perms: Remove execute bit on source files

* Remove the execute bit on source files.
* No functional change.
main: Remove duplicated includes

* Remove duplicate includes from 50391f2c
* No functional change.
autotune: Correct macro name in comments

* Update the comments to reflect the code.
* No functional change.
Merge pull request #187 from kylemanna/cleanup

Various minor cleanups.  Thanks @Kylemanna