Add dotbot package command for syncing .bot changes back to source repo

[ap-cbilgin]

Problem

When developing dotbot, changes are made inside the .bot/ directory of a live project. However, dotbot init is a one-way operation — it copies from profiles/default/ into the project's .bot/, but there's no built-in way to copy changes back. This means after iterating on systems, prompts, workflows, or UI within a project, developers must manually identify and copy modified files back to the dotbot source repo's profiles/default/ directory. This is tedious, error-prone, and doesn't scale.

Solution

Introduces a new dotbot package command that reverses the init flow:

.bot/{path}  -->  {target}/profiles/default/{path}

New file: .bot/package.ps1

A PowerShell script that packages framework files from a project's .bot/ back to the dotbot source repo, with smart filtering to exclude project-specific state.

What gets packaged (framework files):

• systems/ — MCP server, runtime engine, web UI
• prompts/ — agents, skills, workflows, includes
• hooks/ — dev, verify, scripts
• defaults/ — settings, providers, theme
• Root scripts — go.ps1, init.ps1, package.ps1
• Workspace templates/samples only (e.g., TEMPLATE.json, sample tasks)

What gets excluded (project-specific state):

• workspace/ content — tasks, ADRs, sessions, plans, product docs
• .control/ — runtime state, process registry, logs
• .worktrees/ — git worktrees for task isolation
• *.log, *.jsonl, *.tmp files

Features:

• MD5 diffing — only reports/copies files that actually changed ([NEW]/[UPDATE] labels)
• -DryRun — preview all changes before applying
• -SyncFromIDE — pulls agent/skill edits from .claude/ back into .bot/prompts/ before packaging (useful when agents are edited directly in IDE directories)
• -Archive — creates a timestamped .zip for distribution instead of copying to a directory
• -Force — skip hash checks and overwrite everything
• Stale file detection — warns about files present in the target but missing from source, indicating potential cleanup needed
• Target validation — verifies the target directory contains profiles/ before proceeding

CLI integration: install-global.ps1

• Added dotbot package to the CLI wrapper's command switch and help text
• The command delegates to the current project's .bot/package.ps1, so it always uses the version matching the project's dotbot installation

Usage

# Preview what would be synced
dotbot package -Target C:\dotbot-install -DryRun

# Package changes back to source repo
dotbot package -Target C:\dotbot-install

# Sync IDE-edited agents first, then package
dotbot package -Target C:\dotbot-install -SyncFromIDE

# Create a distributable zip archive
dotbot package -Archive

Example output (dry run)

  Found 211 framework files

    [UPDATE] profiles/default/systems/ui/server.ps1
    [UPDATE] profiles/default/systems/ui/static/modules/tasks.js
    [UPDATE] profiles/default/prompts/workflows/99-autonomous-task.md
    [NEW]    profiles/default/package.ps1

  SUMMARY
    New files:     1
    Updated:       22
    Unchanged:     188
    Total files:   211

Test plan

• Run .bot\package.ps1 -Target C:\dotbot-install -DryRun — verify correct [NEW]/[UPDATE] labeling
• Run .bot\package.ps1 -Target C:\dotbot-install — verify files are copied to profiles/default/
• Run .bot\package.ps1 -Archive — verify zip is created with correct structure
• Run .bot\package.ps1 -SyncFromIDE -DryRun — verify IDE agent changes are detected
• Run with no -Target — verify helpful error message is shown
• Run against a non-dotbot directory — verify target validation error
• After packaging, run dotbot init -Force in a fresh project — verify round-trip works
• Verify workspace content (tasks, ADRs, sessions) is NOT included in package

[andresharpe]

I do this differently and a bit safer.

Here is my workflow.

1. I start claude code up in ~/repos/dotbot-v3
2. I tell it that i am testing dotbot-v3 and my target folder that i installed dotbot into is ~/repos/
   2b. I optionally ask it to scan all *.jsonl logs in ~/repos//.bot/ and subfolders and find recurring problems
3. That i must make all changes in ~/repos/dotbot-v3
4. It must then at end "cycle" dotbot:

• cd ~/repos/dotbot-v3 && pwsh tests/Run-Tests.ps1
• cd ~/repos/dotbot-v3 && pwsh install.ps1
• cd ~/repos/ && dotbot init -Profile -Force

5. After the integration test I then do a pull request for changes in ~/repos/dotbot-v3/

this ensures no project specific edits corrupt the main dotbot-v3 repo and makes the changes one way from dotbot to any project..