Bump deps: pyo3 0.22→0.28, bincode 1→2, lru, uuid, assert_cmd - #184

Summary

Combined dependency upgrade that supersedes the open Dependabot PRs:

• Closes Bump assert_cmd from 2.2.0 to 2.2.2 #172 (assert_cmd 2.0 → 2.2)
• Closes Bump bincode from 1.3.3 to 3.0.0 #173 (bincode 1.3.3 → 3.0.0 2.0; see note below)
• Closes Bump uuid from 1.21.0 to 1.23.1 #174 (uuid 1.21 → 1.23)
• Closes Bump lru from 0.16.3 to 0.18.0 #175 (lru 0.16 → 0.18)
• Closes Bump pyo3 from 0.22.6 to 0.28.3 #176 (pyo3 0.22 → 0.28)

What changed

pyo3 0.22 → 0.28

• PyBytes::new_bound / PyDict::new_bound / PyList::new_bound / PyList::empty_bound → unsuffixed new / empty (the Bound variants became the default).
• PyList::new is now fallible (returns PyResult), so call sites add ?.
• py.allow_threads(..) → py.detach(..) and Python::with_gil(..) → Python::attach(..) (0.28 rename).
• value.into_py(py) → value.into_py_any(py).unwrap() via the new IntoPyObjectExt trait.
• obj.downcast::<T>() → obj.cast::<T>() on &Bound<PyAny>.
• Five #[pyclass] types that derive Clone opt in to the legacy FromPyObject derive via from_py_object to silence the 0.28 deprecation warning.

bincode 1.3.3 → 2.0

Note: Dependabot's #173 proposed bincode 3.0.0, but that release is an xkcd-2347 placeholder crate (compile_error!("https://xkcd.com/2347/");) — not a real release. This PR targets bincode 2.0.1, the actual latest stable.

• New crate::serde_bincode helper module wraps bincode::serde::encode_to_vec / decode_from_slice with bincode::config::legacy(), preserving byte-level wire compatibility with bincode 1.3. Existing git blobs, RocksDB rows, and proximity index snapshots written by older versions still round-trip.
• bincode::Error is gone in 2.x. GitKvError::SerializationError splits into SerializationEncodeError(EncodeError) / SerializationDecodeError(DecodeError); StorageError::Serialization likewise splits into SerializationEncode / SerializationDecode.

lru 0.16 → 0.18, uuid 1.0 → 1.23, assert_cmd 2.0 → 2.2

Drop-in — no code changes needed.

Test plan

• cargo build --all clean
• cargo clippy --features "git sql" clean
• cargo clippy --features "git sql rocksdb_storage proximity proximity_text" clean
• cargo clippy --features "python proximity proximity_text rocksdb_storage" clean
• cargo fmt --all -- --check clean
• cargo test --features "git sql" — 225 tests pass, 0 failed
• cargo test --features "git sql rocksdb_storage proximity proximity_text" — 363 tests pass, 0 failed
• maturin build --release --features "python sql" produces a working wheel
• Smoke-test wheel: ProllyTree.insert/find round-trip works
• pytest python/tests/ (without rocksdb-gated tests) — 21 of 22 collected tests pass; the 1 setup error in test_sql.py is pre-existing (test creates a tempfile.mkdtemp() and calls ProllySQLStore(dir) without git init first — fails on main as well).