In the general case there are 2 files of interest:
- The .project file, which contains general eclipse settings.
- The .cproject file, which contains CDT settings (including build configurations).
They are both stored in the root directory of the project.
A few additional settings may be stored in the .settings directory, again in the project root, although whether or not that directory belongs in version control is debated: svn - Which eclipse files belong under Version Control - Stack Overflow
Files related to Processor Expert are described in detail in Erich's slides (Hands-On: Mastering Kinetis Design Studio IDE - Advanced), as is everything else I've mentioned, but hopefully I've saved some people having to open a PDF.