Corrected line endings and BOM issues with several files

- Ensured final end-of-line character in every file.
- Corrected cases of mixed line endings (mostly CR and CRLF within the
  same file.)
- Removed extra BOM  from some scripts, since it causes a parsing error.

Signed-off-by: Haru <haru@dotalux.com>
Merge branch 'master' of https://github.com/HerculesWS/Hercules into ghbb