We look at whether we're trying to replace a blob with a tree during the
update phase, but we fail to look at whether we've just inserted a blob
where we're now trying to insert a tree.

Update the check to look at both places. The test for this was
previously succeeding due to the bu where we did not look at the sorted
output.

The loop is made with the assumption that the inputs are sorted and not
using it leads to bad outputs.

We do not currently use the sorted version of this input in the
function, which means we produce bad results.

giterr format

transports: smart: abort on early end of stream

Update THREADING for OpenSSL 1.1

git_repository_open_ext: fix handling of $GIT_NAMESPACE

fileops: fix typos in `git_futils_creat_locked{,with_path}`

The existing code would set a namespace of "" (empty string) with
GIT_NAMESPACE unset.  In a repository where refs/heads/namespaces/
exists, that can produce incorrect results.  Detect that case and avoid
setting the namespace at all.

Since that makes the last assignment to error conditional, and the
previous assignment can potentially get GIT_ENOTFOUND, set error to 0
explicitly to prevent the call from incorrectly failing with
GIT_ENOTFOUND.

We're recently trying to upgrade to the current master of libgit2
in Cargo but we're unfortunately hitting a segfault in one of our
tests. This particular test is just a small smoke test that https
works (e.g. it's configured in libgit2). It attempts to clone
from a URL which simply immediately drops connections after
they're accepted (e.g. terminate abnormally). We expect to see a
standard error from libgit2 but unfortunately we're seeing a
segfault.

This segfault is happening inside of the `wait_for` function of
`curl_stream.c` at the line `FD_SET(fd, &errfd)` because `fd` is
-1. This ends up doing an out-of-bounds array access that faults
the program. I tracked back to where this -1 came from to the
line here (returned by `CURLINFO_LASTSOCKET`) and added a check
to return an error.

global: synchronize initialization and shutdown with pthreads

The code correctly detects that forced creation of a branch on a
nonbare repo should not be able to overwrite a branch which is
the HEAD reference.  But there's no reason to prevent this on
a bare repo, and in fact, git allows this.  I.e.,

   git branch -f master new_sha

works on a bare repo with HEAD set to master.  This change fixes
that problem, and updates tests so that, for this case, both the
bare and nonbare cases are checked for correct behavior.

add support for OpenSSL 1.1.0 for BIO filter

We need to include the initialisation and construction functions in all
backend, so we include this header when building against SecureTransport
and WinHTTP as well.

pack: fix race in pack_entry_find_offset

For older versions we can fall back on the deprecated ASN1_STRING_data.

We want to program against the interface, so recreate it when we compile
against pre-1.1 versions.

In `pack_entry_find_offset`, we try to find the offset of a
certain object in the pack file. To do so, we first assert if the
packfile has already been opened and open it if not. Opening the
packfile is guarded with a mutex, so concurrent access to this is
in fact safe.

What is not thread-safe though is our calculation of offsets
inside the packfile. Assume two threads calling
`pack_entry_find_offset` at the same time. We first calculate the
offset and index location and only then determine if the pack has
already been opened. If so, we re-calculate the offset and index
address.

Now the case for two threads: thread 1 first calculates the
addresses and is subsequently suspended. The second thread will
now call `pack_index_open` and initialize the pack file,
calculating its addresses correctly. When the first thread is
resumed now, he'll see that the pack file has already been
initialized and will happily proceed with the addresses it has
already calculated before the check. As the pack file was not
initialized before, these addresses are bogus.

Fix the issue by only calculating the addresses after having
checked if the pack file is open.

When trying to receive packets from the remote, we loop until
either an error distinct to `GIT_EBUFS` occurs or until we
successfully parsed the packet. This does not honor the case
where we are looping over an already closed socket which has no
more data, leaving us in an infinite loop if we got a bogus
packet size or if the remote hang up.

Fix the issue by returning `GIT_EEOF` when we cannot read data
from the socket anymore.

When reading a server's reference announcements via the smart
protocol, we expect the server to send multiple flushes before
the protocol is finished. If we fail to receive new data from the
socket, we will only return an end of stream error if we have not
seen any flush yet.

This logic is flawed in that we may run into an infinite loop
when receiving a server's reference announcement with a bogus
flush packet. E.g. assume the last flushing package is changed to
not be '0000' but instead any other value. In this case, we will
still await one more flush package and ignore the fact that we
are not receiving any data from the socket, causing an infinite
loop.

Fix the issue by always returning `GIT_EEOF` if the socket
indicates an end of stream.

pqueue: resolve possible NULL pointer dereference

Exercise the logic surrounding deinitialization of the libgit2
library as well as repeated concurrent de- and reinitialization.
This tries to catch races and makes sure that it is possible to
reinitialize libgit2 multiple times.

After deinitializing libgit2, we have to make sure to setup
options required for testing. Currently, this only includes
setting up the configuration search path again. Before, this has
been set up once in `tests/main.c`.

When threading is not enabled for libgit2, we keep global state
in a simple static variable. When libgit2 is shut down, we clean
up the global state by freeing the global state's dynamically
allocated memory. When libgit2 is built with threading, we
additionally free the thread-local storage and thus completely
remove the global state. In a non-threaded build, though, we
simply leave the global state as-is, which may result in an error
upon reinitializing libgit2.

Fix the issue by zeroing out the variable on a shutdown, thus
returning it to its initial state.

When trying to initialize and tear down global data structures
from different threads at once with `git_libgit2_init` and
`git_libgit2_shutdown`, we race around initializing data. While
we use `pthread_once` to assert that we only initilize data a
single time, we actually reset the `pthread_once_t` on the last
call to `git_libgit2_shutdown`. As resetting this variable is not
synchronized with other threads trying to access it, this is
actually racy when one thread tries to do a complete shutdown of
libgit2 while another thread tries to initialize it.

Fix the issue by creating a mutex which synchronizes `init_once`
and the library shutdown.

CI Improvements

Small documentation improvements

Our valgrind jobs haven't been failing for several builds by now.
This indicates that our tests are sufficiently stable when
running under valgrind. As such, any failures reported by
valgrind become interesting to us and shouldn't be ignored when
causing a build to fail.

Remove the valgrind job from the list of allowed failures.

When running a Coverity build, we have to provide an
authentication token in order to proof that we are actually
allowed to run analysis in the name of a certain project. As this
token should be secret, it is only set on the main repository, so
when we were requested to run the Coverity script on another
repository we do error out. But in fact we do also error out if
the Coverity analysis should _not_ be run if there is no
authentication token provided.

Fix the issue by only checking for the authentication token after
determining if analysis is indeed requested.