audit(issue-12): fix stale msgpack references in docstrings, comments, and tests
- Remove hardcoded _CACHE_VERSION == 3 assertion (bumped to 4 on JSON migration) - Fix TestCacheFormat: use json.loads, .json suffix, drop msgpack import - Fix false-positive shelf tests: glob for no-extension files, not *.msgpack - Rewrite snapshot symlink tests to plant in object store (not legacy snapshots_dir) - Rewrite prune test to walk object store, verify HEAD commit still readable - Remove dead _make_commit helper (used legacy .msgpack commits_dir paths) - Fix corrupt/empty shelf test filenames: no extension matches new format - Update all docstrings: msgpack → JSON in cache_base, paths, store, stat_cache, symbol_cache, callgraph_cache, implicit_edge_cache, indices, test_history, _invariants, bridge, gc, shelf, sign, test_cmd, init, index_rebuild
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