preferences: consolidate the file/project/global preference naming
* always use "Preferences" rather than "Properties"

(integrated from komodo (trunk) change 83459 by toddw)

git-svn-id: http://svn.openkomodo.com/repos/openkomodo/trunk@14132 b87d16e7-d29f-4ee1-b5ec-817d645d335f