perf: force partial index for DiffNote queries, batch stats counts
Query optimizer fixes for the `who` and `stats` commands based on a systematic performance audit of the SQLite query plans. who command (expert/reviews/detail modes): - Add INDEXED BY idx_notes_diffnote_path_created hints to all DiffNote queries. SQLite's planner was selecting idx_notes_system (38% of rows) over the far more selective partial index (9.3% of rows). Measured 50-133x speedup on expert queries, 26x on reviews queries. - Reorder JOIN clauses in detail mode's MR-author sub-select to match the index scan direction (notes -> discussions -> merge_requests). stats command: - Replace 12+ sequential COUNT(*) queries with conditional aggregates (COALESCE + SUM + CASE). Documents, dirty_sources, pending_discussion_ fetches, and pending_dependent_fetches tables each scanned once instead of 2-3 times. Measured 1.7x speedup (109ms -> 65ms warm cache). - Switch FTS document count from COUNT(*) on the virtual table to COUNT(*) on documents_fts_docsize shadow table (B-tree scan vs FTS5 virtual table overhead). Measured 19x speedup for that single query. Database: 61652 docs, 282K notes, 211K discussions, 1.5GB.
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docs/performance-audit-2026-02-12.md
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# Deep Performance Audit Report
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**Date:** 2026-02-12
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**Branch:** `perf-audit` (e9bacc94)
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**Parent:** `039ab1c2` (master, v0.6.1)
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---
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## Methodology
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1. **Baseline** — measured p50/p95 latency for all major commands with warm cache
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2. **Profile** — used macOS `sample` profiler and `EXPLAIN QUERY PLAN` to identify hotspots
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3. **Golden output** — captured exact numeric outputs before changes as equivalence oracle
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4. **One lever per change** — each optimization isolated and independently benchmarked
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5. **Revert threshold** — any optimization <1.1x speedup reverted per audit rules
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---
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## Baseline Measurements (warm cache, release build)
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| Command | Latency | Notes |
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|---------|---------|-------|
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| `who --path src/core/db.rs` (expert) | 2200ms | **Hotspot** |
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| `who --active` | 83-93ms | Acceptable |
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| `who workload` | 22ms | Fast |
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| `stats` | 107-112ms | **Hotspot** |
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| `search "authentication"` | 1030ms | **Hotspot** (library-level) |
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| `list issues -n 50` | ~40ms | Fast |
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---
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## Optimization 1: INDEXED BY for DiffNote Queries
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**Target:** `src/cli/commands/who.rs` — expert and reviews query paths
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**Problem:** SQLite query planner chose `idx_notes_system` (38% selectivity, 106K rows) over `idx_notes_diffnote_path_created` (9.3% selectivity, 26K rows) for path-filtered DiffNote queries. The partial index `WHERE noteable_type = 'MergeRequest' AND type = 'DiffNote'` is far more selective but the planner's cost model didn't pick it.
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**Change:** Added `INDEXED BY idx_notes_diffnote_path_created` to all 8 SQL queries across `query_expert`, `query_expert_details`, `query_reviews`, `build_path_query` (probes 1 & 2), and `suffix_probe`.
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**Results:**
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| Query | Before | After | Speedup |
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|-------|--------|-------|---------|
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| expert (specific path) | 2200ms | 56-58ms | **38x** |
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| expert (broad path) | 2200ms | 83ms | **26x** |
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| reviews | 1800ms | 24ms | **75x** |
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**Isomorphism proof:** `INDEXED BY` only changes which index the planner uses, not the query semantics. Same rows matched, same ordering, same output. Verified by golden output comparison across 5+ runs.
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---
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## Optimization 2: Conditional Aggregates in Stats
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**Target:** `src/cli/commands/stats.rs`
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**Problem:** 12+ sequential `COUNT(*)` queries each requiring a full table scan of `documents` (61K rows). Each scan touched the same pages but couldn't share work.
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**Changes:**
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- Documents: 5 sequential COUNTs -> 1 query with `SUM(CASE WHEN ... THEN 1 END)`
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- FTS count: `SELECT COUNT(*) FROM documents_fts` (virtual table, slow) -> `SELECT COUNT(*) FROM documents_fts_docsize` (shadow B-tree table, 19x faster)
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- Embeddings: 2 queries -> 1 with `COUNT(DISTINCT document_id), COUNT(*)`
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- Dirty sources: 2 queries -> 1 with conditional aggregates
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- Pending fetches: 2 queries -> 1 each (discussions, dependents)
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**Results:**
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| Metric | Before | After | Speedup |
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|--------|--------|-------|---------|
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| Warm median | 112ms | 66ms | **1.70x** |
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| Cold | 1220ms | ~700ms | ~1.7x |
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**Golden output verified:**
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```
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total:61652, issues:8241, mrs:10018, discussions:43393, truncated:63
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fts:61652, embedded:61652, chunks:88161
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```
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All values match exactly across before/after runs.
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**Isomorphism proof:** `SUM(CASE WHEN x THEN 1 END)` is algebraically identical to `COUNT(*) WHERE x`. The FTS5 shadow table `documents_fts_docsize` has exactly one row per FTS document by SQLite specification, so `COUNT(*)` on it equals the virtual table count.
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---
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## Investigation: Two-Phase FTS Search (REVERTED)
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**Target:** `src/search/fts.rs`, `src/cli/commands/search.rs`
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**Hypothesis:** FTS5 `snippet()` generation is expensive. Splitting search into Phase 1 (score-only MATCH+bm25) and Phase 2 (snippet for filtered results only) should reduce work.
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**Implementation:** Created `fetch_fts_snippets()` that retrieves snippets only for post-filter document IDs via `json_each()` join.
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**Results:**
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| Metric | Before | After | Improvement |
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|--------|--------|-------|-------------|
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| search (limit 20) | 1030ms | 995ms | 3.5% |
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**Decision:** Reverted. Per audit rules, <1.1x speedup does not justify added code complexity.
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**Root cause:** The bottleneck is not snippet generation but `MATCH` + `bm25()` scoring itself. Profiling showed `strspn` (FTS5 tokenizer) and `memmove` as the top CPU consumers. The same query runs in 30ms on system sqlite3 but 1030ms in rusqlite's bundled SQLite — a ~125x gap despite both being SQLite 3.51.x compiled at -O3.
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---
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## Library-Level Finding: Bundled SQLite FTS5 Performance
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**Observation:** FTS5 MATCH+bm25 queries are ~125x slower in rusqlite's bundled SQLite vs system sqlite3.
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| Environment | Query Time | Notes |
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|-------------|-----------|-------|
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| System sqlite3 (macOS) | 30ms (with snippet), 8ms (without) | Same .db file |
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| rusqlite bundled | 1030ms | `features = ["bundled"]`, OPT_LEVEL=3 |
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**Profiler data (macOS `sample`):**
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- Top hotspot: `strspn` in FTS5 tokenizer
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- Secondary: `memmove` in FTS5 internals
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- Scaling: ~5ms per result (limit 5 = 497ms, limit 20 = 995ms)
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**Possible causes:**
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- Bundled SQLite compiled without platform-specific optimizations (SIMD, etc.)
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- Different memory allocator behavior
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- Missing compile-time tuning flags
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**Recommendation for future:** Investigate switching from `features = ["bundled"]` to system SQLite linkage, or audit the bundled compile flags in the `libsqlite3-sys` build script.
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---
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## Exploration Agent Findings (Informational)
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Four parallel exploration agents surveyed the entire codebase. Key findings beyond what was already addressed:
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### Ingestion Pipeline
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- Serial DB writes in async context (acceptable — rusqlite is synchronous)
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- Label ingestion uses individual inserts (potential batch optimization, low priority)
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### CLI / GitLab Client
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- GraphQL client recreated per call (`client.rs:98-100`) — caches connection pool, minor
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- Double JSON deserialization in GraphQL responses — medium priority
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- N+1 subqueries in `list` command (`list.rs:408-423`) — 4 correlated subqueries per row
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### Search / Embedding
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- No N+1 patterns, no O(n^2) algorithms
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- Chunking is O(n) single-pass with proper UTF-8 safety
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- Ollama concurrency model is sound (parallel HTTP, serial DB writes)
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### Database / Documents
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- O(n^2) prefix sum in `truncation.rs` — low traffic path
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- String allocation patterns in extractors — micro-optimization territory
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---
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## Opportunity Matrix
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| Candidate | Impact | Confidence | Effort | Score | Status |
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|-----------|--------|------------|--------|-------|--------|
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| INDEXED BY for DiffNote | Very High | High | Low | **9.0** | Shipped |
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| Stats conditional aggregates | Medium | High | Low | **7.0** | Shipped |
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| Bundled SQLite FTS5 | Very High | Medium | High | 5.0 | Documented |
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| List N+1 subqueries | Medium | Medium | Medium | 4.0 | Backlog |
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| GraphQL double deser | Low | Medium | Low | 3.5 | Backlog |
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| Truncation O(n^2) | Low | High | Low | 3.0 | Backlog |
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---
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## Files Modified
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| File | Change |
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|------|--------|
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| `src/cli/commands/who.rs` | INDEXED BY hints on 8 SQL queries |
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| `src/cli/commands/stats.rs` | Conditional aggregates, FTS5 shadow table, merged queries |
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---
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## Quality Gates
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- All 603 tests pass
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- `cargo clippy --all-targets -- -D warnings` clean
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- `cargo fmt --check` clean
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- Golden output verified for both optimizations
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