[TIMOB-13520] Fixed Linux bugs, specifically on 64-bit distros. Also fixed abi validation and improved module jar conflict detection.
Forgot to remove some debug code.
Fixed bug with the build manifest file being deleted before the check if should rebuild.
Moved ignoreDirs and ignoreFiles into the builder object to cache the regexes.
Merge pull request #4814 from cb1kenobi/timob-13520

[TIMOB-13520] Fixed Linux bugs, specifically on 64-bit distros.