Merge pull request #169 from chuckdumont/nio

Fix alias resolution issues
Replace reference of AbstractDojoHttpTransport to
DojoHttpTransport in plugin.xml
Merge pull request #170 from projsaha/JAGGR_master_merge_3

Replace reference of AbstractDojoHttpTransport to
Change module name id map generation to include only scanned resources
and not resources obtained from module dependencies so as to avoid alias
mapped modules.
Merge remote-tracking branch 'jaggr/master' into nio
Remove Rhino dependencies from config interface to make the interface
independent of the javascript parser implementation.