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.