The reload_all call could end up dereferencing a NULL pointer if
there was an error while attempting to load the submodules config
data (i.e. invalid content in the gitmodules file).  This fixes it.

`git_submodule` objects were already refcounted internally in case
the submodule name was different from the path at which it was
stored.  This makes that refcounting externally used as well, so
`git_submodule_lookup` and `git_submodule_add_setup` return an
object that requires a `git_submodule_free` when done.

This removes the fetchRecurse compiler warnings and makes the
behavior match the other submodule options (i.e. the in-memory
setting can be reset to the on-disk value).

Extend the "unmodified" submodule workdir test to include
uninitialized submodules, to prevent reporting submodules as
modified when they're not in the workdir at all.

submodule branch option + little VS2013 fix