Hi Alice,
I managed to fix my .gitignore over the weekend, mostly thanks to Erich's blog.
The linked page really helped with the Processor Expert files.
With the help of other pages on the blog, I realized that my big mistake had been adding my workspace to my repository and not just the projects.
As of now, my project safely moves from machine to machine via GitHub. I am getting identical binaries from my development machine and my build system. No files were lost, and no large number of log, lock, and config files asked to be updated every time I clean or build.
Cheers
Alex