Rename org.topazproject packages to org.ambraproject

Any packages of the form org.topazproject.ambra.* had the "ambra" removed.
Update references to Topaz in comments
Incrementing release version
FEND-884 added plos currents to journal footer
Delete org.ambraproject.Constants.ROOT_PACKAGE

Nothing was visibly using it, and it was set to the obsolete
"org.topazproject.ambra" package.
Merge remote-tracking branch 'origin/rename-topaz' into release/feb_r2
Adding new permission for TNG-2
Adding method to empty the security cache
FEND -888 Extra text showing up above the saved search email body
FEND-905- article reference is missing
Merge remote-tracking branch 'origin/release/feb_r2' into release/feb_r2
FEND-882 Expressions of Concern: Display pink notice at top of articles
Resolving merge conflict
FEND-882 Code review comments
FEND-882 Code review comments
PBUG-106, updating the comment why sometime citedArticle object can be less than references in article.xml
FEND-882 Minor change
FEND-882 Minor change
Merge remote-tracking branch 'origin/master' into FEND-882
Merge remote-tracking branch 'origin/master' into FEND-882