Item11267: Files in top directory need a home.

git-svn-id: http://svn.foswiki.org/trunk/core@17895 0b4bb1d4-4e5a-0410-9cc4-b2b747904278
Item11267: check_manifest.pl should handle git

Also a shell script to check all the default extensions.

git-svn-id: http://svn.foswiki.org/trunk/core@17896 0b4bb1d4-4e5a-0410-9cc4-b2b747904278