1. Fix sort order problem with submodules where "mod" was sorting
   after "mod-plus" because they were being sorted as "mod/" and
   "mod-plus/".  This involved pushing the "contains a .git entry"
   test significantly lower in the stack.
2. Reinstate behavior that a directory which contains a .git entry
   will be treated as a submodule during iteration even if it is
   not yet added to the .gitmodules.
3. Now that any directory containing .git is reported as submodule,
   we have to be more careful checking for GIT_EEXISTS when we
   do a submodule lookup, because that is the error code that is
   returned by git_submodule_lookup when you try to look up a
   directory containing .git that has no record in gitmodules or
   the index.