Add support for free-threaded CPython 3.13t

[andfoy]

What does this PR do?

See #1197

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[rgommers]

The commenting out of pygit2 is for debug/workaround purposes only it looks like. pygit2 doesn't build under free-threading by default yet, but it's installable locally as outlined in libgit2/pygit2#1367. So better to do that, and not include other changes to handle it not being installed in this PR.