Fix duplicate files in query results with explicit dedup

Added safety net deduplication after reranking to prevent the same
file appearing multiple times in results. Uses Set to keep only
first (highest-scored) occurrence of each file.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.beads/issues.jsonl

@@ -10,6 +10,7 @@
 {"id":"qmd-6s5","title":"Export current database to index.yml","description":"Write a script to export current collections and path_contexts from SQLite to ~/.config/qmd/index.yml format. Include all collection metadata and contexts.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:52.707844-05:00","updated_at":"2025-12-13T09:57:36.650437-05:00","closed_at":"2025-12-13T09:57:36.650437-05:00","dependencies":[{"issue_id":"qmd-6s5","depends_on_id":"qmd-3z9","type":"blocks","created_at":"2025-12-13T09:55:07.606834-05:00","created_by":"daemon"}]}
 {"id":"qmd-7ss","title":"remove all the symlinks and stuff in the git repo, clean up the root directory","description":"","status":"closed","priority":4,"issue_type":"task","created_at":"2025-12-12T16:40:00.744982-05:00","updated_at":"2025-12-12T17:11:18.034215-05:00","closed_at":"2025-12-12T17:11:18.034215-05:00"}
 {"id":"qmd-8eu","title":"Update documents table schema for collection names","description":"Change documents.collection_id (integer FK) to documents.collection (text). Update all queries and indices. Keep backwards compatibility during transition.","design":"Schema change:\n- Add `collection TEXT` column\n- Migrate data: UPDATE documents SET collection = (SELECT name FROM collections WHERE id = collection_id)\n- Drop collection_id column\n- Update FTS5 trigger\n- Update all queries in store.ts","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:52.830305-05:00","updated_at":"2025-12-13T10:08:24.88716-05:00","closed_at":"2025-12-13T10:08:24.88716-05:00","dependencies":[{"issue_id":"qmd-8eu","depends_on_id":"qmd-6s5","type":"blocks","created_at":"2025-12-13T09:55:07.662048-05:00","created_by":"daemon"}]}
+{"id":"qmd-9ij","title":"Conditional query expansion based on BM25 signal strength","description":"Query expansion helps recall but injects false positives. Skip expansion if original BM25 top-5 has strong signals (exact term hits, high proximity). Only expand when recall is weak.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-20T17:18:41.806447-05:00","updated_at":"2025-12-20T17:18:41.806447-05:00"}
 {"id":"qmd-9ua","title":"Update all qmd commands for YAML-based collections","description":"Update qmd.ts commands: collection add/list/remove/rename, status, update, ls. All should use collections.ts instead of store.ts collection functions.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:54:53.14644-05:00","updated_at":"2025-12-13T10:17:39.67707-05:00","closed_at":"2025-12-13T10:17:39.67707-05:00","dependencies":[{"issue_id":"qmd-9ua","depends_on_id":"qmd-u84","type":"blocks","created_at":"2025-12-13T09:55:07.893268-05:00","created_by":"daemon"},{"issue_id":"qmd-9ua","depends_on_id":"qmd-oxy","type":"blocks","created_at":"2025-12-13T09:55:07.942221-05:00","created_by":"daemon"}]}
 {"id":"qmd-afe","title":"implement qmd collection rename, which changes the global path prefix for the collection","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T15:55:54.779325-05:00","updated_at":"2025-12-12T16:29:24.153196-05:00","closed_at":"2025-12-12T16:29:24.153196-05:00"}
 {"id":"qmd-ama","title":"Refactor database system","description":"All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection, path, hash,\n┃ created_at, updated_at. (collection,path)\n┃\n┃\n\n┃ All documents should be stored as content addressable hash, e.g. hash, doc, created_at,\n┃ updated_at. documents should be a file system layer on top e.g. collection_id, path, hash,\n┃ created_at, updated_at. (collection,path) is unique. There is also collection which stores PWD\n┃ + glob pattern, name (\\w+). Every document is treated as path qmd://collection.name/","notes":"## Completed\n- ✅ Implemented content-addressable storage (content table with hash→doc mapping)\n- ✅ Refactored documents table as file system layer (collection_id, path, hash)\n- ✅ Added collection names (e.g., \"pages\", \"journals\", \"archive\")\n- ✅ Implemented virtual paths (qmd://collection-name/path/to/file.md)\n- ✅ Added hierarchical context support (collection-scoped)\n- ✅ Successfully migrated existing database\n- ✅ Updated search functions to work with new schema\n- ✅ Updated indexing logic to use content-addressable storage\n- ✅ Orphaned content hash cleanup\n\n## Still TODO\n- Fix migration SQL to properly extract basename (currently needs manual fix)\n- Implement `qmd collection add . --name \u003cname\u003e --mask '**/*.md'`\n- Implement `qmd ls [path]` for exploring virtual file tree","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:57:35.497489-05:00","updated_at":"2025-12-12T15:39:48.879143-05:00","closed_at":"2025-12-12T15:39:48.879143-05:00"}
@@ -18,7 +19,9 @@
 {"id":"qmd-bx1","title":"Fix migration SQL for proper basename extraction","description":"The migration currently generates collection names incorrectly (uses full path instead of basename). Need to fix the SQL in migrateToContentAddressable to properly extract the directory basename.","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-12-12T15:29:53.757723-05:00","updated_at":"2025-12-12T15:50:29.349134-05:00","closed_at":"2025-12-12T15:50:29.349134-05:00","dependencies":[{"issue_id":"qmd-bx1","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.758524-05:00","created_by":"daemon"}]}
 {"id":"qmd-c0m","title":"Comprehensive CLI review and consistency pass","description":"Review entire CLI command structure:\n- Consistent naming (add vs create, remove vs delete)\n- Consistent flag usage (--name, --mask, etc)\n- Update help text for all commands\n- Ensure virtual paths work everywhere\n- Test all commands end-to-end","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-12T15:29:38.083564-05:00","updated_at":"2025-12-12T16:06:51.544695-05:00","closed_at":"2025-12-12T16:06:51.544695-05:00"}
 {"id":"qmd-clr","title":"fix embed","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-12T16:14:55.292114-05:00","updated_at":"2025-12-12T16:31:27.661829-05:00","closed_at":"2025-12-12T16:31:27.661829-05:00"}
+{"id":"qmd-d00","title":"Add offline evaluation harness for tuning","description":"Create a small benchmark with ~100 labeled queries from real searches. Would enable tuning: expansion on/off threshold, candidate count (30 vs 100), blending weights, reranker threshold.","status":"open","priority":3,"issue_type":"feature","created_at":"2025-12-20T17:18:42.007265-05:00","updated_at":"2025-12-20T17:18:42.007265-05:00"}
 {"id":"qmd-deh","title":"Refactor database introduce qmd collection *","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-12-10T10:56:04.516137-05:00","updated_at":"2025-12-12T16:12:12.349428-05:00","closed_at":"2025-12-12T16:12:12.349428-05:00"}
+{"id":"qmd-df5","title":"Rerank multiple chunks per document with score aggregation","description":"Currently we only rerank 1 chunk per doc (selected by keyword heuristic). Should rerank top 2-3 chunks per document, then aggregate scores (max, softmax, or top-2 average). This improves ranking for long documents where the keyword-matched chunk isn't always the most relevant.","status":"open","priority":2,"issue_type":"feature","created_at":"2025-12-20T17:18:41.592575-05:00","updated_at":"2025-12-20T17:18:41.592575-05:00"}
 {"id":"qmd-dmi","title":"Implement 'qmd collection' commands","description":"Add explicit collection management:\n- qmd collection add . --name \u003cname\u003e --mask '**/*.md'\n- qmd collection list\n- qmd collection remove \u003cname\u003e\n\nThis gives users control over collection names and patterns.","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.810666-05:00","updated_at":"2025-12-12T16:02:08.079158-05:00","closed_at":"2025-12-12T16:02:08.079158-05:00","dependencies":[{"issue_id":"qmd-dmi","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.811294-05:00","created_by":"daemon"}]}
 {"id":"qmd-dt1","title":"Redesign context add command for better usability","description":"Current issues: \n1. Virtual path qmd://journals/ is rejected as invalid\n2. Syntax is confusing - sometimes path is first arg, sometimes second\n3. Need to support collection root context (qmd://name/)\n4. Should be intuitive: qmd context add \u003cwhere\u003e \u003cwhat\u003e\nDesign goals:\n- Support qmd://collection/ for collection root context\n- Support qmd://collection/path for path-specific context\n- Clear, consistent syntax\n- Good error messages","status":"closed","priority":1,"issue_type":"task","created_at":"2025-12-13T09:39:19.764114-05:00","updated_at":"2025-12-13T09:41:38.467861-05:00","closed_at":"2025-12-13T09:41:38.467861-05:00"}
 {"id":"qmd-e2c","title":"Implement 'qmd ls' command","description":"Add command to explore virtual file tree:\n- qmd ls → list all collections\n- qmd ls \u003ccollection\u003e → list files in collection\n- qmd ls \u003ccollection\u003e/\u003cpath\u003e → list files under path\nOutput: flat list of qmd:// paths","status":"closed","priority":1,"issue_type":"feature","created_at":"2025-12-12T15:29:53.859804-05:00","updated_at":"2025-12-12T15:55:12.777701-05:00","closed_at":"2025-12-12T15:55:12.777701-05:00","dependencies":[{"issue_id":"qmd-e2c","depends_on_id":"qmd-ama","type":"discovered-from","created_at":"2025-12-12T15:29:53.860535-05:00","created_by":"daemon"}]}

src/qmd.ts

@@ -2164,8 +2164,16 @@ async function querySearch(query: string, opts: OutputOptions, embedModel: strin
     };
   }).sort((a, b) => b.score - a.score);
 
+  // Deduplicate by file (safety net - shouldn't happen but prevents duplicate output)
+  const seenFiles = new Set<string>();
+  const dedupedResults = finalResults.filter(r => {
+    if (seenFiles.has(r.file)) return false;
+    seenFiles.add(r.file);
+    return true;
+  });
+
   closeDb();
-  outputResults(finalResults, query, opts);
+  outputResults(dedupedResults, query, opts);
 }
 
 // Parse CLI arguments using util.parseArgs