git__timer: Allow compilation on systems without CLOCK_MONOTONIC

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

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.

The name of libgit2's main branch is now "main" but contributing.md and
release.md still reference "master" as the main branch.  Fix it.

This is what git.git does, so we should follow suit.

Tolerate readlink size less than st_size

Patch documentation

In https://github.com/libgit2/libgit2/pull/5723/files/fc46dc06f52f854f74371682f911f13856c68edb#r540092847, I was confused by the semantics of `git_index_find`. The documentation says both that it returns the output value in `at_pos` and that it returns it directly as an `int`. This is incorrect; the return value is only returned via `at_pos`.

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

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

The call to git_proxy_options_dup will replace the url pointer of the
proxy.
But if the url pointer is already set, the old address will be lost
forever and will never be free.