Fixes #1762

This adds correct support for an equivalent to --ignore-submodules
in diff, where an actual ignore value can be passed to diff to
override the per submodule settings in the configuration.

This required tweaking the constants for ignore values so that
zero would not be used and could represent an unset option to the
diff.  This was an opportunity to move the submodule values into
include/git2/types.h and to rename the poorly named DEFAULT values
for ignore and update constants to RESET instead.

Now the GIT_DIFF_IGNORE_SUBMODULES flag is exactly the same as
setting the ignore_submodules option to GIT_SUBMODULE_IGNORE_ALL
(which is actually a minor change from the old behavior in that
submodules will now be treated as UNMODIFIED deltas instead of
being left out totally - if you set GIT_DIFF_INCLUDE_UNMODIFIED).

This includes tests for the various new settings.

This fixes the way that submodule status is checked to bypass just
about all of the caching in the submodule object.  Based on the
ignore value, it will try to do the minimum work necessary to find
the current status of the submodule - but it will actually go to
disk to get all of the current values.

This also removes the custom refcounting stuff in favor of the
common git_refcount style.  Right now, it is still for internal
purposes only, but it should make it easier to add true submodule
refcounting in the future with a public git_submodule_free call
that will allow bindings not to worry about the submodule object
getting freed from underneath them.

Fixed a few header @param and @return typos with the help of -Wdocumentation in Xcode.

The following warnings have not been fixed:
common.h:213 - Not sure how the documentation format is for '...'
notes.h:102 - Correct @param name but empty text
notes.h:111 - Correct @param name but empty text
pack.h:140 - @return missing text
pack.h:148 - @return missing text

When diff encounters an untracked directory, there was a shortcut
that it took which is not compatible with core git.  This makes
the default behavior no longer take that shortcut and instead look
inside the untracked directory to see if there are any untracked
files within it.  If there are not, then the directory is treated
as an ignore directory instead of an untracked directory.  This
has implications for the git_status APIs.

This adds tests for diffs with submodules in them and (perhaps
unsurprisingly) requires further fixes to be made.  Specifically,
this fixes:

- when considering if a submodule is dirty in the workdir, it was
  being treated as dirty even if only the index was dirty.
- git_diff_patch_to_str (and git_diff_patch_print) were "printing"
  the headers for files (and submodules) that were unmodified or
  had no meaningful content.
- added comment to previous fix and removed unneeded parens.

This adds a new API to the submodule interface that just returns
where information about the submodule was found (e.g. config file
only or in the HEAD, index, or working directory).

Also, the old "refresh" call was potentially keeping some stale
submodule data around, so this simplfies that code and literally
discards the old cache, then reallocates.

The adds a test for the submodule diff capabilities and then
fixes a few bugs with how the output is generated.  It improves
the accuracy of OIDs in the diff delta object and makes the
submodule output more closely mirror the OIDs that will be used
by core git.