This change makes calculations of merge-bases a bit faster when there
are complex graphs and the commit times cause visiting nodes multiple
times. This is done by visiting the nodes in the graph in reverse
generation order when the generation number is available instead of
commit timestamp. If the generation number is missing in any pair of
commits, it can safely fall back to the old heuristic with no negative
side-effects.

Part of: #5757

commit-graph: Use the commit-graph in revwalks

[Submodule] Git submodule dup

Optional stricter allocation checking (for `malloc(0)` cases)

Co-authored-by: lhchavez <lhchavez@lhchavez.com>

Add `GIT_DEBUG_STRICT_ALLOC` to help identify problematic callers of
allocation code that pass a `0` size to the allocators and then expect a
non-`NULL` return.

When given a 0-size allocation, `malloc` _may_ return either a `NULL`
_or_ a pointer that is not writeable.  Most systems return a non-`NULL`
pointer; AIX is an outlier.  We should be able to cope with this AIXy
behavior, so this adds an option to emulate it.

This refactors this to a wrapper function, as well as changing the
existing API have a va_list and ... version.

stdintification: use int64_t and INT64_C instead of long long

git__timer: Allow compilation on systems without CLOCK_MONOTONIC

For 32-bit int: There's no real reason for that ifdef if we explicitly
specify the stdint.h type.

For 64-bit int: ope, I made it signed accidentally

Makes usage of CLOCK_MONOTONIC conditional and makes functions that uses
git__timer handle clock resynchronization.

Call gettimeofday with tzp set to NULL as required by
https://pubs.opengroup.org/onlinepubs/9699919799/functions/gettimeofday.html

Make `FIND_PACKAGE(PythonInterp)` prefer `python3`

fix check for ignoring of negate rules

Fix wrong time_t used in function

config: fix included configs not refreshed more than once

This change makes it possible to prefer a python (version 3) interpreter
on systems where python2 and python3 coexist (where python2 is found as
`/usr/bin/python`).

Fix memory leak in git_smart__connect

git__timer: Limit ITimer usage to AmigaOS4

Passes w/ gcc 11 on Fedora x64.

Protip: So you don;t have to suffer,

```
perl -pe 's/(-?(?:0x)?[A-Fa-f0-9]+)([Uu])?[Ll][Ll]/\U$2INT64_C(\E$1)/mg'
```

Even on systems without C99 where long long and stdint are both
missing, we can shim stdint and point it to any compiler-specific
type (i.e long long, _int64, etc.).

Also next is constant suffixes and determining what needs to
include stdint.

This function doesn't interoperate with any system functions that
use the system time_t, but rather only works with the git_time_t
type in libgit2, which could be a different width than the system
one. Fixes a compile warning.

Consider files executable only if the user can execute them

Update from regex to pcre licensing information in docs/contributing.md

docs: fix some missing includes that cause Docurium to error out

Define WINHTTP_NO_CLIENT_CERT_CONTEXT if needed

docs: stop mentioning libgit2's "master" branch

Co-authored-by: lhchavez <lhchavez@lhchavez.com>

If an included config is refreshed twice, the second update is not taken
into account.

This is because the list of included files is cleared after re-reading
the new configuration, instead of being cleared before.

Fix it and add a test case to check for this bug.