Added Tools, Libs reference menus to Help

Including support for core tools & libs if reqd later
Added many, many more ways for references to be included
Added new class LocalContribWithReference for contribs with reference

And added some documentation for the new functions
Tool and Lib References now show in Help menu

Removing LocalContribWithReference.java
Remove extra ways for references to be included
Merge pull request #2804 from joelmoniz/addReferences

Added References for installed tools and libraries, whenever available, to the Help menu.
add notes about pr
merge and mess