Backports for v0.23

We should explicitly include the declaration of git_strarray
from "include/git2/sys/transport.h"

Using calloc instead of malloc because the parse error will lead to an immediate free of committer (and its properties, which can segfault on free if undefined - test_refs_reflog_reflog__reading_a_reflog_with_invalid_format_returns_error segfaulted before the fix).

#3458

Inserting new REUC entries can quickly become pathological given that
each insert unsorts the REUC vector, and both subsequent lookups *and*
insertions will require sorting it again before being successful.

To avoid this, we're switching to `git_vector_insert_sorted`: this keeps
the REUC vector constantly sorted and lets us use the `on_dup` callback
to skip an extra binary search on each insertion.

Although CMake will correctly configure include directories for us,
some people may use their own build system, and we should reference
`util.h` based on where it actually lives.

Although our index contains the literal time present in the index,
we do not read nanoseconds from disk, and thus we should not use
them in any comparisons, lest we always think our working directory
is dirty.

Guard this behind a `GIT_USE_NSECS` for future improvement.

Test that nanoseconds are round-tripped correctly when we read
an index file that contains them.  We should, however, ignore them
because we don't understand them, and any new entries in the index
should contain a `0` nsecs field, while existing preserving entries.

The reason is that the types defined in libgit2's inttypes.h collide with system inttypes.h
3rd party library header files may directly reference MSVC's built-in inttypes.h

Fixes #3476

For most real use cases, repositories with alternates use them as main
object storage. Checking the alternate for objects before the main
repository should result in measurable speedups.

Because of this, we're changing the sorting algorithm to prioritize
alternates *in cases where two backends have the same priority*. This
means that the pack backend for the alternate will be checked before the
pack backend for the main repository *but* both of them will be checked
before any loose backends.

In the current implementation of ODB backends, each backend is tasked
with refreshing itself after a failed lookup. This is standard Git
behavior: we want to e.g. reload the packfiles on disk in case they have
changed and that's the reason we can't find the object we're looking
for.

This behavior, however, becomes pathological in repositories where
multiple alternates have been loaded. Given that each alternate counts
as a separate backend, a miss in the main repository (which can
potentially be very frequent in cases where object storage comes from
the alternate) will result in refreshing all its packfiles before we
move on to the alternate backend where the object will most likely be
found.

To fix this, the code in `odb.c` has been refactored as to perform the
refresh of all the backends externally, once we've verified that the
object is nowhere to be found.

If the refresh is successful, we then perform the lookup sequentially
through all the backends, skipping the ones that we know for sure
weren't refreshed (because they have no refresh API).

The on-disk pack backend has been adjusted accordingly: it no longer
performs refreshes internally.

We moved the "main" parsing to use 64 bits for the timestamp, but the
quick parsing for the revwalk did not. This means that for large
timestamps we fail to parse the time and thus the walk.

Move this parser to use 64 bits as well.

There's been a few reports of users not understanding what the python
error means, so spell out the options they have.

SSL_shutdown() does not like it when we pass an unitialized ssl context
to it. This means that when we fail to connect to a host, we hide the
error message saying so with OpenSSL's indecipherable error message.

git expects an empty line after the binary data:

literal X
...binary data...
<empty_line>

The last literal block of the generated patches were not containing the required empty line. Example:

	diff --git a/binary_file b/binary_file
	index 3f1b3f9098131cfecea4a50ff8afab349ea66d22..86e5c1008b5ce635d3e3fffa4434c5eccd8f00b6 100644
	GIT binary patch
	literal 8
	Pc${NM&PdElPvrst3ey5{

	literal 6
	Nc${NM%g@i}0ssZ|0lokL
	diff --git a/binary_file2 b/binary_file2
	index 31be99be19470da4af5b28b21e27896a2f2f9ee2..86e5c1008b5ce635d3e3fffa4434c5eccd8f00b6 100644
	GIT binary patch
	literal 8
	Pc${NM&PdElPvrst3ey5{

	literal 13
	Sc${NMEKbZyOexL+Qd|HZV+4u-

git apply of that diff results in:

	error: corrupt binary patch at line 9: diff --git a/binary_file2 b/binary_file2
	fatal: patch with only garbage at line 10

The proper formating is:

	diff --git a/binary_file b/binary_file
	index 3f1b3f9098131cfecea4a50ff8afab349ea66d22..86e5c1008b5ce635d3e3fffa4434c5eccd8f00b6 100644
	GIT binary patch
	literal 8
	Pc${NM&PdElPvrst3ey5{

	literal 6
	Nc${NM%g@i}0ssZ|0lokL
	diff --git a/binary_file2 b/binary_file2
	index 31be99be19470da4af5b28b21e27896a2f2f9ee2..86e5c1008b5ce635d3e3fffa4434c5eccd8f00b6 100644
	GIT binary patch
	literal 8
	Pc${NM&PdElPvrst3ey5{

	literal 13
	Sc${NMEKbZyOexL+Qd|HZV+4u-

Check that the repository directory is beneath the workdir before
adding it to the list of reserved paths.  If it is not, then there
is no possibility of checking out files into it, and it should not
be a reserved word.

This is a particular problem with submodules where the repo directory
may be in the super's .git directory.

Before:
libdir=/usr//usr/lib64
includedir=/usr//usr/include

After:
libdir=/usr/lib64
includedir=/usr/include

(note the duplication of /usr in the before case)

Don't coalesce all errors into ENOENT.  At least identify EACCES.
All callers should be handling this case already, as the POSIX
`lstat` will return this.

When a file exists on disk and we're checking out a file that differs
in executableness, remove the old file.  This allows us to recreate the
new file with p_open, which will take the new mode into account and
handle setting the umask properly.

Remove any notion of chmod'ing existing files, since it is now handled
by the aforementioned removal and was incorrect, as it did not take
umask into account.

It calls git_mempack_reset which reallocates the object array. git_oidmap_free is now called on it explicitly.

git_mempack_reset was leaving free'd pointers in the oidmap.