diff --git a/csharp/autobuilder/Semmle.Autobuild.Tests/BuildScripts.cs b/csharp/autobuilder/Semmle.Autobuild.Tests/BuildScripts.cs
index 4cd50926dba1..2b655310e09a 100644
--- a/csharp/autobuilder/Semmle.Autobuild.Tests/BuildScripts.cs
+++ b/csharp/autobuilder/Semmle.Autobuild.Tests/BuildScripts.cs
@@ -130,7 +130,7 @@ IEnumerable<string> IBuildActions.EnumerateDirectories(string dir)
 
         string IBuildActions.PathCombine(params string[] parts)
         {
-            return string.Join('\\', parts.Where(p => !string.IsNullOrWhiteSpace(p)));
+            return string.Join(IsWindows ? '\\' : '/', parts.Where(p => !string.IsNullOrWhiteSpace(p)));
         }
 
         string IBuildActions.GetFullPath(string path) => path;
@@ -146,6 +146,13 @@ XmlDocument IBuildActions.LoadXml(string filename)
                 return xml;
             throw new ArgumentException("Missing LoadXml " + filename);
         }
+
+        public string EnvironmentExpandEnvironmentVariables(string s)
+        {
+            foreach (var kvp in GetEnvironmentVariable)
+                s = s.Replace($"%{kvp.Key}%", kvp.Value);
+            return s;
+        }
     }
 
     /// <summary>
@@ -394,9 +401,9 @@ public void TestLinuxCSharpAutoBuilder()
             Actions.RunProcess["dotnet --info"] = 0;
             Actions.RunProcess["dotnet clean test.csproj"] = 0;
             Actions.RunProcess["dotnet restore test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.FileExists["test.csproj"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
@@ -470,6 +477,7 @@ public void TestCppAutobuilderSuccess()
         [Fact]
         public void TestVsWhereSucceeded()
         {
+            Actions.IsWindows = true;
             Actions.GetEnvironmentVariable["ProgramFiles(x86)"] = @"C:\Program Files (x86)";
             Actions.FileExists[@"C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe"] = true;
             Actions.RunProcess[@"C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe -prerelease -legacy -property installationPath"] = 0;
@@ -487,6 +495,7 @@ public void TestVsWhereSucceeded()
         [Fact]
         public void TestVsWhereNotExist()
         {
+            Actions.IsWindows = true;
             Actions.GetEnvironmentVariable["ProgramFiles(x86)"] = @"C:\Program Files (x86)";
             Actions.FileExists[@"C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe"] = false;
 
@@ -497,6 +506,7 @@ public void TestVsWhereNotExist()
         [Fact]
         public void TestVcVarsAllBatFiles()
         {
+            Actions.IsWindows = true;
             Actions.GetEnvironmentVariable["ProgramFiles(x86)"] = @"C:\Program Files (x86)";
             Actions.FileExists[@"C:\Program Files (x86)\Microsoft Visual Studio\Installer\vswhere.exe"] = false;
             Actions.FileExists[@"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\vcvarsall.bat"] = true;
@@ -511,9 +521,9 @@ public void TestVcVarsAllBatFiles()
         [Fact]
         public void TestLinuxBuildlessExtractionSuccess()
         {
-            Actions.RunProcess[@"C:\odasa\tools\csharp\Semmle.Extraction.CSharp.Standalone --references:."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools/csharp/Semmle.Extraction.CSharp.Standalone --references:."] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
@@ -527,9 +537,7 @@ public void TestLinuxBuildlessExtractionSuccess()
         [Fact]
         public void TestLinuxBuildlessExtractionFailed()
         {
-            Actions.RunProcess[@"C:\odasa\tools\csharp\Semmle.Extraction.CSharp.Standalone --references:."] = 10;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools/csharp/Semmle.Extraction.CSharp.Standalone --references:."] = 10;
             Actions.FileExists["csharp.log"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
@@ -543,9 +551,9 @@ public void TestLinuxBuildlessExtractionFailed()
         [Fact]
         public void TestLinuxBuildlessExtractionSolution()
         {
-            Actions.RunProcess[@"C:\odasa\tools\csharp\Semmle.Extraction.CSharp.Standalone foo.sln --references:."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools/csharp/Semmle.Extraction.CSharp.Standalone foo.sln --references:."] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
@@ -587,9 +595,9 @@ void TestAutobuilderScript(Autobuilder autobuilder, int expectedOutput, int comm
         [Fact]
         public void TestLinuxBuildCommand()
         {
-            Actions.RunProcess["C:\\odasa\\tools\\odasa index --auto \"./build.sh --skip-tests\""] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto ""./build.sh --skip-tests"""] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
@@ -610,10 +618,10 @@ public void TestLinuxBuildSh()
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
             Actions.RunProcess["/bin/chmod u+x build/build.sh"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto build/build.sh"] = 0;
-            Actions.RunProcessWorkingDirectory[@"C:\odasa\tools\odasa index --auto build/build.sh"] = "build";
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto build/build.sh"] = 0;
+            Actions.RunProcessWorkingDirectory[@"C:\odasa/tools/odasa index --auto build/build.sh"] = "build";
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
 
             var autobuilder = CreateAutoBuilder("csharp", false);
@@ -629,8 +637,8 @@ public void TestLinuxBuildShCSharpLogMissing()
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
 
             Actions.RunProcess["/bin/chmod u+x build.sh"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto build.sh"] = 0;
-            Actions.RunProcessWorkingDirectory[@"C:\odasa\tools\odasa index --auto build.sh"] = "";
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto build.sh"] = 0;
+            Actions.RunProcessWorkingDirectory[@"C:\odasa/tools/odasa index --auto build.sh"] = "";
             Actions.FileExists["csharp.log"] = false;
 
             var autobuilder = CreateAutoBuilder("csharp", false);
@@ -646,8 +654,8 @@ public void TestLinuxBuildShFailed()
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
 
             Actions.RunProcess["/bin/chmod u+x build.sh"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto build.sh"] = 5;
-            Actions.RunProcessWorkingDirectory[@"C:\odasa\tools\odasa index --auto build.sh"] = "";
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto build.sh"] = 5;
+            Actions.RunProcessWorkingDirectory[@"C:\odasa/tools/odasa index --auto build.sh"] = "";
             Actions.FileExists["csharp.log"] = true;
 
             var autobuilder = CreateAutoBuilder("csharp", false);
@@ -796,9 +804,9 @@ public void TestSkipNugetMsBuild()
         [Fact]
         public void TestSkipNugetBuildless()
         {
-            Actions.RunProcess[@"C:\odasa\tools\csharp\Semmle.Extraction.CSharp.Standalone foo.sln --references:. --skip-nuget"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools/csharp/Semmle.Extraction.CSharp.Standalone foo.sln --references:. --skip-nuget"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
             Actions.GetEnvironmentVariable["SOURCE_ARCHIVE"] = null;
@@ -816,9 +824,9 @@ public void TestSkipNugetDotnet()
             Actions.RunProcess["dotnet --info"] = 0;
             Actions.RunProcess["dotnet clean test.csproj"] = 0;
             Actions.RunProcess["dotnet restore test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto dotnet build --no-incremental /p:UseSharedCompilation=false --no-restore test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto dotnet build --no-incremental /p:UseSharedCompilation=false --no-restore test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.FileExists["test.csproj"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
@@ -846,13 +854,13 @@ public void TestDotnetVersionNotInstalled()
             Actions.RunProcessOut["dotnet --list-sdks"] = "2.1.2 [C:\\Program Files\\dotnet\\sdks]\n2.1.4 [C:\\Program Files\\dotnet\\sdks]";
             Actions.RunProcess[@"curl -sO https://dot.net/v1/dotnet-install.sh"] = 0;
             Actions.RunProcess[@"chmod u+x dotnet-install.sh"] = 0;
-            Actions.RunProcess[@"./dotnet-install.sh --channel release --version 2.1.3 --install-dir C:\Project\.dotnet"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet --info"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet clean test.csproj"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet restore test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto C:\Project\.dotnet\dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"./dotnet-install.sh --channel release --version 2.1.3 --install-dir C:\Project/.dotnet"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet --info"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet clean test.csproj"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet restore test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto C:\Project/.dotnet/dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.FileExists["test.csproj"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
@@ -881,13 +889,13 @@ public void TestDotnetVersionAlreadyInstalled()
             Actions.RunProcessOut["dotnet --list-sdks"] = "2.1.3 [C:\\Program Files\\dotnet\\sdks]\n2.1.4 [C:\\Program Files\\dotnet\\sdks]";
             Actions.RunProcess[@"curl -sO https://dot.net/v1/dotnet-install.sh"] = 0;
             Actions.RunProcess[@"chmod u+x dotnet-install.sh"] = 0;
-            Actions.RunProcess[@"./dotnet-install.sh --channel release --version 2.1.3 --install-dir C:\Project\.dotnet"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet --info"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet clean test.csproj"] = 0;
-            Actions.RunProcess[@"C:\Project\.dotnet\dotnet restore test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto C:\Project\.dotnet\dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"./dotnet-install.sh --channel release --version 2.1.3 --install-dir C:\Project/.dotnet"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet --info"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet clean test.csproj"] = 0;
+            Actions.RunProcess[@"C:\Project/.dotnet/dotnet restore test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto C:\Project/.dotnet/dotnet build --no-incremental /p:UseSharedCompilation=false test.csproj"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.FileExists["test.csproj"] = true;
             Actions.GetEnvironmentVariable["TRAP_FOLDER"] = null;
@@ -988,10 +996,10 @@ public void TestDirsProjWindows()
         [Fact]
         public void TestDirsProjLinux()
         {
-            Actions.RunProcess[@"mono C:\odasa\tools\csharp\nuget\nuget.exe restore dirs.proj"] = 1;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --auto msbuild dirs.proj /p:UseSharedCompilation=false /t:rebuild /p:MvcBuildViews=true"] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\java\bin\java -jar C:\odasa\tools\extractor-asp.jar ."] = 0;
-            Actions.RunProcess[@"C:\odasa\tools\odasa index --xml --extensions config csproj props xml"] = 0;
+            Actions.RunProcess[@"mono C:\odasa\tools/csharp/nuget/nuget.exe restore dirs.proj"] = 1;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --auto msbuild dirs.proj /p:UseSharedCompilation=false /t:rebuild /p:MvcBuildViews=true"] = 0;
+            Actions.RunProcess[@"C:\odasa\tools\java/bin/java -jar C:\odasa/tools/extractor-asp.jar ."] = 0;
+            Actions.RunProcess[@"C:\odasa/tools/odasa index --xml --extensions config csproj props xml"] = 0;
             Actions.FileExists["csharp.log"] = true;
             Actions.FileExists["a/test.csproj"] = true;
             Actions.FileExists["dirs.proj"] = true;
@@ -1042,5 +1050,21 @@ public void TestCyclicDirsProj()
             var autobuilder = CreateAutoBuilder("csharp", false);
             TestAutobuilderScript(autobuilder, 1, 0);
         }
+
+        [Fact]
+        public void TestAsStringWithExpandedEnvVarsWindows()
+        {
+            Actions.IsWindows = true;
+            Actions.GetEnvironmentVariable["LGTM_SRC"] = @"C:\repo";
+            Assert.Equal(@"C:\repo\test", @"%LGTM_SRC%\test".AsStringWithExpandedEnvVars(Actions));
+        }
+
+        [Fact]
+        public void TestAsStringWithExpandedEnvVarsLinux()
+        {
+            Actions.IsWindows = false;
+            Actions.GetEnvironmentVariable["LGTM_SRC"] = "/tmp/repo";
+            Assert.Equal("/tmp/repo/test", "$LGTM_SRC/test".AsStringWithExpandedEnvVars(Actions));
+        }
     }
 }
diff --git a/csharp/autobuilder/Semmle.Autobuild/AspBuildRule.cs b/csharp/autobuilder/Semmle.Autobuild/AspBuildRule.cs
index 7765e94f5e16..a39481545d88 100644
--- a/csharp/autobuilder/Semmle.Autobuild/AspBuildRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/AspBuildRule.cs
@@ -7,7 +7,7 @@ namespace Semmle.Autobuild
     /// </summary>
     class AspBuildRule : IBuildRule
     {
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             var command = new CommandBuilder(builder.Actions).
                 RunCommand(builder.Actions.PathCombine(builder.SemmleJavaHome, "bin", "java")).
diff --git a/csharp/autobuilder/Semmle.Autobuild/AutobuildOptions.cs b/csharp/autobuilder/Semmle.Autobuild/AutobuildOptions.cs
index 53ecf697721e..4a2e906fc81a 100644
--- a/csharp/autobuilder/Semmle.Autobuild/AutobuildOptions.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/AutobuildOptions.cs
@@ -1,5 +1,6 @@
 using System;
 using System.Linq;
+using System.Text.RegularExpressions;
 
 namespace Semmle.Autobuild
 {
@@ -37,14 +38,14 @@ public void ReadEnvironment(IBuildActions actions)
         {
             RootDirectory = actions.GetCurrentDirectory();
             VsToolsVersion = actions.GetEnvironmentVariable(prefix + "VSTOOLS_VERSION");
-            MsBuildArguments = actions.GetEnvironmentVariable(prefix + "MSBUILD_ARGUMENTS");
+            MsBuildArguments = actions.GetEnvironmentVariable(prefix + "MSBUILD_ARGUMENTS").AsStringWithExpandedEnvVars(actions);
             MsBuildPlatform = actions.GetEnvironmentVariable(prefix + "MSBUILD_PLATFORM");
             MsBuildConfiguration = actions.GetEnvironmentVariable(prefix + "MSBUILD_CONFIGURATION");
             MsBuildTarget = actions.GetEnvironmentVariable(prefix + "MSBUILD_TARGET");
-            DotNetArguments = actions.GetEnvironmentVariable(prefix + "DOTNET_ARGUMENTS");
+            DotNetArguments = actions.GetEnvironmentVariable(prefix + "DOTNET_ARGUMENTS").AsStringWithExpandedEnvVars(actions);
             DotNetVersion = actions.GetEnvironmentVariable(prefix + "DOTNET_VERSION");
             BuildCommand = actions.GetEnvironmentVariable(prefix + "BUILD_COMMAND");
-            Solution = actions.GetEnvironmentVariable(prefix + "SOLUTION").AsList(new string[0]);
+            Solution = actions.GetEnvironmentVariable(prefix + "SOLUTION").AsListWithExpandedEnvVars(actions, new string[0]);
 
             IgnoreErrors = actions.GetEnvironmentVariable(prefix + "IGNORE_ERRORS").AsBool("ignore_errors", false);
             Buildless = actions.GetEnvironmentVariable(prefix + "BUILDLESS").AsBool("buildless", false);
@@ -92,12 +93,29 @@ public static Language AsLanguage(this string key)
             }
         }
 
-        public static string[] AsList(this string value, string[] defaultValue)
+        public static string[] AsListWithExpandedEnvVars(this string value, IBuildActions actions, string[] defaultValue)
         {
             if (value == null)
                 return defaultValue;
 
-            return value.Split(new[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries).ToArray();
+            return value.
+                Split(new[] { '\r', '\n' }, StringSplitOptions.RemoveEmptyEntries).
+                Select(s => AsStringWithExpandedEnvVars(s, actions)).ToArray();
+        }
+
+        static readonly Regex linuxEnvRegEx = new Regex(@"\$([a-zA-Z_][a-zA-Z_0-9]*)", RegexOptions.Compiled);
+
+        public static string AsStringWithExpandedEnvVars(this string value, IBuildActions actions)
+        {
+            if (string.IsNullOrEmpty(value))
+                return value;
+
+            // `Environment.ExpandEnvironmentVariables` only works with Windows-style
+            // environment variables
+            var windowsStyle = actions.IsWindows()
+                ? value
+                : linuxEnvRegEx.Replace(value, m => $"%{m.Groups[1].Value}%");
+            return actions.EnvironmentExpandEnvironmentVariables(windowsStyle);
         }
     }
 }
diff --git a/csharp/autobuilder/Semmle.Autobuild/Autobuilder.cs b/csharp/autobuilder/Semmle.Autobuild/Autobuilder.cs
index 02e3b672511f..1734afc8b856 100644
--- a/csharp/autobuilder/Semmle.Autobuild/Autobuilder.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/Autobuilder.cs
@@ -16,7 +16,8 @@ interface IBuildRule
         /// Analyse the files and produce a build script.
         /// </summary>
         /// <param name="builder">The files and options relating to the build.</param>
-        BuildScript Analyse(Autobuilder builder);
+        /// <param name="auto">Whether this build rule is being automatically applied.</param>
+        BuildScript Analyse(Autobuilder builder, bool auto);
     }
 
     /// <summary>
@@ -135,9 +136,9 @@ public Autobuilder(IBuildActions actions, AutobuildOptions options)
                     foreach (var solution in options.Solution)
                     {
                         if (actions.FileExists(solution))
-                            ret.Add(new Solution(this, solution));
+                            ret.Add(new Solution(this, solution, true));
                         else
-                            Log(Severity.Error, $"The specified solution file {solution} was not found");
+                            Log(Severity.Error, $"The specified project or solution file {solution} was not found");
                     }
                     return ret;
                 }
@@ -172,7 +173,7 @@ IEnumerable<IProjectOrSolution> FindFiles(string extension, Func<string, Project
                     return ret;
 
                 // Then look for `.sln` files
-                ret = FindFiles(".sln", f => new Solution(this, f))?.ToList();
+                ret = FindFiles(".sln", f => new Solution(this, f, false))?.ToList();
                 if (ret != null)
                     return ret;
 
@@ -250,17 +251,17 @@ BuildScript CheckExtractorRun(bool warnOnFailure) =>
             switch (GetCSharpBuildStrategy())
             {
                 case CSharpBuildStrategy.CustomBuildCommand:
-                    attempt = new BuildCommandRule().Analyse(this) & CheckExtractorRun(true);
+                    attempt = new BuildCommandRule().Analyse(this, false) & CheckExtractorRun(true);
                     break;
                 case CSharpBuildStrategy.Buildless:
                     // No need to check that the extractor has been executed in buildless mode
-                    attempt = new StandaloneBuildRule().Analyse(this);
+                    attempt = new StandaloneBuildRule().Analyse(this, false);
                     break;
                 case CSharpBuildStrategy.MSBuild:
-                    attempt = new MsBuildRule().Analyse(this) & CheckExtractorRun(true);
+                    attempt = new MsBuildRule().Analyse(this, false) & CheckExtractorRun(true);
                     break;
                 case CSharpBuildStrategy.DotNet:
-                    attempt = new DotNetRule().Analyse(this) & CheckExtractorRun(true);
+                    attempt = new DotNetRule().Analyse(this, false) & CheckExtractorRun(true);
                     break;
                 case CSharpBuildStrategy.Auto:
                     var cleanTrapFolder =
@@ -285,11 +286,11 @@ BuildScript IntermediateAttempt(BuildScript s) =>
 
                     attempt =
                         // First try .NET Core
-                        IntermediateAttempt(new DotNetRule().Analyse(this)) |
+                        IntermediateAttempt(new DotNetRule().Analyse(this, true)) |
                         // Then MSBuild
-                        (() => IntermediateAttempt(new MsBuildRule().Analyse(this))) |
+                        (() => IntermediateAttempt(new MsBuildRule().Analyse(this, true))) |
                         // And finally look for a script that might be a build script
-                        (() => new BuildCommandAutoRule().Analyse(this) & CheckExtractorRun(true)) |
+                        (() => new BuildCommandAutoRule().Analyse(this, true) & CheckExtractorRun(true)) |
                         // All attempts failed: print message
                         AutobuildFailure();
                     break;
@@ -297,8 +298,8 @@ BuildScript IntermediateAttempt(BuildScript s) =>
 
             return
                 attempt &
-                (() => new AspBuildRule().Analyse(this)) &
-                (() => new XmlBuildRule().Analyse(this));
+                (() => new AspBuildRule().Analyse(this, false)) &
+                (() => new XmlBuildRule().Analyse(this, false));
         }
 
         /// <summary>
@@ -337,13 +338,13 @@ enum CSharpBuildStrategy
         BuildScript GetCppBuildScript()
         {
             if (Options.BuildCommand != null)
-                return new BuildCommandRule().Analyse(this);
+                return new BuildCommandRule().Analyse(this, false);
 
             return
                 // First try MSBuild
-                new MsBuildRule().Analyse(this) |
+                new MsBuildRule().Analyse(this, true) |
                 // Then look for a script that might be a build script
-                (() => new BuildCommandAutoRule().Analyse(this)) |
+                (() => new BuildCommandAutoRule().Analyse(this, true)) |
                 // All attempts failed: print message
                 AutobuildFailure();
         }
diff --git a/csharp/autobuilder/Semmle.Autobuild/BuildActions.cs b/csharp/autobuilder/Semmle.Autobuild/BuildActions.cs
index 433598c5c16c..edf4fc752c1c 100644
--- a/csharp/autobuilder/Semmle.Autobuild/BuildActions.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/BuildActions.cs
@@ -113,6 +113,12 @@ public interface IBuildActions
         /// Loads the XML document from <paramref name="filename"/>.
         /// </summary>
         XmlDocument LoadXml(string filename);
+
+        /// <summary>
+        /// Expand all Windows-style environment variables in <paramref name="s"/>,
+        /// Environment.ExpandEnvironmentVariables()
+        /// </summary>
+        string EnvironmentExpandEnvironmentVariables(string s);
     }
 
     /// <summary>
@@ -187,6 +193,8 @@ XmlDocument IBuildActions.LoadXml(string filename)
 
         string IBuildActions.GetFullPath(string path) => Path.GetFullPath(path);
 
+        public string EnvironmentExpandEnvironmentVariables(string s) => Environment.ExpandEnvironmentVariables(s);
+
         public static readonly IBuildActions Instance = new SystemBuildActions();
     }
 }
diff --git a/csharp/autobuilder/Semmle.Autobuild/BuildCommandAutoRule.cs b/csharp/autobuilder/Semmle.Autobuild/BuildCommandAutoRule.cs
index 9ec8a3e16eb0..8ae3ee609667 100644
--- a/csharp/autobuilder/Semmle.Autobuild/BuildCommandAutoRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/BuildCommandAutoRule.cs
@@ -25,7 +25,7 @@ class BuildCommandAutoRule : IBuildRule
             "build"
         };
 
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             builder.Log(Severity.Info, "Attempting to locate build script");
 
diff --git a/csharp/autobuilder/Semmle.Autobuild/BuildCommandRule.cs b/csharp/autobuilder/Semmle.Autobuild/BuildCommandRule.cs
index 2dd3a1442223..8019b5798bc5 100644
--- a/csharp/autobuilder/Semmle.Autobuild/BuildCommandRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/BuildCommandRule.cs
@@ -5,7 +5,7 @@
     /// </summary>
     class BuildCommandRule : IBuildRule
     {
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             if (builder.Options.BuildCommand == null)
                 return BuildScript.Failure;
diff --git a/csharp/autobuilder/Semmle.Autobuild/DotNetRule.cs b/csharp/autobuilder/Semmle.Autobuild/DotNetRule.cs
index c9622d2cf26f..9cce54ab50ef 100644
--- a/csharp/autobuilder/Semmle.Autobuild/DotNetRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/DotNetRule.cs
@@ -14,22 +14,25 @@ namespace Semmle.Autobuild
     /// </summary>
     class DotNetRule : IBuildRule
     {
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             if (!builder.ProjectsOrSolutionsToBuild.Any())
                 return BuildScript.Failure;
 
-            var notDotNetProject = builder.ProjectsOrSolutionsToBuild.
-                SelectMany(p => Enumerators.Singleton(p).Concat(p.IncludedProjects)).
-                OfType<Project>().
-                FirstOrDefault(p => !p.DotNetProject);
-            if (notDotNetProject != null)
+            if (auto)
             {
-                builder.Log(Severity.Info, "Not using .NET Core because of incompatible project {0}", notDotNetProject);
-                return BuildScript.Failure;
-            }
+                var notDotNetProject = builder.ProjectsOrSolutionsToBuild.
+                  SelectMany(p => Enumerators.Singleton(p).Concat(p.IncludedProjects)).
+                  OfType<Project>().
+                  FirstOrDefault(p => !p.DotNetProject);
+                if (notDotNetProject != null)
+                {
+                    builder.Log(Severity.Info, "Not using .NET Core because of incompatible project {0}", notDotNetProject);
+                    return BuildScript.Failure;
+                }
 
-            builder.Log(Severity.Info, "Attempting to build using .NET Core");
+                builder.Log(Severity.Info, "Attempting to build using .NET Core");
+            }
 
             return WithDotNet(builder, dotNet =>
                 {
diff --git a/csharp/autobuilder/Semmle.Autobuild/MsBuildRule.cs b/csharp/autobuilder/Semmle.Autobuild/MsBuildRule.cs
index 2b46d8d526e8..593039919ed9 100644
--- a/csharp/autobuilder/Semmle.Autobuild/MsBuildRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/MsBuildRule.cs
@@ -13,12 +13,13 @@ class MsBuildRule : IBuildRule
         /// </summary>
         const string MsBuild = "msbuild";
 
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             if (!builder.ProjectsOrSolutionsToBuild.Any())
                 return BuildScript.Failure;
 
-            builder.Log(Severity.Info, "Attempting to build using MSBuild");
+            if (auto)
+                builder.Log(Severity.Info, "Attempting to build using MSBuild");
 
             var vsTools = GetVcVarsBatFile(builder);
 
diff --git a/csharp/autobuilder/Semmle.Autobuild/Project.cs b/csharp/autobuilder/Semmle.Autobuild/Project.cs
index 87088d1edfb5..47752f691a49 100644
--- a/csharp/autobuilder/Semmle.Autobuild/Project.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/Project.cs
@@ -39,9 +39,9 @@ public Project(Autobuilder builder, string path) : base(builder, path)
             {
                 projFile = builder.Actions.LoadXml(FullPath);
             }
-            catch (XmlException)
+            catch (Exception e) when (e is XmlException || e is FileNotFoundException)
             {
-                builder.Log(Severity.Info, $"Skipping project file {path} as it is not a valid XML document.");
+                builder.Log(Severity.Info, $"Unable to read project file {path}.");
                 return;
             }
 
@@ -80,7 +80,7 @@ public Project(Autobuilder builder, string path) : base(builder, path)
                     var projectFilesIncludes = root.SelectNodes("//msbuild:Project/msbuild:ItemGroup/msbuild:ProjectFiles/@Include", mgr).OfType<XmlNode>();
                     foreach (var include in projectFileIncludes.Concat(projectFilesIncludes))
                     {
-                        var includePath = builder.Actions.IsWindows() ? include.Value : include.Value.Replace("\\", "/");
+                        var includePath = builder.Actions.PathCombine(include.Value.Split('\\', StringSplitOptions.RemoveEmptyEntries));
                         ret.Add(new Project(builder, builder.Actions.PathCombine(Path.GetDirectoryName(this.FullPath), includePath)));
                     }
                     return ret;
diff --git a/csharp/autobuilder/Semmle.Autobuild/Solution.cs b/csharp/autobuilder/Semmle.Autobuild/Solution.cs
index 312e7deeb54b..a5512a84ea66 100644
--- a/csharp/autobuilder/Semmle.Autobuild/Solution.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/Solution.cs
@@ -4,6 +4,8 @@
 using System.Collections.Generic;
 using System.Linq;
 using Semmle.Util;
+using System.IO;
+using Semmle.Util.Logging;
 
 namespace Semmle.Autobuild
 {
@@ -55,25 +57,33 @@ class Solution : ProjectOrSolution, ISolution
         public string DefaultPlatformName =>
             solution == null ? "" : solution.GetDefaultPlatformName();
 
-        public Solution(Autobuilder builder, string path) : base(builder, path)
+        public Solution(Autobuilder builder, string path, bool allowProject) : base(builder, path)
         {
             try
             {
                 solution = SolutionFile.Parse(FullPath);
-
-                includedProjects =
-                    solution.ProjectsInOrder.
-                    Where(p => p.ProjectType == SolutionProjectType.KnownToBeMSBuildFormat).
-                    Select(p => builder.Actions.GetFullPath(FileUtils.ConvertToNative(p.AbsolutePath))).
-                    Select(p => new Project(builder, p)).
-                    ToArray();
             }
-            catch (InvalidProjectFileException)
+            catch (Exception e) when (e is InvalidProjectFileException || e is FileNotFoundException)
             {
                 // We allow specifying projects as solutions in lgtm.yml, so model
                 // that scenario as a solution with just that one project
-                includedProjects = new[] { new Project(builder, path) };
+                if (allowProject)
+                {
+                    includedProjects = new[] { new Project(builder, path) };
+                    return;
+                }
+
+                builder.Log(Severity.Info, $"Unable to read solution file {path}.");
+                includedProjects = new Project[0];
+                return;
             }
+
+            includedProjects =
+                solution.ProjectsInOrder.
+                Where(p => p.ProjectType == SolutionProjectType.KnownToBeMSBuildFormat).
+                Select(p => builder.Actions.PathCombine(Path.GetDirectoryName(path), builder.Actions.PathCombine(p.RelativePath.Split('\\', StringSplitOptions.RemoveEmptyEntries)))).
+                Select(p => new Project(builder, p)).
+                ToArray();
         }
 
         IEnumerable<Version> ToolsVersions => includedProjects.Where(p => p.ValidToolsVersion).Select(p => p.ToolsVersion);
diff --git a/csharp/autobuilder/Semmle.Autobuild/StandaloneBuildRule.cs b/csharp/autobuilder/Semmle.Autobuild/StandaloneBuildRule.cs
index 3fafa84e454b..366ce1f08fc6 100644
--- a/csharp/autobuilder/Semmle.Autobuild/StandaloneBuildRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/StandaloneBuildRule.cs
@@ -7,7 +7,7 @@ namespace Semmle.Autobuild
     /// </summary>
     class StandaloneBuildRule : IBuildRule
     {
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             BuildScript GetCommand(string solution)
             {
diff --git a/csharp/autobuilder/Semmle.Autobuild/XmlBuildRule.cs b/csharp/autobuilder/Semmle.Autobuild/XmlBuildRule.cs
index 420fc508bfb7..8d34fde6413a 100644
--- a/csharp/autobuilder/Semmle.Autobuild/XmlBuildRule.cs
+++ b/csharp/autobuilder/Semmle.Autobuild/XmlBuildRule.cs
@@ -7,7 +7,7 @@ namespace Semmle.Autobuild
     /// </summary>
     class XmlBuildRule : IBuildRule
     {
-        public BuildScript Analyse(Autobuilder builder)
+        public BuildScript Analyse(Autobuilder builder, bool auto)
         {
             var command = new CommandBuilder(builder.Actions).
                 RunCommand(builder.Odasa).