
 <p>To download the latest quickstart ZIP file, browse to: <a href="https://github.com/windup/windup-quickstarts/releases" class="bare">https://github.com/windup/windup-quickstarts/releases</a></p>
 </div>
@@ -3480,7 +3480,7 @@ <h4 id="_download_the_latest_zip_2">Download the Latest ZIP</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_fork_and_clone_the_github_project_2">Fork and Clone the GitHub Project</h4>
+<h4 id="_fork_and_clone_the_github_project_2">10.2.2. Fork and Clone the GitHub Project</h4>
 <div class="paragraph">
 <p>If you don&#8217;t have the GitHub client (<code>git</code>), download it from: <a href="http://git-scm.com/" class="bare">http://git-scm.com/</a></p>
 </div>
@@ -3526,15 +3526,15 @@ <h4 id="_fork_and_clone_the_github_project_2">Fork and Clone the GitHub Project<
 </div>
 </div>
 <div class="sect2">
-<h3 id="Known-Issues">Known Windup Issues</h3>
+<h3 id="Known-Issues">10.3. Known Windup Issues</h3>
 <div class="paragraph">
 <p>Windup known issues are tracked here: <a href="https://issues.jboss.org/browse/WINDUP-496?jql=project%20%3D%20WINDUP%20AND%20issuetype%20%3D%20Bug%20AND%20status%20in%20%28Open%2C%20%22Coding%20In%20Progress%22%2C%20Reopened%2C%20%22Pull%20Request%20Sent%22%29">Open Windup issues</a></p>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Glossary">Glossary of Terms Used in Windup</h3>
+<h3 id="Glossary">10.4. Glossary of Terms Used in Windup</h3>
 <div class="sect3">
-<h4 id="_rules_terms">Rules Terms</h4>
+<h4 id="_rules_terms">10.4.1. Rules Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Rule</dt>
@@ -3597,7 +3597,7 @@ <h4 id="_rules_terms">Rules Terms</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reporting_terms">Reporting Terms</h4>
+<h4 id="_reporting_terms">10.4.2. Reporting Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Lift and Shift (Level of effort)</dt>
@@ -3623,10 +3623,10 @@ <h4 id="_reporting_terms">Reporting Terms</h4>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_appendix">Appendix</h2>
+<h2 id="_appendix">11. Appendix</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
+<h3 id="Windup-Architectural-Components">11.1. Windup Architectural Components</h3>
 <div class="paragraph">
 <p>The following open source software, tools, and APIs are used within
 Windup to analyze and provide migration information. If you plan to
@@ -3634,7 +3634,7 @@ <h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
 familiar with them.</p>
 </div>
 <div class="sect3">
-<h4 id="_forge">Forge</h4>
+<h4 id="_forge">11.1.1. Forge</h4>
 <div class="paragraph">
 <p>Forge is an open source, extendable, rapid application development tool
 for creating Java EE applications using Maven. For more information
@@ -3642,7 +3642,7 @@ <h4 id="_forge">Forge</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_forge_furnace">Forge Furnace</h4>
+<h4 id="_forge_furnace">11.1.2. Forge Furnace</h4>
 <div class="paragraph">
 <p>Forge Furnace is a modular runtime container behind Forge that provides
 the ability to run Forge addons in an embedded application. For more
@@ -3651,21 +3651,21 @@ <h4 id="_forge_furnace">Forge Furnace</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_tinkerpop">TinkerPop</h4>
+<h4 id="_tinkerpop">11.1.3. TinkerPop</h4>
 <div class="paragraph">
 <p>TinkerPop is an open source graph computing framework. For more
 information, see: <a href="http://www.tinkerpop.com/">TinkerPop</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_titan">Titan</h4>
+<h4 id="_titan">11.1.4. Titan</h4>
 <div class="paragraph">
 <p>Titan is a scalable graph database optimized for storing and querying graphs.
 For more information, see: <a href="http://thinkaurelius.github.io/titan/">Titan Distributed Graph Database</a> and <a href="https://github.com/thinkaurelius/titan/wiki/Beginner%27s-Guide">Titan Beginner&#8217;s Guide</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_frames">Frames</h4>
+<h4 id="_frames">11.1.5. Frames</h4>
 <div class="paragraph">
 <p>Frames represents graph data in the form of interrelated Java Objects or
 a collection of annotated Java Interfaces. For more information, see:
@@ -3677,7 +3677,7 @@ <h4 id="_frames">Frames</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_gremlin">Gremlin</h4>
+<h4 id="_gremlin">11.1.6. Gremlin</h4>
 <div class="paragraph">
 <p>Gremlin is a graph traversal language that allows you to query, analyze,
 and manipulate property graphs that implement the Blueprints property
@@ -3686,7 +3686,7 @@ <h4 id="_gremlin">Gremlin</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_blueprints">Blueprints</h4>
+<h4 id="_blueprints">11.1.7. Blueprints</h4>
 <div class="paragraph">
 <p>Blueprints is an industry standard API used to access graph databases.
 For more information about Blueprints, see:
@@ -3694,7 +3694,7 @@ <h4 id="_blueprints">Blueprints</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_pipes">Pipes</h4>
+<h4 id="_pipes">11.1.8. Pipes</h4>
 <div class="paragraph">
 <p>Pipes is a dataflow framework used to process graph data. It for the
 transformation of data from input to output. For more information, see:
@@ -3702,14 +3702,14 @@ <h4 id="_pipes">Pipes</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rexster">Rexster</h4>
+<h4 id="_rexster">11.1.9. Rexster</h4>
 <div class="paragraph">
 <p>Rexster is a graph server that exposes any Blueprints graph through HTTP/REST and a binary protocol called RexPro. Rexster makes extensive use of Blueprints, Pipes, and Gremlin. For more information, see:
 <a href="https://github.com/tinkerpop/rexster/wiki">TinkerPop Rexster Wiki</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
+<h4 id="_ocpsoft_rewrite">11.1.10. OCPsoft Rewrite</h4>
 <div class="paragraph">
 <p>OCPsoft Rewrite is an open source routing and URL rewriting solution for
 Servlets, Java Web Frameworks, and Java EE. For more information about
@@ -3718,7 +3718,7 @@ <h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Dev-Dependencies">Dependencies (Forge add-ons)</h3>
+<h3 id="Dev-Dependencies">11.2. Dependencies (Forge add-ons)</h3>
 <div class="paragraph">
 <div class="title">DRAFT</div>
 <p><em>Based on
@@ -3726,7 +3726,7 @@ <h3 id="Dev-Dependencies">Dependencies (Forge add-ons)</h3>
 discussion.</em></p>
 </div>
 <div class="sect3">
-<h4 id="_maven_add_on_structure">Maven Add-on Structure</h4>
+<h4 id="_maven_add_on_structure">11.2.1. Maven Add-on Structure</h4>
 <div class="paragraph">
 <p>The following is the typical structure of Maven <code>add-on</code> modules.</p>
 </div>
@@ -3776,7 +3776,7 @@ <h4 id="_maven_add_on_structure">Maven Add-on Structure</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_add_on_sub_parts">Add-on sub-parts</h4>
+<h4 id="_add_on_sub_parts">11.2.2. Add-on sub-parts</h4>
 <div class="paragraph">
 <p>Add-on sub-parts declare dependency preferably on forge add-on APIs, not
 on the add-ons themselves, wherever possible (wherever an add-on has an
@@ -3834,7 +3834,7 @@ <h4 id="_add_on_sub_parts">Add-on sub-parts</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_test_dependencies">Test dependencies</h4>
+<h4 id="_test_dependencies">11.2.3. Test dependencies</h4>
 <div class="paragraph">
 <p>For test dependencies on add-ons: Any addon/sub-part requiring an addon
 for testing purposes should use <code>&lt;scope&gt;test&lt;/scope&gt;</code>.</p>
@@ -3852,7 +3852,7 @@ <h4 id="_test_dependencies">Test dependencies</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_dependencies_between_sub_parts_within_the_same_add_on">Dependencies between sub-parts within the same add-on</h4>
+<h4 id="_dependencies_between_sub_parts_within_the_same_add_on">11.2.4. Dependencies between sub-parts within the same add-on</h4>
 <div class="paragraph">
 <p>Subpart may declare dependency on other subpart. E.g. <code>impl</code> typically
 depends on <code>api</code>. In that case, the scope should be set appropriately
@@ -3870,7 +3870,7 @@ <h4 id="_dependencies_between_sub_parts_within_the_same_add_on">Dependencies bet
 </div>
 </div>
 <div class="sect2">
-<h3 id="Rules-Windup-Models">Windup Models</h3>
+<h3 id="Rules-Windup-Models">11.3. Windup Models</h3>
 <div class="paragraph">
 <p>Windup models are the classes extending WindupVertexFrame.
 They are used to model the data in the graph database to Java objects.</p>
@@ -3883,7 +3883,7 @@ <h3 id="Rules-Windup-Models">Windup Models</h3>
 <p><span class="image"><img src="images/WindupModels-NbScreenshot.png" alt="Windup Models Graphic"></span></p>
 </div>
 <div class="sect3">
-<h4 id="_meta_models">Meta Models</h4>
+<h4 id="_meta_models">11.3.1. Meta Models</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -3896,17 +3896,17 @@ <h4 id="_meta_models">Meta Models</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_core_models">Core Models</h4>
+<h4 id="_core_models">11.3.2. Core Models</h4>
 <div class="paragraph">
 <p>FileModel ArchiveModel</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reporting_models">Reporting Models</h4>
+<h4 id="_reporting_models">11.3.3. Reporting Models</h4>
 
 </div>
 <div class="sect3">
-<h4 id="_custom_models_coming_from_addons">Custom Models (coming from Addons)</h4>
+<h4 id="_custom_models_coming_from_addons">11.3.4. Custom Models (coming from Addons)</h4>
 <div class="paragraph">
 <p>See respective ruleset&#8217;s documentation.</p>
 </div>
@@ -3917,7 +3917,7 @@ <h4 id="_custom_models_coming_from_addons">Custom Models (coming from Addons)</h
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2015-02-04 16:09:16 EST
+Last updated 2015-02-09 14:16:34 EST
 </div>
 </div>
 </body>
diff --git a/html/WindupUserGuide.html b/html/WindupUserGuide.html
index 4f3e9913a4..11cfeb12c0 100644
--- a/html/WindupUserGuide.html
+++ b/html/WindupUserGuide.html
@@ -415,29 +415,29 @@ <h1>Windup User Guide</h1>
 <div id="toc" class="toc">
 <div id="toctitle">Table of Contents</div>
 <ul class="sectlevel1">
-<li><a href="#_overview">Overview</a>
+<li><a href="#_overview">1. Overview</a>
 <ul class="sectlevel2">
-<li><a href="#What-is-Windup">What is Windup?</a></li>
-<li><a href="#Features-of-Windup-2.0">Features of Windup 2.0</a></li>
-<li><a href="#Windup-Processing-Overview">Windup Processing Overview</a></li>
-<li><a href="#Get-Involved">Get Involved</a></li>
-<li><a href="#Report-Issues-with-Windup">Report Issues with Windup</a></li>
-<li><a href="#About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</a></li>
+<li><a href="#What-is-Windup">1.1. What is Windup?</a></li>
+<li><a href="#Features-of-Windup-2.0">1.2. Features of Windup 2.0</a></li>
+<li><a href="#Windup-Processing-Overview">1.3. Windup Processing Overview</a></li>
+<li><a href="#Get-Involved">1.4. Get Involved</a></li>
+<li><a href="#Report-Issues-with-Windup">1.5. Report Issues with Windup</a></li>
+<li><a href="#About-the-WINDUP_HOME-Variable">1.6. About the WINDUP_HOME Variable</a></li>
 </ul>
 </li>
-<li><a href="#_run_windup">Run Windup</a>
+<li><a href="#_run_windup">2. Run Windup</a>
 <ul class="sectlevel2">
-<li><a href="#Install-Windup">Install Windup</a></li>
-<li><a href="#Execute-Windup">Execute Windup</a></li>
-<li><a href="#Review-the-Report">Review the Report</a></li>
+<li><a href="#Install-Windup">2.1. Install Windup</a></li>
+<li><a href="#Execute-Windup">2.2. Execute Windup</a></li>
+<li><a href="#Review-the-Report">2.3. Review the Report</a></li>
 </ul>
 </li>
-<li><a href="#_additional_resources">Additional Resources</a>
+<li><a href="#_additional_resources">3. Additional Resources</a>
 <ul class="sectlevel2">
-<li><a href="#Review-the-Windup-Quickstarts">Review the Windup Quickstarts</a></li>
-<li><a href="#Known-Issues">Known Windup Issues</a></li>
-<li><a href="#Glossary">Glossary of Terms Used in Windup</a></li>
-<li><a href="#Windup-Architectural-Components">Windup Architectural Components</a></li>
+<li><a href="#Review-the-Windup-Quickstarts">3.1. Review the Windup Quickstarts</a></li>
+<li><a href="#Known-Issues">3.2. Known Windup Issues</a></li>
+<li><a href="#Glossary">3.3. Glossary of Terms Used in Windup</a></li>
+<li><a href="#Windup-Architectural-Components">3.4. Windup Architectural Components</a></li>
 </ul>
 </li>
 </ul>
@@ -445,14 +445,14 @@ <h1>Windup User Guide</h1>
 </div>
 <div id="content">
 <div class="sect1">
-<h2 id="_overview">Overview</h2>
+<h2 id="_overview">1. Overview</h2>
 <div class="sectionbody">
 <div class="paragraph">
 <p>This guide is for engineers, consultants, and others who plan to use
 Windup 2.0 to migrate Java applications or other components.</p>
 </div>
 <div class="sect2">
-<h3 id="What-is-Windup">What is Windup?</h3>
+<h3 id="What-is-Windup">1.1. What is Windup?</h3>
 <div class="paragraph">
 <p><span class="image"><img src="images/windup-logo-wiki-header.jpg" alt="Windup Logo"></span></p>
 </div>
@@ -467,13 +467,13 @@ <h3 id="What-is-Windup">What is Windup?</h3>
 migrating from other containers to JBoss EAP a piece of cake.</p>
 </div>
 <div class="sect3">
-<h4 id="_windup_2_0_vs_windup_0_7_x">Windup 2.0 vs. Windup 0.7.x</h4>
+<h4 id="_windup_2_0_vs_windup_0_7_x">1.1.1. Windup 2.0 vs. Windup 0.7.x</h4>
 <div class="paragraph">
 <p>Windup 2.0 aims to deliver the same functionality as legacy Windup, however, the internal architecture and rule structure is very different and allows for the creation of much more complex rules.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?</h4>
+<h4 id="_how_does_windup_simplify_migration">1.1.2. How Does Windup Simplify Migration?</h4>
 <div class="paragraph">
 <p>Windup looks for common resources and highlight technologies and known “trouble
 spots” in migrating applications. The goal of Windup is to provide a
@@ -513,14 +513,14 @@ <h4 id="_how_does_windup_simplify_migration">How Does Windup Simplify Migration?
 </table>
 </div>
 <div class="sect3">
-<h4 id="_follow_windup_on_twitter">Follow Windup on Twitter!</h4>
+<h4 id="_follow_windup_on_twitter">1.1.3. Follow Windup on Twitter!</h4>
 <div class="paragraph">
 <p>Follow Windup on Twitter <a href="https://twitter.com/jbosswindup">@JBossWindup</a> for updates and more!</p>
 </div>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
+<h3 id="Features-of-Windup-2.0">1.2. Features of Windup 2.0</h3>
 <div class="hdlist">
 <table>
 <tr>
@@ -654,7 +654,7 @@ <h3 id="Features-of-Windup-2.0">Features of Windup 2.0</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
+<h3 id="Windup-Processing-Overview">1.3. Windup Processing Overview</h3>
 <div class="paragraph">
 <p>Windup is a rule-based migration tool that allows you to write customized rules to analyze the APIs, technologies, and architectures used by the applications you plan to migrate. The Windup tool also executes its own core rules through all phases of the migration process.</p>
 </div>
@@ -662,7 +662,7 @@ <h3 id="Windup-Processing-Overview">Windup Processing Overview</h3>
 <p>The following is a high level conceptual overview of what happens within Windup when you execute the tool against your application or archive.</p>
 </div>
 <div class="sect3">
-<h4 id="_discovery_phase">Discovery Phase</h4>
+<h4 id="_discovery_phase">1.3.1. Discovery Phase</h4>
 <div class="paragraph">
 <p>Wnen you run the <code>windup-migrate-app</code> command, Windup executes its own core rules to extract files from archives, decompile classes, and analyze the application. In this phase, Windup builds a datamodel, storing component data and relationships in a graph database, which can then be queried and updated as needed by the migration rules and for reporting purposes.</p>
 </div>
@@ -671,7 +671,7 @@ <h4 id="_discovery_phase">Discovery Phase</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_application_migration">Application Migration</h4>
+<h4 id="_application_migration">1.3.2. Application Migration</h4>
 <div class="paragraph">
 <p>The next step in the process is the execution of the migration rules. In this phase, the rules typically do not execute against the application input files. Instead, they execute against the graph database model. Windup rules are independent and decoupled and they communicate with each other using the graph database model. Rules query the graph database to obtain information needed to test the rule condition. They also update the data model with information based on the result of the rule execution. This allows rules to easily interact with other rules and enables the creation of very complex rules.</p>
 </div>
@@ -680,7 +680,7 @@ <h4 id="_application_migration">Application Migration</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Findings Based on the Rule Execution Results</h4>
+<h4 id="_generate_findings_based_on_the_rule_execution_results">1.3.3. Generate Findings Based on the Rule Execution Results</h4>
 <div class="paragraph">
 <p>The final step in the process is to pull data from the graph database model to generate of reports and optionally generate scripts. Again, Windup uses rules to generate the final output.</p>
 </div>
@@ -706,9 +706,9 @@ <h4 id="_generate_findings_based_on_the_rule_execution_results">Generate Finding
 </div>
 </div>
 <div class="sect2">
-<h3 id="Get-Involved">Get Involved</h3>
+<h3 id="Get-Involved">1.4. Get Involved</h3>
 <div class="sect3">
-<h4 id="_how_can_you_help">How can you help?</h4>
+<h4 id="_how_can_you_help">1.4.1. How can you help?</h4>
 <div class="paragraph">
 <p>To help us make Windup cover most application constructs and server configurations, including yours, you can help with any of the following items. Some items require only a few minutes of your time!</p>
 </div>
@@ -775,7 +775,7 @@ <h4 id="_how_can_you_help">How can you help?</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_helpful_links">Helpful links</h4>
+<h4 id="_helpful_links">1.4.2. Helpful links</h4>
 <div class="ulist">
 <ul>
 <li>
@@ -820,12 +820,12 @@ <h4 id="_helpful_links">Helpful links</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Report-Issues-with-Windup">Report Issues with Windup</h3>
+<h3 id="Report-Issues-with-Windup">1.5. Report Issues with Windup</h3>
 <div class="paragraph">
 <p>Windup uses JIRA as its issue tracking system. If you encounter an issue executing Windup, please file a Windup JIRA Issue.</p>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_account">Create a JIRA Account</h4>
+<h4 id="_create_a_jira_account">1.5.1. Create a JIRA Account</h4>
 <div class="paragraph">
 <p>If you do not yet have a JIRA account, create one using the following procedure.</p>
 </div>
@@ -847,7 +847,7 @@ <h4 id="_create_a_jira_account">Create a JIRA Account</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
+<h4 id="_create_a_jira_issue">1.5.2. Create a JIRA Issue</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -906,7 +906,7 @@ <h4 id="_create_a_jira_issue">Create a JIRA Issue</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</h3>
+<h3 id="About-the-WINDUP_HOME-Variable">1.6. About the WINDUP_HOME Variable</h3>
 <div class="paragraph">
 <p>This documentation uses the <code>WINDUP_HOME</code> <strong>replaceable</strong> value to denote the path to the Windup distribution. When you encounter this value in the documentation, be sure to replace it with the actual path to your Windup installation.</p>
 </div>
@@ -924,10 +924,10 @@ <h3 id="About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</h3>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_run_windup">Run Windup</h2>
+<h2 id="_run_windup">2. Run Windup</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Install-Windup">Install Windup</h3>
+<h3 id="Install-Windup">2.1. Install Windup</h3>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -953,9 +953,9 @@ <h3 id="Install-Windup">Install Windup</h3>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Execute-Windup">Execute Windup</h3>
+<h3 id="Execute-Windup">2.2. Execute Windup</h3>
 <div class="sect3">
-<h4 id="_prerequisites">Prerequisites</h4>
+<h4 id="_prerequisites">2.2.1. Prerequisites</h4>
 <div class="paragraph">
 <p>Before you begin, you must gather the following information.</p>
 </div>
@@ -1020,7 +1020,7 @@ <h4 id="_prerequisites">Prerequisites</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_start_windup">Start Windup</h4>
+<h4 id="_start_windup">2.2.2. Start Windup</h4>
 <div class="paragraph">
 <p>For information about the use of WINDUP_HOME in the instructions below, see <a href="#About-the-WINDUP_HOME-Variable">About the WINDUP_HOME Variable</a>.</p>
 </div>
@@ -1061,7 +1061,7 @@ <h4 id="_start_windup">Start Windup</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migrate-app</code> Command</h4>
+<h4 id="_run_the_code_windup_migrate_app_code_command">2.2.3. Run the <code>windup-migrate-app</code> Command</h4>
 <div class="olist arabic">
 <ol class="arabic">
 <li>
@@ -1144,7 +1144,7 @@ <h4 id="_run_the_code_windup_migrate_app_code_command">Run the <code>windup-migr
 </div>
 </div>
 <div class="sect3">
-<h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
+<h4 id="_run_windup_in_batch_mode">2.2.4. Run Windup in Batch Mode</h4>
 <div class="paragraph">
 <p>Windup can be also executed in batch mode within a shell or batch script using the <code>--evaluate</code> argument as follows.</p>
 </div>
@@ -1166,7 +1166,7 @@ <h4 id="_run_windup_in_batch_mode">Run Windup in Batch Mode</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_windup_help">Windup Help</h4>
+<h4 id="_windup_help">2.2.5. Windup Help</h4>
 <div class="paragraph">
 <p>To see the list of available parameters for the <code>windup-migrate-app</code> command, execute the following command in the Windup prompt:</p>
 </div>
@@ -1177,12 +1177,12 @@ <h4 id="_windup_help">Windup Help</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="windup-command-examples">Windup Command Examples</h4>
+<h4 id="windup-command-examples">2.2.6. Windup Command Examples</h4>
 <div class="paragraph">
 <p>The following Windup command examples report against applications located in the Windup source <a href="https://github.com/windup/windup/tree/master/test-files">test-files</a> directory.</p>
 </div>
 <div class="sect4">
-<h5 id="_source_code_example">Source Code Example</h5>
+<h5 id="_source_code_example">2.2.6.1. Source Code Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/tree/master/test-files/seam-booking-5.2">seam-booking-5.2</a> application source code. It evaluates all <code>org.jboss.seam</code> packages and creates a folder named 'seam-booking-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1193,7 +1193,7 @@ <h5 id="_source_code_example">Source Code Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_example">Archive Example</h5>
+<h5 id="_archive_example">2.2.6.2. Archive Example</h5>
 <div class="paragraph">
 <p>The following command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1204,7 +1204,7 @@ <h5 id="_archive_example">Archive Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_batch_example">Windup Batch Example</h5>
+<h5 id="_windup_batch_example">2.2.6.3. Windup Batch Example</h5>
 <div class="paragraph">
 <p>The following Windup batch command runs against the <a href="https://github.com/windup/windup/blob/master/test-files/jee-example-app-1.0.0.ear">jee-example-app-1.0.0.ear</a> EAR archive. It evaluates all <code>com.acme</code> and <code>org.apache</code> packages and creates a folder named 'jee-example-app-1.0.0.ear-report' in the <code>/home/username/windup-reports/</code> directory to contain the reporting output.</p>
 </div>
@@ -1216,7 +1216,7 @@ <h5 id="_windup_batch_example">Windup Batch Example</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
+<h5 id="_windup_quickstart_examples">2.2.6.4. Windup Quickstart Examples</h5>
 <div class="paragraph">
 <p>For more concrete examples, see the Windup quickstarts located on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a>. If you prefer, you can download the <a href="https://github.com/windup/windup-quickstarts/releases/tag/2.0.0.Alpha1">2.0.0.Alpha1 release</a> ZIP or TAR  distribution of the quickstarts.</p>
 </div>
@@ -1227,9 +1227,9 @@ <h5 id="_windup_quickstart_examples">Windup Quickstart Examples</h5>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Review-the-Report">Review the Report</h3>
+<h3 id="Review-the-Report">2.3. Review the Report</h3>
 <div class="sect3">
-<h4 id="_about_the_report">About the Report</h4>
+<h4 id="_about_the_report">2.3.1. About the Report</h4>
 <div class="paragraph">
 <p>When you execute Windup, the report is generated in the <code>OUTPUT_REPORT_DIRECTORY</code> you specify for the <code>--output</code> argument in the command line. This output directory contains the following files and subdirectories:</p>
 </div>
@@ -1262,7 +1262,7 @@ <h4 id="_about_the_report">About the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_open_the_report">Open the Report</h4>
+<h4 id="_open_the_report">2.3.2. Open the Report</h4>
 <div class="paragraph">
 <p>Use your favorite browser to open the <code>index.html</code> file located in the output report directory. You should see something like the following:</p>
 </div>
@@ -1274,9 +1274,9 @@ <h4 id="_open_the_report">Open the Report</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_report_sections">Report Sections</h4>
+<h4 id="_report_sections">2.3.3. Report Sections</h4>
 <div class="sect4">
-<h5 id="_application_report_page">Application Report Page</h5>
+<h5 id="_application_report_page">2.3.3.1. Application Report Page</h5>
 <div class="paragraph">
 <p>The first section of the application report page summarizes the migration effort. It provides the total <em>Story Points</em> and a graphically displays the effort by technology. A <em>Story Point</em> is a term commonly used in Scrum Agile software development methodology to estimate the level of effort needed to implement a feature or change. It does not necessarily translate to man-hours, but the value should be consistent across tasks.</p>
 </div>
@@ -1298,7 +1298,7 @@ <h5 id="_application_report_page">Application Report Page</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
+<h5 id="_archive_analysis_sections">2.3.3.2. Archive Analysis Sections</h5>
 <div class="paragraph">
 <p>Each archive summary begins with a total of the story points assigned to its migration, followed by a table detailing the changes required for each file in the archive. The report contains the following columns.</p>
 </div>
@@ -1361,7 +1361,7 @@ <h5 id="_archive_analysis_sections">Archive Analysis Sections</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_file_analysis_pages">File Analysis Pages</h5>
+<h5 id="_file_analysis_pages">2.3.3.3. File Analysis Pages</h5>
 <div class="paragraph">
 <p>The analysis of the <code>jee-example-services.jar</code> lists the files in the JAR and the warnings and story points assigned to each one. Notice the <code>com.acme.anvil.listener.AnvilWebLifecycleListener</code> file has 5 warnings and is assigned 7 story points. Click on the file to see the detail.</p>
 </div>
@@ -1390,12 +1390,12 @@ <h5 id="_file_analysis_pages">File Analysis Pages</h5>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_additional_reports">Additional Reports</h4>
+<h4 id="_additional_reports">2.3.4. Additional Reports</h4>
 <div class="paragraph">
 <p>Explore the Windup <code>OUTPUT_REPORT_DIRECTORY/reports</code> folder to find additional reporting information.</p>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report">2.3.4.1. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
@@ -1404,13 +1404,13 @@ <h5 id="_rule_provider_execution_report">Rule Provider Execution Report</h5>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_rule_provider_execution_report_2">Rule Provider Execution Report</h5>
+<h5 id="_rule_provider_execution_report_2">2.3.4.2. Rule Provider Execution Report</h5>
 <div class="paragraph">
 <p>The <code>OUTPUT_REPORT_DIRECTORY/reports/windup_ruleproviders.html</code> page provides the list of rule providers that executed when running the Windup migration command against the application.</p>
 </div>
 </div>
 <div class="sect4">
-<h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
+<h5 id="_individual_file_analysis_reports">2.3.4.3. Individual File Analysis Reports</h5>
 <div class="paragraph">
 <p>You can directly access the the file analysis report pages described above by browsing for them by name in the <code>OUTPUT_REPORT_DIRECTORY/reports/</code> directory. Because the same common file names can exist in multiple archives, for example "manifest.mf" or "web.xml", Windup adds a unique numeric suffix to each report file name.</p>
 </div>
@@ -1423,10 +1423,10 @@ <h5 id="_individual_file_analysis_reports">Individual File Analysis Reports</h5>
 </div>
 </div>
 <div class="sect1">
-<h2 id="_additional_resources">Additional Resources</h2>
+<h2 id="_additional_resources">3. Additional Resources</h2>
 <div class="sectionbody">
 <div class="sect2">
-<h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
+<h3 id="Review-the-Windup-Quickstarts">3.1. Review the Windup Quickstarts</h3>
 <div class="paragraph">
 <p>The Windup quickstarts provide working examples of how to create custom Java-based rule addons and XML rules. You can use them as a starting point for creating your own custom rules. The quickstarts are available on GitHub here: <a href="https://github.com/windup/windup-quickstarts" class="bare">https://github.com/windup/windup-quickstarts</a></p>
 </div>
@@ -1434,7 +1434,7 @@ <h3 id="Review-the-Windup-Quickstarts">Review the Windup Quickstarts</h3>
 <p>You can fork and clone the project to have access to regular updates or you can download a ZIP file of the latest version.</p>
 </div>
 <div class="sect3">
-<h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
+<h4 id="_download_the_latest_zip">3.1.1. Download the Latest ZIP</h4>
 <div class="paragraph">
 <p>To download the latest quickstart ZIP file, browse to: <a href="https://github.com/windup/windup-quickstarts/releases" class="bare">https://github.com/windup/windup-quickstarts/releases</a></p>
 </div>
@@ -1443,7 +1443,7 @@ <h4 id="_download_the_latest_zip">Download the Latest ZIP</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h4>
+<h4 id="_fork_and_clone_the_github_project">3.1.2. Fork and Clone the GitHub Project</h4>
 <div class="paragraph">
 <p>If you don&#8217;t have the GitHub client (<code>git</code>), download it from: <a href="http://git-scm.com/" class="bare">http://git-scm.com/</a></p>
 </div>
@@ -1489,15 +1489,15 @@ <h4 id="_fork_and_clone_the_github_project">Fork and Clone the GitHub Project</h
 </div>
 </div>
 <div class="sect2">
-<h3 id="Known-Issues">Known Windup Issues</h3>
+<h3 id="Known-Issues">3.2. Known Windup Issues</h3>
 <div class="paragraph">
 <p>Windup known issues are tracked here: <a href="https://issues.jboss.org/browse/WINDUP-496?jql=project%20%3D%20WINDUP%20AND%20issuetype%20%3D%20Bug%20AND%20status%20in%20%28Open%2C%20%22Coding%20In%20Progress%22%2C%20Reopened%2C%20%22Pull%20Request%20Sent%22%29">Open Windup issues</a></p>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Glossary">Glossary of Terms Used in Windup</h3>
+<h3 id="Glossary">3.3. Glossary of Terms Used in Windup</h3>
 <div class="sect3">
-<h4 id="_rules_terms">Rules Terms</h4>
+<h4 id="_rules_terms">3.3.1. Rules Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Rule</dt>
@@ -1560,7 +1560,7 @@ <h4 id="_rules_terms">Rules Terms</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_reporting_terms">Reporting Terms</h4>
+<h4 id="_reporting_terms">3.3.2. Reporting Terms</h4>
 <div class="dlist">
 <dl>
 <dt class="hdlist1">Lift and Shift (Level of effort)</dt>
@@ -1584,7 +1584,7 @@ <h4 id="_reporting_terms">Reporting Terms</h4>
 </div>
 </div>
 <div class="sect2">
-<h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
+<h3 id="Windup-Architectural-Components">3.4. Windup Architectural Components</h3>
 <div class="paragraph">
 <p>The following open source software, tools, and APIs are used within
 Windup to analyze and provide migration information. If you plan to
@@ -1592,7 +1592,7 @@ <h3 id="Windup-Architectural-Components">Windup Architectural Components</h3>
 familiar with them.</p>
 </div>
 <div class="sect3">
-<h4 id="_forge">Forge</h4>
+<h4 id="_forge">3.4.1. Forge</h4>
 <div class="paragraph">
 <p>Forge is an open source, extendable, rapid application development tool
 for creating Java EE applications using Maven. For more information
@@ -1600,7 +1600,7 @@ <h4 id="_forge">Forge</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_forge_furnace">Forge Furnace</h4>
+<h4 id="_forge_furnace">3.4.2. Forge Furnace</h4>
 <div class="paragraph">
 <p>Forge Furnace is a modular runtime container behind Forge that provides
 the ability to run Forge addons in an embedded application. For more
@@ -1609,21 +1609,21 @@ <h4 id="_forge_furnace">Forge Furnace</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_tinkerpop">TinkerPop</h4>
+<h4 id="_tinkerpop">3.4.3. TinkerPop</h4>
 <div class="paragraph">
 <p>TinkerPop is an open source graph computing framework. For more
 information, see: <a href="http://www.tinkerpop.com/">TinkerPop</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_titan">Titan</h4>
+<h4 id="_titan">3.4.4. Titan</h4>
 <div class="paragraph">
 <p>Titan is a scalable graph database optimized for storing and querying graphs.
 For more information, see: <a href="http://thinkaurelius.github.io/titan/">Titan Distributed Graph Database</a> and <a href="https://github.com/thinkaurelius/titan/wiki/Beginner%27s-Guide">Titan Beginner&#8217;s Guide</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_frames">Frames</h4>
+<h4 id="_frames">3.4.5. Frames</h4>
 <div class="paragraph">
 <p>Frames represents graph data in the form of interrelated Java Objects or
 a collection of annotated Java Interfaces. For more information, see:
@@ -1635,7 +1635,7 @@ <h4 id="_frames">Frames</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_gremlin">Gremlin</h4>
+<h4 id="_gremlin">3.4.6. Gremlin</h4>
 <div class="paragraph">
 <p>Gremlin is a graph traversal language that allows you to query, analyze,
 and manipulate property graphs that implement the Blueprints property
@@ -1644,7 +1644,7 @@ <h4 id="_gremlin">Gremlin</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_blueprints">Blueprints</h4>
+<h4 id="_blueprints">3.4.7. Blueprints</h4>
 <div class="paragraph">
 <p>Blueprints is an industry standard API used to access graph databases.
 For more information about Blueprints, see:
@@ -1652,7 +1652,7 @@ <h4 id="_blueprints">Blueprints</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_pipes">Pipes</h4>
+<h4 id="_pipes">3.4.8. Pipes</h4>
 <div class="paragraph">
 <p>Pipes is a dataflow framework used to process graph data. It for the
 transformation of data from input to output. For more information, see:
@@ -1660,14 +1660,14 @@ <h4 id="_pipes">Pipes</h4>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_rexster">Rexster</h4>
+<h4 id="_rexster">3.4.9. Rexster</h4>
 <div class="paragraph">
 <p>Rexster is a graph server that exposes any Blueprints graph through HTTP/REST and a binary protocol called RexPro. Rexster makes extensive use of Blueprints, Pipes, and Gremlin. For more information, see:
 <a href="https://github.com/tinkerpop/rexster/wiki">TinkerPop Rexster Wiki</a>.</p>
 </div>
 </div>
 <div class="sect3">
-<h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
+<h4 id="_ocpsoft_rewrite">3.4.10. OCPsoft Rewrite</h4>
 <div class="paragraph">
 <p>OCPsoft Rewrite is an open source routing and URL rewriting solution for
 Servlets, Java Web Frameworks, and Java EE. For more information about
@@ -1680,7 +1680,7 @@ <h4 id="_ocpsoft_rewrite">OCPsoft Rewrite</h4>
 </div>
 <div id="footer">
 <div id="footer-text">
-Last updated 2015-02-04 16:09:16 EST
+Last updated 2015-02-09 14:03:12 EST
 </div>
 </div>
 </body>
diff --git a/scripts/windupDocPublish.sh b/scripts/windupDocPublish.sh
index 42d8847497..396889e89f 100755
--- a/scripts/windupDocPublish.sh
+++ b/scripts/windupDocPublish.sh
@@ -2,11 +2,11 @@
 if [ "$1" == "" ] || [ "$2" == "" ] || [ "$3" == "" ]; then 
 
     echo "You must pass the following arguments on the command line:"
-    echo "    Path to the local windup-documentation GitHub directory"
-    echo "    Path to the local windup source GitHub directory"
-    echo "    Name of the new beta version" 
+    echo "    arg 1: Path to the local windup-documentation GitHub directory"
+    echo "    arg 2: Path to the local windup source GitHub directory"
+    echo "    arg 3: New documentation version" 
     echo "For example:"
-    echo "    scripts/windupDocPublish.sh ~/GitRepos/windup-documentation/ ~/GitRepos/windup/ 2.0.0.Beta8"
+    echo "    scripts/windupDocPublish.sh ~/GitRepos/windup-documentation/ ~/GitRepos/windup/ 2.0.0.Final"
     exit
 else
     echo  "Windup Documentation will be copied from here: " $1
@@ -54,6 +54,13 @@ echo "    git push origin HEAD"
 echo "    (issue a pull and verify)"
 echo "    git push upstream gh-pages"
 echo "    firefox http://windup.github.io/windup/docs/$WINDUP_VERSION/html/WindupUserGuide.html"
+echo "    unlink latest"
+echo "    ln -s $3 latest"
+echo "    git add latest"
+echo "    git commit -m 'Replace symlink for latest to point to 2.0.0.Final'"
+echo "    git push origin HEAD"
+echo "    (issue a pull and verify)"
+echo "    git push upstream gh-pages"
 
 # git push origin HEAD
 ## issue a pull and verify
@@ -62,3 +69,15 @@ echo "    firefox http://windup.github.io/windup/docs/$WINDUP_VERSION/html/Windu
 
 cd $1
 
+## Update the symlink to point to the latest docs
+# cd $2/docs
+# unlink latest
+# ln -s $3 latest
+## for example: ln -s 2.0.0.Final latest
+# git add latest
+# git commit -m 'Replace symlink for latest to point to 2.0.0.Final'
+# git push origin HEAD
+## issuw a pull and verify
+# git push upstream gh-pages
+
+