Hi,
I removed the executable bit from the source files using
chmod a-x | find . -executable -not -type d -name "*.someextension"
commands. Only two batch file and a ".bin" file remained there. (And the ".git/hooks/*.sample" files.)
If you want, you can merge a branch from here:
https://github.com/cim-unito/MITK/tree/bug-9-executable_bit_on_source_files
Miklos