When trying to determine if we can safely overwrite an existing workdir
item, we may need to calculate the oid for the workdir item to determine
if its identical to the old side (and eligible for removal).

We previously did this regardless of the type of entry in the workdir;
if it was a directory, we would open(2) it and then try to read(2).
The read(2) of a directory fails on many platforms, so we would treat it
as if it were unmodified and continue to perform the checkout.

On FreeBSD, you _can_ read(2) a directory, so this pattern failed.  We
would calculate an oid from the data read and determine that the
directory was modified and would therefore generate a checkout conflict.

This reliance on read(2) is silly (and was most likely accidentally
giving us the behavior we wanted), we should be explicit about the
directory test.

tests: index: do not re-allocate index

According to the reference the git_checkout_tree and git_checkout_head
functions should accept NULL in the opts field

This was broken since the opts field was dereferenced and thus lead to a
crash.

README: adjust URL to libqgit2 repository

Plug a memory leak caused by re-allocating a `git_index`
structure which has already been allocated by the test suite's
initializer.

transports: http: set substream as disconnected after closing

Teach `git_patch_from_diff` about parsed diffs

Ensure that `git_patch_from_diff` can return the patch for parsed diffs,
not just generate a patch for a generated diff.

filesystem_iterator: fixed double free on error

Support index v4

ignore: allow unignoring basenames in subdirectories

When calling `http_connect` on a subtransport whose stream is already
connected, we first close the stream in case no keep-alive is in use.
When doing so, we do not reset the transport's connection state,
though. Usually, this will do no harm in case the subsequent connect
will succeed. But when the connection fails we are left with a
substransport which is tagged as connected but which has no valid
stream attached.

Fix the issue by resetting the subtransport's connected-state when
closing its stream in `http_connect`.

The .gitignore file allows for patterns which unignore previous
ignore patterns. When unignoring a previous pattern, there are
basically three cases how this is matched when no globbing is
used:

1. when a previous file has been ignored, it can be unignored by
   using its exact name, e.g.

   foo/bar
   !foo/bar

2. when a file in a subdirectory has been ignored, it can be
   unignored by using its basename, e.g.

   foo/bar
   !bar

3. when all files with a basename are ignored, a specific file
   can be unignored again by specifying its path in a
   subdirectory, e.g.

   bar
   !foo/bar

The first problem in libgit2 is that we did not correctly treat
the second case. While we verified that the negative pattern
matches the tail of the positive one, we did not verify if it
only matches the basename of the positive pattern. So e.g. we
would have also negated a pattern like

    foo/fruz_bar
    !bar

Furthermore, we did not check for the third case, where a
basename is being unignored in a certain subdirectory again.

Both issues are fixed with this commit.

Support reading and writing index v4.  Index v4 uses a very simple
compression scheme for pathnames, but is otherwise similar to index v3.

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

This code is ported from git.git

Signed-off-by: Junio C Hamano <gitster@pobox.com>
Signed-off-by: David Turner <dturner@twopensource.com>

stransport memory management improvements

tests: blob: remove unused callback function

When failing to initialize a new stransport stream, we try to
release already allocated memory by calling out to
`git_stream_free`, which in turn called out to the stream's
`free` function pointer. As we only initialize the function
pointer later on, this leads to a `NULL` pointer exception.

Furthermore, plug another memory leak when failing to create the
SSL context.

odb: only provide the empty tree

stransport: make internal functions static

diff: document `git_diff_from_buffer`

Only provide the empty tree internally, which matches git's behavior.
If we provide the empty blob then any users trying to write it with
libgit2 would omit it from actually landing in the odb, which appear
to git proper as a broken repository (missing that object).

SecureTransport: handle NULL trust on success

The `SSLCopyPeerTrust` call can succeed but fail to return a trust
object if it can't load the certificate chain and thus cannot check the
validity of a certificate. This can lead to us calling `CFRelease` on a
`NULL` trust object, causing a crash.

Handle this by returning ECERTIFICATE.

clar: fix parsing of test suite prefixes

Patch image initialization

odb: freshen existing objects when writing

Since writing multiple objects may all already exist in a single
packfile, avoid freshening that packfile repeatedly in a tight loop.
Instead, only freshen pack files every 2 seconds.

When writing an object, we calculate its OID and see if it exists in the
object database.  If it does, we need to freshen the file that contains
it.

sysdir: don't assume an empty dir is uninitialized