Merge pull request #771 from driusan/PHPCS-Notify

Ran PHPCS on Notify class
Merge pull request #772 from driusan/PHPCS-Message

Ran PHPCS on Message class
Moved timepoint flag module to modules directory
Started PHPCS on HelpFile
Moved HelpFile.class.inc to help module, since that's the only place it's used
Search module directory for requires in ajax scripts too
Remove file that was part of EFax module.

According to the header, Loris doesn't own the copyright to
File.class.inc, and it seems to have only been for the EFax
module.
Fixed most PHPCS errors in User.class
Ran PHPCS on Site and MRIFile
Added files to travis
Ran PHPCBF on Utility class
Ran PHPCS on NDB_BVL_Instrument_instrument_preview.class.inc