added LinkCommands and LinkCommandsTests
fixed up tests, removed unused ReferenceList methods

Reference List is not basically acting like a "set".  Duplicates are not preserved while removing items doesn't complain.
Merge remote-tracking branch 'origin/feature/checks' into feature/referenceList

2 Tests failing

Conflicts:
	src/models/ProjectModel.php
	src/models/UserModel.php
	test/php/commands/AllCommandTests.php
	test/php/model/UserModel_Test.php
fixed up tests
Additional debugging in sf.php
Merge remote-tracking branch 'origin/feature/referenceList' into feature/checks
wip #24: ReferenceList.  All tests pass.

* The tests use the model class in their json rpc, so were passing 'projects' and 'users' in as ReferenceLists.  These were not decoded as a class by the JsonRpcServer::decode method.  The correct behaviour, if these properties are set, is to ignore them.  References have a separate API to create and remove references.
Remove unused link commands.