Add fuzzy key match, pattern mining (P#) and IDF ranking to document …

[hungpham10]

…graph

Phase 3 of the structured document graph: fuzzy retrieval, cross-document pattern mining and rarity-based ranking (rare structure = high information, IDF-style scoring).

• Fuzzy key match: search_key_fuzzy scores distinct keys by exact/prefix/ contains/Levenshtein similarity with an IDF bonus (rarer keys score higher). doc_search accepts ~segment to force fuzzy and falls back exact-substring -> fuzzy when the full-path trie misses.
• Pattern mining: mine_patterns() counts kind chains (wildcard FIELD/IDX payloads) ending at scalar leaves over a max_depth window, assigns stable pattern ids (P#, registry persisted in storage and restored on open) and indexes chains into the previously dead pattern_trie. Results carry node_count / doc_count / doc_freq, sorted by document frequency ascending so characteristic patterns surface first and background (~1.0) sinks.
• Structural search: search_kind_chain() matches nodes whose ancestor kind window ends with the query chain (e.g. "MAP, FIELD, NUMBER"); results are ranked by pattern uniqueness IDF. search_path_scan() complements the radix trie whose leaf holds a single record per chain, returning all nodes with the same key path across documents (spec.replicas: 97 hits on the infra repo instead of 1).
• Depth semantics fixed in doc_search: depth counts extra levels BELOW the pattern, so the radix key-length filter gets pattern_len + depth.
• New MCP tools: doc_mine_patterns, doc_list_patterns, doc_search_struct. New CLI commands: codegraph doc patterns, codegraph doc struct.

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[codspeed]

Merging this PR will not alter performance

✅ 28 untouched benchmarks

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_{Comparing feature/fuzzy-structure-matching (50a6c1f) with main (6a75ca7)}

[codecov-commenter]

Codecov Report

❌ Patch coverage is 54.75460% with 295 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.32%. Comparing base (6a75ca7) to head (50a6c1f).

Files with missing lines	Patch %	Lines
crates/codegraph-mcp/src/tools.rs	0.00%	121 Missing ⚠️
crates/codegraph-docs/src/graph.rs	82.25%	77 Missing ⚠️
crates/codegraph/src/main.rs	0.00%	63 Missing ⚠️
crates/codegraph-mcp/src/lib.rs	0.00%	34 Missing ⚠️

❌ Your patch status has failed because the patch coverage (54.75%) is below the target coverage (100.00%). You can increase the patch coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #30      +/-   ##
==========================================
- Coverage   73.84%   73.32%   -0.53%     
==========================================
  Files          87       87              
  Lines       19286    19915     +629     
==========================================
+ Hits        14242    14602     +360     
- Misses       5044     5313     +269     

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