Shallow (#6396) with some fixes from review

The `depth` field is suitable to specify unshallowing; provide an enum
to aide in specifying the `unshallow` value.

Users should provide us an array of object ids; we don't need a separate
type. And especially, we should not be mutating user-providing values.
Instead, use `git_oid *` in the shallow code.

As reported in https://bugs.freebsd.org/271234, recent versions of
FreeBSD have adjusted the prototype for qsort_r() to match the POSIX
interface. This causes libgit2's CMake configuration check to fail to
detect qsort_r(), making it fall back to qsort_s(), which in libgit2
also has an incompatible interface. With recent versions of clang this
results in a "incompatible function pointer types" compile error.

Summarizing, there are four variations of 'qsort-with-context':
* old style BSD qsort_r(), used in FreeBSD 13 and earlier, where the
  comparison function has the context parameter first
* GNU or POSIX qsort_r(), also used in FreeBSD 14 and later, where the
  comparison function has the context parameter last
* C11 qsort_s(), where the comparison function has the context parameter
  last
* Microsoft qsort_s(), where the comparison function has the context
  parameter first

Add explicit detections for all these variants, so they get detected as
(in the same order as above):

* `GIT_QSORT_R_BSD`
* `GIT_QSORT_R_GNU`
* `GIT_QSORT_S_C11`
* `GIT_QSORT_S_MSC`

An additional complication is that on FreeBSD 14 and later, <stdlib.h>
uses the C11 _Generic() macro mechanism to automatically select the
correct qsort_r() prototype, depending on the caller's comparison
function argument. This breaks CMake's check_prototype_definition()
functionality, since it tries to redefine the function, and _Generic
macro is expanded inline causing a compile error.

Work around that problem by putting the function names in parentheses,
to prevent the preprocessor from using a macro to replace the function
name.

Also, in `git__qsort_r()`, change the `#if` order so the variants that
do not have to use glue are preferred.

The semantics of `from_file` are weird - it looks like a function that
just opens a file, but it actually inspects the pointer, which is
unexpected and could make things very crashy.

Make an `open` function that just does an open, and move the magic to
`open_or_refresh` whose name better indicates that it may do weird
stuff.

Depth of `0` should indicate full depth. Disallow negative values (they
may have a future meaning) and use `0` as the default.

Don't mix parsing by hand and using `git_parse` to parse.