[CI] Upgrade to cargo-deny-action v2

`cargo update` dependencies selectively

[CI] Upgrade mercurial to 7.2

Rename write_object_file accordingly to git-core changes in 2.53.0

Update git-core to 2.53.0

Update git-core to 2.52.0

Import ref_store instead of using it fully qualified

Remove transparent wrapping of the notes API

Fix the definitions of xpparam_t and xdi_diff_outf on the rust side

Upgrade zip to 7

Upgrade lru to 0.16

`cargo update` dependencies selectively

Avoid using as_ref when using version::*

[CI] Upgrade to clang 21

[CI] Upgrade to rust 1.93.0