Removed the executable bit from all .java files
Removed executable bit from *.pde files
Unset the executable bit on xml files
unset executable bit for .txt files
unset executable bit in miscellaneous files
Unset executable bit on a few more files
Bring in upstream changes from 'master'
Merge pull request #2977 from kfeuz/filePermissions

Unset executable bit on non-executable files