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.
Update query to get scan data for the Scans per site chart.

The new query groups by session ID so that one scan session is counted as a scan. Previously the query was just counting the number of files in the files table.
Update new and pending scan query.

The old query was not grouping files by session, as is done in the imaging browser.
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
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_Menu_Filter
Ran PHPCS on NDB_Menu_Filter_Form
Merge pull request #760 from driusan/PHPCS-NDB_Menu_Filter_Form

Ran PHPCS on NDB_Menu_Filter_Form
Fixed PHP syntax error