Modify scripts to support layout reorganization

Teach PopulatePatchesByPackage.py to place patch files in
"Package/{PackageName}/Patches/{PatchName}" instead of
"Package/{PackageName}/{PatchName}".  This allows non-patch elements
such as testing files to be added to the package directories.

Uncategorized and Multibuilds directory layout remain the same.

Also update the layout documentation in README.rst accordingly.

Change-Id: Ib1a1fd01ca9d5c6bfc95eafd859badbd2fd8141c