Package.ini generation
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How Setup Capture decides which EXE will be included in a generated package.ini file

Most larger applications will install many different EXE files during installation; however, not all of the EXE files installed are meant to be used directly by users. During the Setup Capture process, Thinstall will look to see which Desktop and Start Menu shortcuts were created and use these links to generate Thinstall EXEs during build.

For example, Office 2003 installs 44 different EXEs:

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However, Office 2003 only installs Start Menu entries for 13 of these 44 EXE files. Most of the EXE files are probably not intended to invoked directly by the user.

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For a standard capture of Office 2003, Thinstall generates a package.ini which contains entries to generate EXEs for only the shortcuts installed by Office like this:

[EXCEL.EXE]
Source=%ProgramFilesDir%\Microsoft Office\OFFICE11\EXCEL.EXE
ReadOnlyData=bin\Package.ro.tvr

[OUTLOOK.EXE]
Source=%ProgramFilesDir%\Microsoft Office\OFFICE11\OUTLOOK.EXE
Shortcut=EXCEL.EXE

[POWERPNT.EXE]
Source=%ProgramFilesDir%\Microsoft Office\OFFICE11\POWERPNT.EXE
Shortcut=EXCEL.EXE

[WINWORD.EXE]
Source=%ProgramFilesDir%\Microsoft Office\OFFICE11\WINWORD.EXE
Shortcut=EXCEL.EXE

...
 
Note: For each entry in the package file, there is a Source= option which specifies which application will be launched when building the package.  
In this case, [EXCEL.EXE] is set up to host all of the package file/registry data by using ReadOnlyData=, while all the other EXE files simply reference the package data from EXCEL.EXE using Shortcut=  
 
When building this packaging using build.bat, you'll see the following appear in your bin directory.  
 
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Because Thinstall uses shortcuts installed during the capture process to generate the package.ini, make sure you let the installer create shortcuts for you. Many installers offer the option to not write shortcuts; if you disable shortcut creation, Setup Capture won't know what EXEs you intend to generate and will start with an empty project. 
 
If you accidentally disabled shortcuts during install or the application does not install any shortcuts during it's installation process, you can manually tell Thinstall which EXEs the user can access directly by using a text editor to add this information to your package.ini file. Simply add the following lines anywhere in the text file.  
 
[My Application.exe]
Source=%ProgramFilesDir%\My App\My Application.exe
ReadOnlyData=bin\Package.ro.tvr
Where %ProgramFilesDir%\My App\My Application.exe corresponds to a path inside of your Thinstall project.