feat(clones): git-ast clones — structural clone detection (identity index, first slice)

[bdelanghe]

Summary

• Adds src/clones.rs with find_clones() — groups Defs by shape_hash across files, surfaces groups with >1 occurrence as structural clones
• Adds git-ast clones FILE... verb wired into main.rs with extension-based dispatch (mirrors inspect)
• First concrete step of prx-nf1f (identity index): the subtree_hashes / shape_hash computed per-file are now accumulated rather than discarded

Why this is the right first slice:
The shape_hash is already an exact equivalence-class key by construction — equal hash ⟹ same canonical body. No threshold, no heuristics. The identity-index research note calls the occurrence map "trivial"; this PR makes it real, in memory, over a provided file set. The fuzzy/near-clone layer (MinHash + LSH over subtree_hashes) is explicitly deferred.

Example output:

$ git-ast clones src/a.rs src/b.rs
d5e0ebfa8c0dfcfc  3×fn
  src/a.rs  helper
  src/a.rs  aux
  src/b.rs  helper

Groups are sorted by shape_hash (BTreeMap), occurrences in file-then-definition order.

Test plan

• 11 new unit tests: empty input, single file, cross-file, exact-clone, 3-way group, multiple disjoint groups, HTML kinds preserved, sorted output, real Rust round-trip via printer::inspect
• 108 total unit tests pass (was 97 before this PR; includes the 11 new + upgrade brings 0 regressions)
• 5 cucumber integration tests pass
• Smoke-tested against repo's own source (no false positives) and a synthetic known-clone pair (correct 3-occurrence group)

PR checklist

1. Independent PR — new module + verb only; no changes to existing paths
2. Changed codepaths verified — 11 targeted unit tests + smoke test
3. Root cause — N/A (new feature)
4. No duplication — find_clones is pure post-processing; inspect dispatch is one pattern
5. No unrelated changes — only src/clones.rs, src/lib.rs, src/main.rs

Depends on #44 (tree-sitter upgrade) landing first.

🤖 Generated with Claude Code