Instructions for setting up and configuring ASDoc in Flash Builder, where the project is contained in 3 modules inside C:\httpdocs\XX_project_XX:

Run -> External Tools configurations
Right click in left pane and select "New"

 Location: C:\Program Files (x86)\Adobe\Adobe Flash Builder 4\sdks\4.0.0\bin\asdoc.exe

 Working Directory: C:\httpdocs\XX_project_XX

 -source-path MYAPI/src
 -source-path MyGameAPI/src
 -source-path MyGame/src
 
 -doc-sources MYAPI/src
 -doc-sources MyGameAPI/src
 -doc-sources MyGame/src
 
 -external-library-path "C:\httpdocs\XX_project_XX\libs\as3corelib-.92.1"
 -external-library-path "C:\httpdocs\XX_project_XX\libs\as3isolib-.303"
 -external-library-path "C:\httpdocs\XX_project_XX\libs\bulkoader-rev-282"
 -external-library-path "C:\httpdocs\XX_project_XX\libs\parsley-2.2.2-lib"
 -external-library-path "C:\httpdocs\XX_project_XX\libs\parsley-2.2.2-release"
 
 
 -compiler.strict=false
 
 -main-title "MyGame Flash Client Documentation"
 -window-title "MyGame Flash Client Documentation"
 -footer "This is the footer"
 
 -output docs

• Docs
• ASDocs
• ActionScript 3 Documentation
• ASDoc
• AS3Doc