Added `git_repository_submodule_cache_all` to initialze a cache of
submodules on the repository so that operations looking up N
submodules are O(N) and not O(N^2).  Added a
`git_repository_submodule_cache_clear` function to remove the cache.

Also optimized the function that loads all submodules as it was itself
O(N^2) w.r.t the number of submodules, having to loop through the
`.gitmodules` file once per submodule.  I changed it to process the
`.gitmodules` file once, into a map.

Signed-off-by: David Turner <dturner@twosigma.com>

Fixed typo in git_repository_reinit_filesystem() documentation

It was missing "common.h" and "types.h" like other system headers.
This generated compilation errors if including it directly.

When using a bare repo with an index, libgit2 attempts to read
files from the index.  It caches those files based on the path
to the file, specifically the path to the directory that contains
the file.

If there is no working directory, we use `git_path_dirname_r` to
get the path to the containing directory.  However, for the
`.gitattributes` file in the root of the repository, this ends up
normalizing the containing path to `"."` instead of the empty
string and the lookup the `.gitattributes` data fails.

This adds a test of attribute lookups on bare repos and also
fixes the problem by simply rewriting `"."` to be `""`.

Before these changes, looking up a reference would return the
same precomposed or decomposed form of the reference name that
was used to look it up, so on MacOS which ignores the difference
between the two, a single reference could be looked up either way
and git_reference_name would return the form of the name that was
used to look it up!  This change makes lookup always return the
precomposed name if core.precomposeunicode is set regardless of
which version was used to look it up.  The reference iterator was
already returning the precomposed form from earlier work.

This also updates the CMakeLists.txt rules for enabling iconv
usage because the clar tests for this code were actually not being
activated properly with the old version.

Finally, this moves git_repository_reset_filesystem from include/
git2/repository.h to include/git2/sys/repository.h since it is not
really a function that normal library users should have to think
about very often.