arrow

GH-40268: [Archery] Bump the version of pygit2, adapt to API changes (#40269)

### Rationale for this change

`archery crossbow submit ...` fails with newer versions of pygit2

### What changes are included in this PR?

Adapt away from deprecated [sic] APIs in pygit2 to ones that work with current versions, bump the pin

### Are these changes tested?

Manually, yes, I can use `archery crossbow submit ...` again. CI will run using archery in a bunch of places on this PR too.

### Are there any user-facing changes?

No
* GitHub Issue: #40268

Authored-by: Jonathan Keane <jkeane@gmail.com>
Signed-off-by: Jonathan Keane <jkeane@gmail.com>