Improve submodules status data caching and compatibility

This restores a behavior that was accidentally lost during some
diff refactoring where an untracked directory that contains a .git
item should be treated as IGNORED, not as UNTRACKED.  The submodule
code already detects this, but the diff code was not handling the
scenario right.

This also updates a number of existing tests that were actually
exercising the behavior but did not have the right expectations in
place.  It actually makes the new
`test_diff_submodules__diff_ignore_options` test feel much better
because the "not-a-submodule" entries are now ignored instead of
showing up as untracked items.

Fixes #1697

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.

Submodules now expose an internal status API that allows diff to
get back the OID values from the submodule very easily and also
to avoiding caching issues and to override the ignore setting for
the submodule.

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.

This adds a BARE option to git_repository_open_ext which allows
a fast open path that still knows how to read gitlinks and to
search for the actual .git directory from a subdirectory.

`git_repository_open_bare` is still simpler and faster, but having
a gitlink aware fast open is very useful for submodules where we
want to quickly be able to peek at the HEAD and index data without
doing any other meaningful repo operations.

This is probably not the final form of this change, but this is
a preliminary version of checking a timestamp to see if the cached
working directory HEAD OID matches the current.  Right now, this
uses the timestamp on the index and is, like most of our timestamp
checking, subject to having only second accuracy.

The submodules code caches data about submodules in a way that
can cause problems.  This adds some tests that try making various
modifications to the state of a submodule to see where we can
catch out problems in the submodule caching.

Right now, I've put in an extra git_submodule_reload_all so that
the test will pass, but with that commented out, the test fails.
I'm working on fixing the broken version of the test at which
point I'll commit the fix and delete the extra reload that makes
the test pass.

This controls for the diff.mnemonicprefix setting so that can't
break the tests.  Also, this expands one test to emulate an
ObjectiveGit test more closely.

This adds an additional pathspec API that will match a pathspec
against a diff object.  This is convenient if you want to handle
renames (so you need the whole diff and can't use the pathspec
constraint built into the diff API) but still want to tell if the
diff had any files that matched the pathspec.

When the pathspec is matched against a diff, instead of keeping
a list of filenames that matched, instead the API keeps the list
of git_diff_deltas that matched and they can be retrieved via a
new API git_pathspec_match_list_diff_entry.

There are a couple of other minor API extensions here that were
mostly for the sake of convenience and to reduce dependencies
on knowing the internal data structure between files inside the
library.

This is a simple bit vector object that is not resizable after
the initial allocation but can be of arbitrary size.  It will
keep the bti vector entirely on the stack for vectors 64 bits
or less, and will allocate the vector on the heap for larger
sizes.  The API is uniform regardless of storage location.

This is very basic right now and all the APIs are inline functions,
but it is useful for storing an array of boolean values.

This converts the array of parent SHAs from a git_vector where
each SHA has to be separately allocated to a git_array_t where
all the SHAs can be kept in one block.  Since the two collections
have almost identical APIs, there isn't much involved in making
the change.  I did add an API to git_array_t so that it could be
allocated at a precise initial size.

This fixes the way the example log program decides if a merge
commit should be shown when a pathspec is given.  Also makes it
easier to use the pathspec API to just check "does a tree match
anything in the pathspec" without allocating a match list.

This adds more command line processing to the example version of
log.  In particular, this adds the funky command line processing
that allows an arbitrary series of revisions followed by an
arbitrary number of paths and/or glob patterns.

The actual logging part still isn't implemented.

This adds a new public API for compiling pathspecs and matching
them against the working directory, the index, or a tree from the
repository.  This also reworks the pathspec internals to allow the
sharing of code between the existing internal usage of pathspec
matching and the new external API.

While this is working and the new API is ready for discussion, I
think there is still an incorrect behavior in which patterns are
always matched against the full path of an entry without taking
the subdirectories into account (so "s*" will match "subdir/file"
even though it wouldn't with core Git).  Further enhancements are
coming, but this was a good place to take a functional snapshot.

Try harder not to double free index entries

PR 1706 plus error reporting cleanups

The SSH error checking and reporting could still be further
improved by using the libssh2 native methods to get error info,
but at least this ensures that all error codes are checked and
translated into libgit2 error messages.

Conflicts:
	src/transports/ssh.c