Fix trailing slash issue to the gitdir path when the repo is opened through a workdir

repository: ensure that the path to the .git directory ends with a forward slash when opening a repository through a working directory path

This fixes an issue which was detected while using one of the libgit2 bindings [0]. The lack of the trailing forward slash led the name of references returned by git_reference_listall() to be prefixed with a forward slash.

  [0]: https://github.com/libgit2/libgit2sharp/pull/108

Fix the build on Emscripten

struct timeval is used in this file, which requires <sys/time.h> to be
included.

On non-Windows builds, we will now use _GNU_SOURCE so header
files will include modern API extensions.  This should resolve
issue #547.

Add unit tests to confirm ignore directory pattern matches and
to confirm that ignore and attribute files are loaded properly
into the attribute file cache.

Actually look for the file by the same cache key that we
store it under.  Rocket science!

threads: Make the old test suite TLS aware...

Now that is_dir is calculated correctly for attr/ignore paths,
it is possible to use it so that ignoring "dir/" will properly
match the directory name and ignore the entire directory.

When building an attr path object, the code that checks if the
file is a directory was evaluating the file as a relative path
to the current working directory, instead of using the repo root.
This lead to inconsistent behavior.

When status encounters a submodule, right now it is asserting.
This changes it to just skip the file that it can't deal with.

git_refspec_transform_r assumed that the reference name passed would
be only a branch or tag name. This is not the case, and we need to
take into consideration what's in the refspec's source to know how
much of the prefix to ignore.

Those were re-added on the move. Ops!

The object cache is mostly IO-bound, so it makes no sense to have a lock
per node.

This is a MSVC-only issue. All other compilers we support work properly.

Repository re-initialization

This currently only ensures that the version of the repository format isn't greater than zero.

A non migrated yet test has been removed as well as it's mostly redundant.

Rename the Clay test suite to Clar

Clay is the name of a programming language on the makings, and we want
to avoid confusions. Sorry for the huge diff!

This had been left over from a time when I believed what the git
documentation had to say about case-sensitivity. The rest of the code
doesn't recognize this form and we hadn't noticed because most tests
don't try to get a recently-set variable but free and reload the
configuration, causing the right format to be used.

remote: add test which creates a basic remote entry in the repository configuration then loads the remote

This resolves issue #535 and issue #533.

The buffer wasn't getting freed if the last difference was a deletion.

MSVC doesn't think %zd is a valid specifier.

Don't leak when deleting or removing refs

When we remove the ref from the hashtable, we need to free the
packref.

Truncate at the slash; otherwise we get ppack-*.idx filenames.

On error, the pointer could be pointing anywhere.

Fix download segfault

transport: prevent git_remote_download() from segfaulting when being passed a lightweight remote built with git_remote_new()

This takes all of the functions that look up simple data about
paths (such as `git_futils_isdir`) and moves them over to path.h
(becoming `git_path_isdir`).  This leaves fileops.h just with
functions that actually manipulate the filesystem or look at
the file contents in some way.

As part of this, the dir.h header which is really just for win32
support was moved into win32 (with some minor changes).

Fix transport segfault