Fix Conflict Resolver spelling.
Adding Instrument manager and Data Integrity Flag to loris menu.
Remove hardcoding of menu IDs from default schema.
Adding line break on document repository item panels.
Move patch out of the archive since it was not added before the release.:
Moved timepoint flag module to modules directory
Fix ordering and added comma to patch.
Change <br> tag formatting.
Fixed formatting errors in NDB_Reliability
Run PHPCS on NDB_Reliability automagically
Started PHPCS on HelpFile
Moved HelpFile.class.inc to help module, since that's the only place it's used
Ran PHPCS on NDB_Factory
Search module directory for requires in ajax scripts too
Add showDatabaseQueries back to config.xml

This setting was accidentally removed during the creation of the configuration module, but should be there as it is not stored in the config database tables and cannot be edited from the frontend.
Removed HelpFile from travis since it's no longer in php/libraries
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.
Ran PHPCS on NDB_Caller
Added NDB_Caller to Travis PHPCS
Merge pull request #751 from driusan/PHPCS-NDB_Factory

Ran PHPCS on NDB_Factory