Test submodules with empty index or orphaned head

In both of these cases, the submodule data should still be loaded
just (obviously) without the data that comes from either the index
or the HEAD.

This fixes a bug in the orphaned head case.

Dirty submodules do not correctly appear in diffs

There was a bug where submodules whose HEAD had not been moved
were being marked as having an UNMODIFIED delta record instead
of being left MODIFIED.  This fixes that and fixes the tests to
notice if a submodule has been incorrectly marked as UNMODIFIED.

Prefer younger merge bases over older ones.

Unbreak git_remote_ls on a local transport after disconnecting.

Correctly handle win32 junctions

git-core prefers younger merge bases over older ones in case that multiple valid merge bases exists.

A junction has S_IFDIR | S_IFLNK set, however, only one makes sense.

Signed-off-by: Sven Strickroth <email@cs-ware.de>

This reverts commit 32c12ea6.

Minor point release! We got a lot of rather large features that we
wanted to get settled in:

- New (threadsafe) cache for objects
- Iterator for Status
- New Merge APIs
- SSH support on *NIX
- Function context on diff
- Namespaces support
- Index add/update/remove with wildcard support
- Iterator for References
- Fetch and push refspecs for Remotes
- Rename support in Status
- New 'sys/` namespace for external headers with low-level APIs

As always, this comes with hundreds of bug fixes and performance
improvements. We're faster and better than ever. And we haven't broken
many APIs this time!

Build stuff.

Fix a leak in the local transport code.

Fix checkout tests on Windows

Fixed most documentation header bugs

Add O_CLOEXEC to open calls

In loose objects backend, constrain mkdir calls to avoid extra mkdirs

In theory, p_stat should never return an S_ISLNK result, but due
to the current implementation on Windows with mount points it is
possible that it will.  For now, work around that by allowing a
link in the path to a directory being created.  If it is really a
problem, then the issue will be caught on the next iteration of
the loop, but typically this will be the right thing to do.

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

Do not redefine WC_ERR_INVALID_CHARS

This updates the calls that make the subdirectories for objects
to use a base directory above which git_futils_mkdir won't walk
any higher.  This prevents attempts to mkdir all the way up to
the root of the filesystem.

Also, this moves the objects_dir into the loose backend structure
and removes the separate allocation, plus does some preformatting
of the objects_dir value to guarantee a trailing slash, etc.

WC_ERR_INVALID_CHARS might be already defined by the Windows SDK.

Signed-off-by: Sven Strickroth <email@cs-ware.de>

Add target directory to checkout options

This adds additonal tests of the checkout target directory option
including using it to dump data from bare repos.

With the new target directory option to checkout, the non-bareness
of the repository should be checked much later in the parameter
validation process - actually that check was already in place, but
I was doing it redundantly in the checkout APIs.

This removes the now unnecessary early check for bare repos.  It
also adds some other parameter validation and makes it so that
implied parameters can actually be passed as NULL (i.e. if you
pass a git_index, you don't have to pass the git_repository - we
can get it from index).

This adds the ability for checkout to write to a target directory
instead of having to use the working directory of the repository.
This makes it easier to do exports of repository data and the like.

This is similar to, but not quite the same as, the --prefix option
to `git checkout-index` (this will always be treated as a directory
name, not just as a simple text prefix).

As part of this, the workdir iterator was extended to take the
path to the working directory as a parameter and fallback on the
git_repository_workdir result only if it's not specified.

Fixes #1332

Checkout should not recreate deleted files - with fix

This fixes the checkout case when a file is modified between the
baseline and the target and yet missing in the working directory.
The logic for that case appears to have been wrong.

This also adds a useful checkout notify callback to the checkout
test helpers that will count notifications and also has a debug
mode to visualize what checkout thinks that it's doing.

Command line status example (with bug fixes)

Add test for bug fixed in 852ded96
Sorry, I wrote that bug fix and forgot to check in a test at the
same time.  Here is one that fails on the old version of the code
and now works.