Update repository documentation manual:
- Start to reorganize repository documentaiton manual layout. Now,
the filesystem is considered a chapter, like might be
introduction or theme production.
- Inside filesystem chapter all documentation entries start as
section in just one file. Directories like trunk, tags and
branches are no longer cosidered chapters, but a section
instead. Likewise trunk/Identity, trunk/Identity/Themes, no
matter what directory level be they always be treated as section
entries inside the repository documentation manual.