I guess I found the source of the problem: I had decided to store the workspace in a folder shared with the host (this is because I use git from OS X, not from Windows). And it seems that PSoC Creator did not like to read/write files from/to a VirtualBox shared folder...
So, easy correction: my workspace is now stored inside the virtual machine. And when I want to commit my work, I copy the workspace to the shared folder...
For me its even worse - Creator tells me it cannot find the files on a shared VBox folder, even though it was happy to navigate me to there :(
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You can find this issue is addressed in PSoC Creator 3.1 release note. :
If you run PSoC Creator on a virtual machine and access source files from a shared folder, you must disable Semantic Parsing using the Tools > Options > Semantic Parsing menu item. There is a known issue with a third-party tool that is used to support the Semantic Parsing features. For more information, refer to the bug report for that tool (http://llvm.org/bugs/show_bug.cgi?id=21143).
Thanks a lot for the information, Jobin! This will allow me to improve the way I handle my source code.