Implement hybrid search with adaptive recall

## Background
Hybrid search is the top-level search orchestrator that combines FTS5 lexical results with sqlite-vec semantic results via RRF ranking. It supports three modes (Lexical, Semantic, Hybrid) and implements adaptive recall (wider initial fetch when filters are applied) and graceful degradation (falls back to FTS when Ollama is unavailable). All modes use RRF for consistent --explain output.

## Approach
Create `src/search/hybrid.rs` per PRD Section 5.3.

**Key types:**
```rust
#[derive(Debug, Clone, Copy, PartialEq, Eq)]
pub enum SearchMode {
    Hybrid,    // Vector + FTS with RRF
    Lexical,   // FTS only
    Semantic,  // Vector only
}

impl SearchMode {
    pub fn from_str(s: &str) -> Option<Self> {
        match s.to_lowercase().as_str() {
            "hybrid" => Some(Self::Hybrid),
            "lexical" | "fts" => Some(Self::Lexical),
            "semantic" | "vector" => Some(Self::Semantic),
            _ => None,
        }
    }

    pub fn as_str(&self) -> &'static str {
        match self {
            Self::Hybrid => "hybrid",
            Self::Lexical => "lexical",
            Self::Semantic => "semantic",
        }
    }
}

pub struct HybridResult {
    pub document_id: i64,
    pub score: f64,          // Normalized RRF score (0-1)
    pub vector_rank: Option<usize>,
    pub fts_rank: Option<usize>,
    pub rrf_score: f64,      // Raw RRF score
}
```

**Core function (ASYNC, PRD-exact signature):**
```rust
pub async fn search_hybrid(
    conn: &Connection,
    client: Option<&OllamaClient>,      // None if Ollama unavailable
    ollama_base_url: Option<&str>,       // For actionable error messages
    query: &str,
    mode: SearchMode,
    filters: &SearchFilters,
    fts_mode: FtsQueryMode,
) -> Result<(Vec<HybridResult>, Vec<String>)>
```

**IMPORTANT — client is `Option<&OllamaClient>`:** This enables graceful degradation. When Ollama is unavailable, the caller passes `None` and hybrid mode falls back to FTS-only with a warning. The `ollama_base_url` is separate so error messages can include it even when client is None.

**Adaptive recall constants (PRD Section 5.3):**
```rust
const BASE_RECALL_MIN: usize = 50;
const FILTERED_RECALL_MIN: usize = 200;
const RECALL_CAP: usize = 1500;
```

**Recall formula:**
```rust
let requested = filters.clamp_limit();
let top_k = if filters.has_any_filter() {
    (requested * 50).max(FILTERED_RECALL_MIN).min(RECALL_CAP)
} else {
    (requested * 10).max(BASE_RECALL_MIN).min(RECALL_CAP)
};
```

**Mode behavior:**
- **Lexical:** FTS only -> rank_rrf with empty vector list (single-list RRF)
- **Semantic:** Vector only -> requires client (error if None) -> rank_rrf with empty FTS list
- **Hybrid:** Both FTS + vector -> rank_rrf with both lists
- **Hybrid with client=None:** Graceful degradation to Lexical with warning, NOT error

**Graceful degradation logic:**
```rust
SearchMode::Hybrid => {
    let fts_results = search_fts(conn, query, top_k, fts_mode)?;
    let fts_tuples: Vec<_> = fts_results.iter().map(|r| (r.document_id, r.rank)).collect();

    match client {
        Some(client) => {
            let query_embedding = client.embed_batch(vec\![query.to_string()]).await?;
            let embedding = query_embedding.into_iter().next().unwrap();
            let vec_results = search_vector(conn, &embedding, top_k)?;
            let vec_tuples: Vec<_> = vec_results.iter().map(|r| (r.document_id, r.distance)).collect();
            let ranked = rank_rrf(&vec_tuples, &fts_tuples);
            // ... map to HybridResult
            Ok((results, warnings))
        }
        None => {
            warnings.push("Ollama unavailable, falling back to lexical search".into());
            let ranked = rank_rrf(&[], &fts_tuples);
            // ... map to HybridResult
            Ok((results, warnings))
        }
    }
}
```

## Acceptance Criteria
- [ ] Function is `async` (per PRD — Ollama client methods are async)
- [ ] Signature takes `client: Option<&OllamaClient>` (not required)
- [ ] Signature takes `ollama_base_url: Option<&str>` for actionable error messages
- [ ] Returns `(Vec<HybridResult>, Vec<String>)` — results + warnings
- [ ] Lexical mode: FTS-only results ranked via RRF (single list)
- [ ] Semantic mode: vector-only results ranked via RRF; error if client is None
- [ ] Hybrid mode: both FTS + vector results merged via RRF
- [ ] Graceful degradation: client=None in Hybrid falls back to FTS with warning (not error)
- [ ] Adaptive recall: unfiltered max(50, limit*10), filtered max(200, limit*50), capped 1500
- [ ] All modes produce consistent --explain output (vector_rank, fts_rank, rrf_score)
- [ ] SearchMode::from_str accepts aliases: "fts" for Lexical, "vector" for Semantic
- [ ] `cargo build` succeeds

## Files
- `src/search/hybrid.rs` — new file
- `src/search/mod.rs` — add `pub use hybrid::{search_hybrid, HybridResult, SearchMode};`

## TDD Loop
RED: Tests (some integration, some unit):
- `test_lexical_mode` — FTS results only
- `test_semantic_mode` — vector results only
- `test_hybrid_mode` — both lists merged
- `test_graceful_degradation` — None client falls back to FTS with warning in warnings vec
- `test_adaptive_recall_unfiltered` — recall = max(50, limit*10)
- `test_adaptive_recall_filtered` — recall = max(200, limit*50)
- `test_recall_cap` — never exceeds 1500
- `test_search_mode_from_str` — "hybrid", "lexical", "fts", "semantic", "vector", invalid
GREEN: Implement search_hybrid
VERIFY: `cargo test hybrid`

## Edge Cases
- Both FTS and vector return zero results: empty output (not error)
- FTS returns results but vector returns empty: RRF still works (single-list)
- Very high limit (100) with filters: recall = min(5000, 1500) = 1500
- Semantic mode with client=None: error (OllamaUnavailable), not degradation
- Semantic mode with 0% coverage: return LoreError::EmbeddingsNotBuilt

Implemented hybrid search with 3 modes (lexical/semantic/hybrid), graceful degradation when Ollama unavailable, adaptive recall (50-1500), RRF fusion. 6 tests pass.


Implement RRF ranking

## Background
Reciprocal Rank Fusion (RRF) combines results from multiple retrieval systems (FTS5 lexical + sqlite-vec semantic) into a single ranked list without requiring score normalization. Documents appearing in both lists rank higher than single-list documents. This is the core ranking algorithm for hybrid search in Gate B.

## Approach
Create \`src/search/rrf.rs\` per PRD Section 5.2.

```rust
use std::collections::HashMap;

const RRF_K: f64 = 60.0;

pub struct RrfResult {
    pub document_id: i64,
    pub rrf_score: f64,           // Raw RRF score
    pub normalized_score: f64,    // Normalized to 0-1 (rrf_score / max)
    pub vector_rank: Option<usize>,  // 1-indexed rank in vector list
    pub fts_rank: Option<usize>,     // 1-indexed rank in FTS list
}

/// Input: tuples of (document_id, score/distance) — already sorted by retriever.
/// Ranks are 1-indexed (first result = rank 1).
/// Score = sum of 1/(k + rank) for each list containing the document.
pub fn rank_rrf(
    vector_results: &[(i64, f64)],  // (doc_id, distance)
    fts_results: &[(i64, f64)],     // (doc_id, bm25_score)
) -> Vec<RrfResult>
```

**Algorithm (per PRD):**
1. Build HashMap<doc_id, (rrf_score, vector_rank, fts_rank)>
2. For each vector result at position i: score += 1/(K + (i+1)), record vector_rank = i+1 (**1-indexed**)
3. For each FTS result at position i: score += 1/(K + (i+1)), record fts_rank = i+1 (**1-indexed**)
4. Sort descending by rrf_score
5. Normalize: each result.normalized_score = result.rrf_score / max_score (best = 1.0)

**Key PRD details:**
- Ranks are **1-indexed** (rank 1 = best, not rank 0)
- Input is \`&[(i64, f64)]\` tuples, NOT custom structs
- Output has both \`rrf_score\` (raw) and \`normalized_score\` (0-1)

## Acceptance Criteria
- [ ] Documents in both lists score higher than single-list documents
- [ ] Single-list documents are included (not dropped)
- [ ] Ranks are 1-indexed (first element = rank 1)
- [ ] Raw RRF score available in rrf_score field
- [ ] Normalized score: best = 1.0, all in [0, 1]
- [ ] Results sorted descending by rrf_score
- [ ] vector_rank and fts_rank tracked per result for --explain
- [ ] Empty input lists handled (return empty)
- [ ] One empty list + one non-empty returns results from non-empty list

## Files
- \`src/search/rrf.rs\` — new file
- \`src/search/mod.rs\` — add \`mod rrf; pub use rrf::{rank_rrf, RrfResult};\`

## TDD Loop
RED: Tests in \`#[cfg(test)] mod tests\`:
- \`test_dual_list_ranks_higher\` — doc in both lists scores > doc in one list
- \`test_single_list_included\` — FTS-only and vector-only docs appear
- \`test_normalization\` — best score is 1.0, all in [0, 1]
- \`test_empty_inputs\` — empty returns empty
- \`test_ranks_are_1_indexed\` — verify vector_rank/fts_rank start at 1
- \`test_raw_and_normalized_scores\` — both fields populated correctly
GREEN: Implement rank_rrf()
VERIFY: \`cargo test rrf\`

## Edge Cases
- Duplicate document_id within same list: shouldn't happen, use first occurrence
- Single result in one list, zero in other: normalized_score = 1.0
- Very large input lists: HashMap handles efficiently

Completed: RRF ranking with 1-indexed ranks, raw+normalized scores, vector_rank/fts_rank provenance, 7 tests pass


[CP1] Test fixtures for mocked GitLab responses

Create mock response files for integration tests using wiremock.

## Fixtures to Create

### tests/fixtures/gitlab_issue.json
Single issue with labels:
- id, iid, project_id, title, description, state
- author object
- labels array (string names)
- timestamps
- web_url

### tests/fixtures/gitlab_issues_page.json
Array of issues simulating paginated response:
- 3-5 issues with varying states
- Mix of labels

### tests/fixtures/gitlab_discussion.json
Single discussion:
- id (string)
- individual_note: false
- notes array with 2+ notes
- Include one system note

### tests/fixtures/gitlab_discussions_page.json
Array of discussions:
- Mix of individual_note true/false
- Include resolvable/resolved examples

## Edge Cases to Cover
- Issue with no labels (empty array)
- Issue with labels_details (ignored in CP1)
- Discussion with individual_note=true (single note)
- System notes with system=true
- Resolvable notes

Files: tests/fixtures/gitlab_issue.json, gitlab_issues_page.json, gitlab_discussion.json, gitlab_discussions_page.json
Done when: wiremock handlers can use fixtures for deterministic tests


Fetch closes_issues API and populate entity_references

## Background
GET /projects/:id/merge_requests/:iid/closes_issues returns issues that will close when MR merges. This is the most reliable source for MR→issue relationships. Uses the generic dependent fetch queue (job_type = 'mr_closes_issues').

## Approach

**1. Add API endpoint to GitLab client (src/gitlab/client.rs):**
```rust
/// Fetch issues that will be closed when this MR merges.
pub async fn fetch_mr_closes_issues(
    &self,
    project_id: i64,
    iid: i64
) -> Result<Vec<GitLabIssueRef>>
```

New type in src/gitlab/types.rs:
```rust
#[derive(Debug, Clone, Deserialize)]
pub struct GitLabIssueRef {
    pub id: i64,
    pub iid: i64,
    pub project_id: i64,
    pub title: String,
    pub state: String,
    pub web_url: String,
}
```

URL: `GET /api/v4/projects/{project_id}/merge_requests/{iid}/closes_issues?per_page=100`

**2. Enqueue jobs during MR ingestion:**
In orchestrator.rs, after MR upsert:
```rust
enqueue_job(conn, project_id, "merge_request", iid, local_id, "mr_closes_issues", None)?;
```

This is always enqueued (not gated by a config flag) because cross-reference data is fundamental to all temporal queries.

**3. Process jobs in drain step:**
In the drain dispatcher (from bd-1ep), handle "mr_closes_issues" job_type:
```rust
let closes_issues = client.fetch_mr_closes_issues(gitlab_project_id, job.entity_iid).await?;
for issue_ref in &closes_issues {
    let target_id = resolve_issue_local_id(conn, project_id, issue_ref.iid);
    insert_entity_reference(conn, EntityReference {
        source_entity_type: "merge_request",
        source_entity_id: job.entity_local_id,
        target_entity_type: "issue",
        target_entity_id: target_id,            // Some(id) or None for cross-project
        target_project_path: if target_id.is_none() { Some(resolve_project_path(issue_ref.project_id)) } else { None },
        target_entity_iid: if target_id.is_none() { Some(issue_ref.iid) } else { None },
        reference_type: "closes",
        source_method: "api_closes_issues",
        created_at: None,
    })?;
}
```

**4. Insert helper for entity_references:**
Add to src/core/references.rs:
```rust
pub fn insert_entity_reference(conn: &Connection, ref_: &EntityReference) -> Result<bool>
// INSERT OR IGNORE, returns true if inserted
```

## Acceptance Criteria
- [ ] closes_issues API called for all MRs during sync
- [ ] Entity references created with reference_type='closes', source_method='api_closes_issues'
- [ ] Source = MR, target = issue (correct directionality)
- [ ] Cross-project issues stored as unresolved (target_entity_id=NULL, target_project_path set)
- [ ] Idempotent: re-sync doesn't create duplicate references
- [ ] 404 on deleted MR handled gracefully (fail_job)

## Files
- src/gitlab/client.rs (add fetch_mr_closes_issues)
- src/gitlab/types.rs (add GitLabIssueRef)
- src/core/references.rs (add insert_entity_reference helper)
- src/ingestion/orchestrator.rs (enqueue mr_closes_issues jobs)
- src/core/drain.rs or sync.rs (handle mr_closes_issues in drain dispatcher)

## TDD Loop
RED: tests/references_tests.rs:
- `test_closes_issues_creates_references` - mock closes_issues response, verify entity_references rows
- `test_closes_issues_cross_project_unresolved` - issue from different project stored as unresolved
- `test_closes_issues_idempotent` - process same job twice, verify no duplicates

tests/gitlab_types_tests.rs:
- `test_deserialize_issue_ref` - verify GitLabIssueRef deserialization

GREEN: Implement API endpoint, enqueue hook, drain handler, insert helper

VERIFY: `cargo test references -- --nocapture && cargo test gitlab_types -- --nocapture`

## Edge Cases
- closes_issues API returns issues from OTHER projects (cross-project closing) — must check if issue is in local DB
- Empty response (MR doesn't close any issues) — no refs created, job still completed
- MR may close the same issue via description ("Closes #123") and via commits — API deduplicates, but our INSERT OR IGNORE handles it too
- The closes_issues API may return stale data for draft MRs (issues that *would* close but haven't yet)


Add database migration 006_merge_requests.sql

## Background
Foundation for all CP2 MR features. This migration defines the schema that all other MR components depend on. Must complete BEFORE any other CP2 work can proceed.

## Approach
Create migration file that adds:
1. `merge_requests` table with all CP2 fields
2. `mr_labels`, `mr_assignees`, `mr_reviewers` junction tables
3. Indexes on discussions for MR queries
4. DiffNote position columns on notes table

## Files
- `migrations/006_merge_requests.sql` - New migration file
- `src/core/db.rs` - Update MIGRATIONS const to include version 6

## Acceptance Criteria
- [ ] Migration file exists at `migrations/006_merge_requests.sql`
- [ ] `merge_requests` table has columns: id, gitlab_id, project_id, iid, title, description, state, draft, author_username, source_branch, target_branch, head_sha, references_short, references_full, detailed_merge_status, merge_user_username, created_at, updated_at, merged_at, closed_at, last_seen_at, discussions_synced_for_updated_at, discussions_sync_last_attempt_at, discussions_sync_attempts, discussions_sync_last_error, web_url, raw_payload_id
- [ ] `mr_labels` junction table exists with (merge_request_id, label_id) PK
- [ ] `mr_assignees` junction table exists with (merge_request_id, username) PK
- [ ] `mr_reviewers` junction table exists with (merge_request_id, username) PK
- [ ] `idx_discussions_mr_id` and `idx_discussions_mr_resolved` indexes exist
- [ ] `notes` table has new columns: position_type, position_line_range_start, position_line_range_end, position_base_sha, position_start_sha, position_head_sha
- [ ] `gi doctor` runs without migration errors
- [ ] `cargo test` passes

## TDD Loop
RED: Cannot open DB with version 6 schema
GREEN: Add migration file with full SQL
VERIFY: `cargo run -- doctor` shows healthy DB

## SQL Reference (from PRD)
```sql
-- Merge requests table
CREATE TABLE merge_requests (
  id INTEGER PRIMARY KEY,
  gitlab_id INTEGER UNIQUE NOT NULL,
  project_id INTEGER NOT NULL REFERENCES projects(id),
  iid INTEGER NOT NULL,
  title TEXT,
  description TEXT,
  state TEXT,                         -- opened | merged | closed | locked
  draft INTEGER NOT NULL DEFAULT 0,   -- SQLite boolean
  author_username TEXT,
  source_branch TEXT,
  target_branch TEXT,
  head_sha TEXT,
  references_short TEXT,
  references_full TEXT,
  detailed_merge_status TEXT,
  merge_user_username TEXT,
  created_at INTEGER,                 -- ms epoch UTC
  updated_at INTEGER,
  merged_at INTEGER,
  closed_at INTEGER,
  last_seen_at INTEGER NOT NULL,
  discussions_synced_for_updated_at INTEGER,
  discussions_sync_last_attempt_at INTEGER,
  discussions_sync_attempts INTEGER DEFAULT 0,
  discussions_sync_last_error TEXT,
  web_url TEXT,
  raw_payload_id INTEGER REFERENCES raw_payloads(id)
);
CREATE INDEX idx_mrs_project_updated ON merge_requests(project_id, updated_at);
CREATE UNIQUE INDEX uq_mrs_project_iid ON merge_requests(project_id, iid);
-- ... (see PRD for full index list)

-- Junction tables
CREATE TABLE mr_labels (
  merge_request_id INTEGER REFERENCES merge_requests(id) ON DELETE CASCADE,
  label_id INTEGER REFERENCES labels(id) ON DELETE CASCADE,
  PRIMARY KEY(merge_request_id, label_id)
);

CREATE TABLE mr_assignees (
  merge_request_id INTEGER REFERENCES merge_requests(id) ON DELETE CASCADE,
  username TEXT NOT NULL,
  PRIMARY KEY(merge_request_id, username)
);

CREATE TABLE mr_reviewers (
  merge_request_id INTEGER REFERENCES merge_requests(id) ON DELETE CASCADE,
  username TEXT NOT NULL,
  PRIMARY KEY(merge_request_id, username)
);

-- DiffNote position columns (ALTER TABLE)
ALTER TABLE notes ADD COLUMN position_type TEXT;
ALTER TABLE notes ADD COLUMN position_line_range_start INTEGER;
ALTER TABLE notes ADD COLUMN position_line_range_end INTEGER;
ALTER TABLE notes ADD COLUMN position_base_sha TEXT;
ALTER TABLE notes ADD COLUMN position_start_sha TEXT;
ALTER TABLE notes ADD COLUMN position_head_sha TEXT;

INSERT INTO schema_version (version, applied_at, description)
VALUES (6, strftime('%s', 'now') * 1000, 'Merge requests, MR labels, assignees, reviewers');
```

## Edge Cases
- SQLite does not support ADD CONSTRAINT - FK defined as nullable in CP1
- `locked` state is transitional (merge-in-progress) - store as first-class
- discussions_synced_for_updated_at prevents redundant discussion refetch

Migration 006_merge_requests.sql created and verified. Schema v6 applied successfully with all tables, indexes, and position columns.


Add transform_mr_discussion and transform_notes_with_diff_position

## Background
Extends discussion transformer for MR context. MR discussions can contain DiffNotes with file position metadata. This is critical for code review context in CP3 document generation.

## Approach
Add two new functions to existing `src/gitlab/transformers/discussion.rs`:
1. `transform_mr_discussion()` - Transform discussion with MR reference
2. `transform_notes_with_diff_position()` - Extract DiffNote position metadata

CP1 already has the polymorphic `NormalizedDiscussion` with `NoteableRef` enum - reuse that pattern.

## Files
- `src/gitlab/transformers/discussion.rs` - Add new functions
- `tests/diffnote_tests.rs` - DiffNote position extraction tests
- `tests/mr_discussion_tests.rs` - MR discussion transform tests

## Acceptance Criteria
- [ ] `transform_mr_discussion()` returns `NormalizedDiscussion` with `merge_request_id: Some(local_mr_id)`
- [ ] `transform_notes_with_diff_position()` returns `Result<Vec<NormalizedNote>, String>`
- [ ] DiffNote position fields extracted: `position_old_path`, `position_new_path`, `position_old_line`, `position_new_line`
- [ ] Extended position fields extracted: `position_type`, `position_line_range_start`, `position_line_range_end`
- [ ] SHA triplet extracted: `position_base_sha`, `position_start_sha`, `position_head_sha`
- [ ] Strict timestamp parsing - returns `Err` on invalid timestamps (no `unwrap_or(0)`)
- [ ] `cargo test diffnote` passes
- [ ] `cargo test mr_discussion` passes

## TDD Loop
RED: `cargo test diffnote_position` -> test fails
GREEN: Add position extraction logic
VERIFY: `cargo test diffnote`

## Function Signatures
```rust
/// Transform GitLab discussion for MR context.
/// Reuses existing transform_discussion logic, just with MR reference.
pub fn transform_mr_discussion(
    gitlab_discussion: &GitLabDiscussion,
    local_project_id: i64,
    local_mr_id: i64,
) -> NormalizedDiscussion {
    // Use existing transform_discussion with NoteableRef::MergeRequest(local_mr_id)
    transform_discussion(
        gitlab_discussion,
        local_project_id,
        NoteableRef::MergeRequest(local_mr_id),
    )
}

/// Transform notes with DiffNote position extraction.
/// Returns Result to enforce strict timestamp parsing.
pub fn transform_notes_with_diff_position(
    gitlab_discussion: &GitLabDiscussion,
    local_project_id: i64,
) -> Result<Vec<NormalizedNote>, String>
```

## DiffNote Position Extraction
```rust
// Extract position metadata if present
let (old_path, new_path, old_line, new_line, position_type, lr_start, lr_end, base_sha, start_sha, head_sha) = note
    .position
    .as_ref()
    .map(|pos| (
        pos.old_path.clone(),
        pos.new_path.clone(),
        pos.old_line,
        pos.new_line,
        pos.position_type.clone(),                    // "text" | "image" | "file"
        pos.line_range.as_ref().map(|r| r.start_line),
        pos.line_range.as_ref().map(|r| r.end_line),
        pos.base_sha.clone(),
        pos.start_sha.clone(),
        pos.head_sha.clone(),
    ))
    .unwrap_or((None, None, None, None, None, None, None, None, None, None));
```

## Strict Timestamp Parsing
```rust
// CRITICAL: Return error on invalid timestamps, never zero
let created_at = iso_to_ms(&note.created_at)
    .ok_or_else(|| format\!(
        "Invalid note.created_at for note {}: {}",
        note.id, note.created_at
    ))?;
```

## NormalizedNote Fields for DiffNotes
```rust
NormalizedNote {
    // ... existing fields ...
    // DiffNote position metadata
    position_old_path: old_path,
    position_new_path: new_path,
    position_old_line: old_line,
    position_new_line: new_line,
    // Extended position
    position_type,
    position_line_range_start: lr_start,
    position_line_range_end: lr_end,
    // SHA triplet
    position_base_sha: base_sha,
    position_start_sha: start_sha,
    position_head_sha: head_sha,
}
```

## Edge Cases
- Notes without position should have all position fields as None
- Invalid timestamp should fail the entire discussion (no partial results)
- File renames: `old_path \!= new_path` indicates a renamed file
- Multi-line comments: `line_range` present means comment spans lines 45-48

Implemented transform_mr_discussion() and transform_notes_with_diff_position() with full DiffNote position extraction:
- Extended NormalizedNote with 10 DiffNote position fields (path, line, type, line_range, SHA triplet)
- Added strict timestamp parsing that returns Err on invalid timestamps
- Created 13 diffnote_position_tests covering all extraction paths and error cases
- Created 6 mr_discussion_tests verifying MR reference handling
- All 161 tests passing


Implement MR CLI commands (list, show, count)

## Background
CLI commands for viewing and filtering merge requests. Includes list, show, and count commands with MR-specific filters.

## Approach
Update existing CLI command files:
1. `list.rs` - Add MR listing with filters
2. `show.rs` - Add MR detail view with discussions
3. `count.rs` - Add MR counting with state breakdown

## Files
- `src/cli/commands/list.rs` - Add MR subcommand
- `src/cli/commands/show.rs` - Add MR detail view
- `src/cli/commands/count.rs` - Add MR counting

## Acceptance Criteria
- [ ] `gi list mrs` shows MR table with iid, title, state, author, branches
- [ ] `gi list mrs --state=merged` filters by state
- [ ] `gi list mrs --state=locked` filters locally (not server-side)
- [ ] `gi list mrs --draft` shows only draft MRs
- [ ] `gi list mrs --no-draft` excludes draft MRs
- [ ] `gi list mrs --reviewer=username` filters by reviewer
- [ ] `gi list mrs --target-branch=main` filters by target branch
- [ ] `gi list mrs --source-branch=feature/x` filters by source branch
- [ ] Draft MRs show `[DRAFT]` prefix in title
- [ ] `gi show mr <iid>` displays full detail including discussions
- [ ] DiffNote shows file context: `[src/file.ts:45]`
- [ ] Multi-line DiffNote shows: `[src/file.ts:45-48]`
- [ ] `gi show mr` shows `detailed_merge_status`
- [ ] `gi count mrs` shows total with state breakdown
- [ ] `gi sync-status` shows MR cursor positions
- [ ] `cargo test cli_commands` passes

## TDD Loop
RED: `cargo test list_mrs` -> command not found
GREEN: Add MR subcommand
VERIFY: `gi list mrs --help`

## gi list mrs Output
```
Merge Requests (showing 20 of 1,234)

  !847  Refactor auth to use JWT tokens           merged   @johndoe   main <- feature/jwt   3 days ago
  !846  Fix memory leak in websocket handler      opened   @janedoe   main <- fix/websocket 5 days ago
  !845  [DRAFT] Add dark mode CSS variables       opened   @bobsmith  main <- ui/dark-mode  1 week ago
```

## SQL for MR Listing
```sql
SELECT
    m.iid, m.title, m.state, m.draft, m.author_username,
    m.target_branch, m.source_branch, m.updated_at
FROM merge_requests m
WHERE m.project_id = ?
  AND (? IS NULL OR m.state = ?)           -- state filter
  AND (? IS NULL OR m.draft = ?)           -- draft filter
  AND (? IS NULL OR m.author_username = ?) -- author filter
  AND (? IS NULL OR m.target_branch = ?)   -- target-branch filter
  AND (? IS NULL OR m.source_branch = ?)   -- source-branch filter
  AND (? IS NULL OR EXISTS (               -- reviewer filter
    SELECT 1 FROM mr_reviewers r
    WHERE r.merge_request_id = m.id AND r.username = ?
  ))
ORDER BY m.updated_at DESC
LIMIT ?
```

## gi show mr Output
```
Merge Request !847: Refactor auth to use JWT tokens
================================================================================

Project:        group/project-one
State:          merged
Draft:          No
Author:         @johndoe
Assignees:      @janedoe, @bobsmith
Reviewers:      @alice, @charlie
Source:         feature/jwt
Target:         main
Merge Status:   mergeable
Merged By:      @alice
Merged At:      2024-03-20 14:30:00
Labels:         enhancement, auth, reviewed

Description:
  Moving away from session cookies to JWT-based authentication...

Discussions (8):

  @janedoe (2024-03-16) [src/auth/jwt.ts:45]:
    Should we use a separate signing key for refresh tokens?

    @johndoe (2024-03-16):
      Good point. I'll add a separate key with rotation support.

  @alice (2024-03-18) [RESOLVED]:
    Looks good! Just one nit about the token expiry constant.
```

## DiffNote File Context Display
```rust
// Build file context string
let file_context = match (note.position_new_path, note.position_new_line, note.position_line_range_end) {
    (Some(path), Some(line), Some(end_line)) if line != end_line => {
        format!("[{}:{}-{}]", path, line, end_line)
    }
    (Some(path), Some(line), _) => {
        format!("[{}:{}]", path, line)
    }
    _ => String::new(),
};
```

## gi count mrs Output
```
Merge Requests: 1,234
  opened: 89
  merged: 1,045
  closed: 100
```

## Filter Arguments (clap)
```rust
#[derive(Parser)]
struct ListMrsArgs {
    #[arg(long)]
    state: Option<String>,  // opened|merged|closed|locked|all
    #[arg(long)]
    draft: bool,
    #[arg(long)]
    no_draft: bool,
    #[arg(long)]
    author: Option<String>,
    #[arg(long)]
    assignee: Option<String>,
    #[arg(long)]
    reviewer: Option<String>,
    #[arg(long)]
    target_branch: Option<String>,
    #[arg(long)]
    source_branch: Option<String>,
    #[arg(long)]
    label: Vec<String>,
    #[arg(long)]
    project: Option<String>,
    #[arg(long, default_value = "20")]
    limit: u32,
}
```

## Edge Cases
- `--state=locked` must filter locally (GitLab API doesn't support it)
- Ambiguous MR iid across projects: prompt for `--project`
- Empty discussions: show "No discussions" message
- Multi-line DiffNotes: show line range in context


[CP0] gi version, backup, reset, sync-status commands

## Background

These are the remaining utility commands for CP0. version is trivial. backup creates safety copies before destructive operations. reset provides clean-slate capability. sync-status is a stub for CP0 that will be implemented in CP1.

Reference: docs/prd/checkpoint-0.md sections "gi version", "gi backup", "gi reset", "gi sync-status"

## Approach

**src/cli/commands/version.ts:**
```typescript
import { Command } from 'commander';
import { version } from '../../../package.json' with { type: 'json' };

export const versionCommand = new Command('version')
  .description('Show version information')
  .action(() => {
    console.log(\`gi version \${version}\`);
  });
```

**src/cli/commands/backup.ts:**
```typescript
import { Command } from 'commander';
import { copyFileSync, mkdirSync } from 'node:fs';
import { loadConfig } from '../../core/config';
import { getDbPath, getBackupDir } from '../../core/paths';

export const backupCommand = new Command('backup')
  .description('Create timestamped database backup')
  .action(async (options, command) => {
    const globalOpts = command.optsWithGlobals();
    const config = loadConfig(globalOpts.config);

    const dbPath = getDbPath(config.storage?.dbPath);
    const backupDir = getBackupDir(config.storage?.backupDir);

    mkdirSync(backupDir, { recursive: true });

    // Format: data-2026-01-24T10-30-00.db (colons replaced for Windows compat)
    const timestamp = new Date().toISOString().replace(/:/g, '-').replace(/\\..*/, '');
    const backupPath = \`\${backupDir}/data-\${timestamp}.db\`;

    copyFileSync(dbPath, backupPath);
    console.log(\`Created backup: \${backupPath}\`);
  });
```

**src/cli/commands/reset.ts:**
```typescript
import { Command } from 'commander';
import { unlinkSync, existsSync } from 'node:fs';
import { createInterface } from 'node:readline';
import { loadConfig } from '../../core/config';
import { getDbPath } from '../../core/paths';

export const resetCommand = new Command('reset')
  .description('Delete database and reset all state')
  .option('--confirm', 'Skip confirmation prompt')
  .action(async (options, command) => {
    const globalOpts = command.optsWithGlobals();
    const config = loadConfig(globalOpts.config);
    const dbPath = getDbPath(config.storage?.dbPath);

    if (!existsSync(dbPath)) {
      console.log('No database to reset.');
      return;
    }

    if (!options.confirm) {
      console.log(\`This will delete:\n  - Database: \${dbPath}\n  - All sync cursors\n  - All cached data\n\`);
      // Prompt for 'yes' confirmation
      // If not 'yes', exit 2
    }

    unlinkSync(dbPath);
    // Also delete WAL and SHM files if they exist
    if (existsSync(\`\${dbPath}-wal\`)) unlinkSync(\`\${dbPath}-wal\`);
    if (existsSync(\`\${dbPath}-shm\`)) unlinkSync(\`\${dbPath}-shm\`);

    console.log("Database reset. Run 'gi sync' to repopulate.");
  });
```

**src/cli/commands/sync-status.ts:**
```typescript
// CP0 stub - full implementation in CP1
export const syncStatusCommand = new Command('sync-status')
  .description('Show sync state')
  .action(() => {
    console.log("No sync runs yet. Run 'gi sync' to start.");
  });
```

## Acceptance Criteria

- [ ] `gi version` outputs "gi version X.Y.Z"
- [ ] `gi backup` creates timestamped copy of database
- [ ] Backup filename is Windows-compatible (no colons)
- [ ] Backup directory created if missing
- [ ] `gi reset` prompts for 'yes' confirmation
- [ ] `gi reset --confirm` skips prompt
- [ ] Reset deletes .db, .db-wal, and .db-shm files
- [ ] Reset exits 2 if user doesn't type 'yes'
- [ ] `gi sync-status` outputs stub message

## Files

CREATE:
- src/cli/commands/version.ts
- src/cli/commands/backup.ts
- src/cli/commands/reset.ts
- src/cli/commands/sync-status.ts

## TDD Loop

N/A - simple commands, verify manually:

```bash
gi version
gi backup
ls ~/.local/share/gi/backups/
gi reset  # type 'no'
gi reset --confirm
ls ~/.local/share/gi/data.db  # should not exist
gi sync-status
```

## Edge Cases

- Backup when database doesn't exist - show clear error
- Reset when database doesn't exist - show "No database to reset"
- WAL/SHM files may not exist - check before unlinking
- Timestamp with milliseconds could cause very long filename
- readline prompt in non-interactive terminal - handle SIGINT


Rename GiError to LoreError across codebase

## Background
The codebase currently uses `GiError` as the primary error enum name (legacy from when the project was called "gi"). Checkpoint 3 introduces new modules (documents, search, embedding) that import error types. Renaming before Gate A work begins prevents every subsequent bead from needing to reference the old name and avoids merge conflicts across parallel work streams.

## Approach
Mechanical find-and-replace using `ast-grep` or `sed`:
1. Rename the enum declaration in `src/core/error.rs`: `pub enum GiError` -> `pub enum LoreError`
2. Update the type alias: `pub type Result<T> = std::result::Result<T, LoreError>;`
3. Update re-exports in `src/core/mod.rs` and `src/lib.rs`
4. Update all `use` statements across ~16 files that import `GiError`
5. Update any `GiError::` variant construction sites
6. Run `cargo build` to verify no references remain

**Do NOT change:**
- Error variant names (ConfigNotFound, etc.) — only the enum name
- ErrorCode enum — it's already named correctly
- RobotError — already named correctly

## Acceptance Criteria
- [ ] `cargo build` succeeds with zero warnings about GiError
- [ ] `rg GiError src/` returns zero results
- [ ] `rg LoreError src/core/error.rs` shows the enum declaration
- [ ] `src/core/mod.rs` re-exports `LoreError` (not `GiError`)
- [ ] `src/lib.rs` re-exports `LoreError`
- [ ] All `use crate::core::error::LoreError` imports compile

## Files
- `src/core/error.rs` — enum rename + type alias
- `src/core/mod.rs` — re-export update
- `src/lib.rs` — re-export update
- All files matching `rg 'GiError' src/` (~16 files: ingestion/*.rs, cli/commands/*.rs, gitlab/*.rs, main.rs)

## TDD Loop
RED: `cargo build` fails after renaming enum but before fixing imports
GREEN: Fix all imports; `cargo build` succeeds
VERIFY: `cargo build && rg GiError src/ && echo "FAIL: GiError references remain" || echo "PASS: clean"`

## Edge Cases
- Some files may use `GiError` in string literals (error messages) — do NOT rename those, only type references
- `impl From<X> for GiError` blocks must become `impl From<X> for LoreError`
- The `thiserror` derive macro on the enum does not reference the name, so no macro changes needed

Completed: renamed GiError to LoreError across all 16 files, cargo build + 164 tests pass


Implement lore search CLI command (lexical mode)

## Background
The search CLI command is the user-facing entry point for Gate A lexical search. It orchestrates the search pipeline: query parsing -> FTS5 search -> filter application -> result hydration (single round-trip) -> display. Gate B extends this same command with --mode=hybrid and --mode=semantic. The hydration query is critical for performance — it fetches all display fields + labels + paths in one SQL query using json_each() + json_group_array().

## Approach
Create `src/cli/commands/search.rs` per PRD Section 3.4.

**Key types:**
- `SearchResultDisplay` — display-ready result with all fields (dates as ISO via `ms_to_iso`)
- `ExplainData` — ranking explanation for --explain flag (vector_rank, fts_rank, rrf_score)
- `SearchResponse` — wrapper with query, mode, total_results, results, warnings

**Core function:**
```rust
pub fn run_search(
    config: &Config,
    query: &str,
    mode: SearchMode,
    filters: SearchFilters,
    explain: bool,
) -> Result<SearchResponse>
```

**Pipeline:**
1. Parse query + filters
2. Execute search based on mode -> ranked doc_ids (+ explain ranks)
3. Apply post-retrieval filters via apply_filters() preserving ranking order
4. Hydrate results in single DB round-trip using json_each + json_group_array
5. Attach snippets: prefer FTS snippet, fallback to `generate_fallback_snippet()` for semantic-only
6. Convert timestamps via `ms_to_iso()` from `crate::core::time`
7. Build SearchResponse

**Hydration query (critical — single round-trip, replaces 60 queries with 1):**
```sql
SELECT d.id, d.source_type, d.title, d.url, d.author_username,
       d.created_at, d.updated_at, d.content_text,
       p.path_with_namespace AS project_path,
       (SELECT json_group_array(dl.label_name)
        FROM document_labels dl WHERE dl.document_id = d.id) AS labels,
       (SELECT json_group_array(dp.path)
        FROM document_paths dp WHERE dp.document_id = d.id) AS paths
FROM json_each(?) AS j
JOIN documents d ON d.id = j.value
JOIN projects p ON p.id = d.project_id
ORDER BY j.key
```

**Human output uses `console::style` for terminal formatting:**
```rust
use console::style;
// Type prefix in cyan
println!("[{}] {} - {} ({})", i+1, style(type_prefix).cyan(), title, score);
// URL in dim
println!("    {}", style(url).dim());
```

**JSON robot mode includes elapsed_ms in meta (PRD Section 3.4):**
```rust
pub fn print_search_results_json(response: &SearchResponse, elapsed_ms: u64) {
    let output = serde_json::json!({
        "ok": true,
        "data": response,
        "meta": { "elapsed_ms": elapsed_ms }
    });
    println!("{}", serde_json::to_string_pretty(&output).unwrap());
}
```

**CLI args in `src/cli/mod.rs` (PRD Section 3.4):**
```rust
#[derive(Args)]
pub struct SearchArgs {
    query: String,
    #[arg(long, default_value = "hybrid")]
    mode: String,
    #[arg(long, value_name = "TYPE")]
    r#type: Option<String>,
    #[arg(long)]
    author: Option<String>,
    #[arg(long)]
    project: Option<String>,
    #[arg(long, action = clap::ArgAction::Append)]
    label: Vec<String>,
    #[arg(long)]
    path: Option<String>,
    #[arg(long)]
    after: Option<String>,
    #[arg(long)]
    updated_after: Option<String>,
    #[arg(long, default_value = "20")]
    limit: usize,
    #[arg(long)]
    explain: bool,
    #[arg(long, default_value = "safe")]
    fts_mode: String,
}
```

**IMPORTANT: default_value = "hybrid"** — When Ollama is unavailable, hybrid mode gracefully degrades to FTS-only with a warning (not an error). `lore search` works without Ollama.

## Acceptance Criteria
- [ ] Default mode is "hybrid" (not "lexical") per PRD
- [ ] Hybrid mode degrades gracefully to FTS-only when Ollama unavailable (warning, not error)
- [ ] All filters work (type, author, project, label, path, after, updated_after, limit)
- [ ] Label filter uses `clap::ArgAction::Append` for repeatable --label flags
- [ ] Hydration in single query (not N+1) — uses json_each + json_group_array
- [ ] Timestamps converted via `ms_to_iso()` for display (ISO format)
- [ ] Human output uses `console::style` for colored type prefix (cyan) and dim URLs
- [ ] JSON robot mode includes `elapsed_ms` in `meta` field
- [ ] Semantic-only results get fallback snippets via `generate_fallback_snippet()`
- [ ] Empty results show friendly message: "No results found for 'query'"
- [ ] "No data indexed" message if documents table empty
- [ ] --explain shows vector_rank, fts_rank, rrf_score per result
- [ ] --fts-mode=safe preserves prefix `*` while escaping special chars
- [ ] --fts-mode=raw passes FTS5 MATCH syntax through unchanged
- [ ] --mode=semantic with 0% embedding coverage returns LoreError::EmbeddingsNotBuilt (not OllamaUnavailable)
- [ ] SearchArgs registered in cli/mod.rs with Clap derive
- [ ] `cargo build` succeeds

## Files
- `src/cli/commands/search.rs` — new file
- `src/cli/commands/mod.rs` — add `pub mod search;`
- `src/cli/mod.rs` — add SearchArgs struct, wire up search subcommand
- `src/main.rs` — add search command handler

## TDD Loop
RED: Integration test requiring DB with documents
- `test_lexical_search_returns_results` — FTS search returns hits
- `test_hydration_single_query` — verify no N+1 (mock/inspect query count)
- `test_json_output_includes_elapsed` — robot mode JSON has meta.elapsed_ms
- `test_empty_results_message` — zero results shows friendly message
- `test_fallback_snippet` — semantic-only result uses truncated content
GREEN: Implement run_search + hydrate_results + print functions
VERIFY: `cargo build && cargo test search`

## Edge Cases
- Zero results: display friendly empty message, JSON returns empty array
- --mode=semantic with 0% embedding coverage: return LoreError::EmbeddingsNotBuilt
- json_group_array returns "[]" for documents with no labels — parse as empty array
- Very long snippets: truncated at display time
- Hybrid default works without Ollama: degrades to FTS-only with warning
- ms_to_iso with epoch 0: return valid ISO string (not crash)

Implemented search CLI with FTS5 + RRF ranking, single-query hydration (json_each + json_group_array), adaptive recall, all filters, --explain, human + JSON output. Builds clean.


WHO: Robot JSON output for all 5 modes

## Background

Robot-mode JSON output following the standard lore envelope: `{"ok":true,"data":{...},"meta":{"elapsed_ms":N}}`. Includes both raw CLI args (input) and computed values (resolved_input) for agent reproducibility.

## Approach

### Envelope structs:
```rust
#[derive(Serialize)]
struct WhoJsonEnvelope { ok: bool, data: WhoJsonData, meta: RobotMeta }

#[derive(Serialize)]
struct WhoJsonData {
    mode: String,
    input: serde_json::Value,
    resolved_input: serde_json::Value,
    #[serde(flatten)]
    result: serde_json::Value,
}
```

### print_who_json(run, args, elapsed_ms):
- `input`: raw CLI args `{ target, path, project, since, limit }`
- `resolved_input`: `{ mode, project_id, project_path, since_ms, since_iso, since_mode, limit }`
- `result`: mode-specific JSON via *_to_json() functions using serde_json::json\!() macro

### Mode-specific JSON fields:
- **Expert**: path_query, path_match, truncated, experts[] with ISO last_seen_at
- **Workload**: username, 4 entity arrays with ref/project_path/ISO timestamps, summary{} counts, truncation{} per-section bools
- **Reviews**: username, total_diffnotes, categorized_count, mrs_reviewed, categories[] with rounded percentages
- **Active**: total_unresolved_in_window, truncated, discussions[] with discussion_id + participants + participants_total + participants_truncated
- **Overlap**: path_query, path_match, truncated, users[] with role + touch counts + mr_refs + mr_refs_total + mr_refs_truncated

### Key implementation detail — #[serde(flatten)] on result field:
The `result` field uses `#[serde(flatten)]` so mode-specific keys are merged into the top-level data object rather than nested. This means `data.experts` (not `data.result.experts`).

### Timestamps: all use ms_to_iso() for ISO 8601 format in JSON output

### Percentage rounding: Reviews categories use `(percentage * 10.0).round() / 10.0` for single decimal precision

## Files

- `src/cli/commands/who.rs`

## TDD Loop

No unit tests for JSON serialization — the serde_json::json\!() macro produces correct JSON by construction. Verification via manual robot mode invocation.
VERIFY: `cargo check && cargo run --release -- -J who src/features/global-search/ | python3 -m json.tool`

## Acceptance Criteria

- [ ] cargo check passes
- [ ] JSON output validates (valid JSON, no trailing content)
- [ ] input echoes raw CLI args
- [ ] resolved_input includes since_mode tri-state (default/explicit/none)
- [ ] All timestamps in ISO 8601 format
- [ ] Bounded metadata present (participants_total, mr_refs_total, truncation object)
- [ ] #[serde(flatten)] correctly merges result keys into data object

## Edge Cases

- `#[serde(flatten)]` on the result Value means mode-specific keys must not collide with mode/input/resolved_input — verified by convention (expert uses "experts", workload uses "username", etc.)
- serde_json::json\!() panics are impossible for valid Rust expressions, but verify that all row.get() values in *_to_json() handle None fields correctly (author_username in WorkloadMr is Option<String> — json\!() serializes None as null, which is correct)
- ms_to_iso() must handle 0 and very old timestamps gracefully — produces "1970-01-01T00:00:00Z" for epoch 0, which is valid
- Reviews percentage rounding: categories summing to >100% due to rounding is acceptable (display artifact) — agent consumers should not assert sum == 100
- println\!() for JSON output (not eprintln\!) — errors go to stderr, data to stdout, matching all other robot-mode commands
- If a mode returns empty results, the JSON should still be valid (empty arrays, zero counts) — serde handles this correctly

Implemented by agent team: migration 017, CLI skeleton, all 5 query modes, human+robot output, 20 tests. All quality gates pass.


[CP1] gi list issues command

List issues from the database.

Flags:
- --limit=N (default: 20)
- --project=PATH (filter by project)
- --state=opened|closed|all (default: all)

Output: Table with iid, title, state, author, relative time

Files: src/cli/commands/list.ts
Done when: List displays issues with proper filtering and formatting


[CP1] gi list issues command

## Background

The `gi list issues` command displays a paginated list of issues from the local database. It supports filtering by project and state, with configurable limit. This provides quick access to synced issues without opening GitLab.

## Approach

### Module: src/cli/commands/list.rs

### Clap Definition

```rust
#[derive(Args)]
pub struct ListArgs {
    /// Entity type to list
    #[arg(value_parser = ["issues", "mrs"])]
    pub entity: String,

    /// Maximum results
    #[arg(long, default_value = "20")]
    pub limit: usize,

    /// Filter by project path
    #[arg(long)]
    pub project: Option<String>,

    /// Filter by state
    #[arg(long, value_parser = ["opened", "closed", "all"])]
    pub state: Option<String>,
}
```

### Handler Function

```rust
pub async fn handle_list(args: ListArgs, conn: &Connection) -> Result<()>
```

### Query (for issues)

```sql
SELECT i.iid, i.title, i.state, i.author_username, i.updated_at, p.path
FROM issues i
JOIN projects p ON i.project_id = p.id
WHERE (p.path = ? OR ? IS NULL)
  AND (i.state = ? OR ? IS NULL OR ? = 'all')
ORDER BY i.updated_at DESC
LIMIT ?
```

### Output Format (matches PRD)

```
Issues (showing 20 of 3,801)

  #1234  Authentication redesign                       opened   @johndoe   3 days ago
  #1233  Fix memory leak in cache                      closed   @janedoe   5 days ago
  #1232  Add dark mode support                         opened   @bobsmith  1 week ago
  ...
```

### Column Layout

| Column | Width | Alignment |
|--------|-------|-----------|
| IID | 6 | right |
| Title | 45 | left (truncate) |
| State | 8 | left |
| Author | 12 | left |
| Updated | 12 | right (relative) |

### Relative Time Formatting

```rust
fn format_relative_time(ms_epoch: i64) -> String {
    let now = now_ms();
    let diff = now - ms_epoch;
    match diff {
        d if d < 60_000 => "just now".to_string(),
        d if d < 3_600_000 => format!("{} min ago", d / 60_000),
        d if d < 86_400_000 => format!("{} hours ago", d / 3_600_000),
        d if d < 604_800_000 => format!("{} days ago", d / 86_400_000),
        d if d < 2_592_000_000 => format!("{} weeks ago", d / 604_800_000),
        _ => format!("{} months ago", diff / 2_592_000_000),
    }
}
```

## Acceptance Criteria

- [ ] Lists issues ordered by updated_at DESC
- [ ] Shows "showing X of Y" with total count
- [ ] Respects --limit parameter
- [ ] --project filters to single project
- [ ] --state filters to opened/closed/all
- [ ] Title truncated if longer than column width
- [ ] Updated time shown as relative ("3 days ago")

## Files

- src/cli/commands/mod.rs (add `pub mod list;`)
- src/cli/commands/list.rs (create)
- src/cli/mod.rs (add List variant to Commands enum)

## TDD Loop

RED:
```rust
#[tokio::test] async fn list_issues_shows_correct_columns()
#[tokio::test] async fn list_issues_respects_limit()
#[tokio::test] async fn list_issues_filters_by_project()
#[tokio::test] async fn list_issues_filters_by_state()
```

GREEN: Implement handler with query and formatting

VERIFY: `cargo test list_issues`

## Edge Cases

- No issues match filters - show "No issues found"
- Title exactly 45 chars - no truncation
- Title 46+ chars - truncate with "..."
- --state=all shows both opened and closed
- Default state filter is all (not just opened)


[CP1] Issue transformer with label extraction

## Background

The issue transformer converts GitLab API responses into our local schema format. It extracts core fields and, critically, the array of label names from each issue. This transformer is pure logic with no I/O, making it easy to test.

## Approach

Create a transformer module with a function that:
1. Takes a `GitLabIssue` and returns an `IssueRow` struct
2. Extracts the `labels: Vec<String>` directly from the issue (GitLab returns label names as strings)

### Structs

```rust
// src/gitlab/transformers/issue.rs

pub struct IssueRow {
    pub gitlab_id: i64,
    pub iid: i64,
    pub project_id: i64,
    pub title: String,
    pub description: Option<String>,
    pub state: String,
    pub author_username: String,
    pub created_at: i64,      // ms epoch UTC
    pub updated_at: i64,      // ms epoch UTC
    pub web_url: String,
}

pub struct IssueWithLabels {
    pub issue: IssueRow,
    pub label_names: Vec<String>,
}
```

### Function

```rust
pub fn transform_issue(issue: GitLabIssue) -> Result<IssueWithLabels, TransformError> {
    // Parse ISO 8601 timestamps to ms epoch
    // Extract author.username
    // Return IssueWithLabels with label_names from issue.labels
}
```

## Acceptance Criteria

- [ ] `IssueRow` struct exists with all fields from schema
- [ ] `IssueWithLabels` struct bundles issue + label names
- [ ] `transform_issue` parses ISO 8601 to ms epoch correctly
- [ ] `transform_issue` handles missing description (None)
- [ ] Label names are preserved exactly as received from GitLab
- [ ] Unit tests cover all edge cases

## Files

- src/gitlab/transformers/mod.rs (create, add `pub mod issue;`)
- src/gitlab/transformers/issue.rs (create)

## TDD Loop

RED:
```rust
// tests/unit/issue_transformer_test.rs
#[test] fn transforms_issue_with_all_fields()
#[test] fn handles_missing_description()
#[test] fn extracts_label_names()
#[test] fn parses_timestamps_to_ms_epoch()
```

GREEN: Implement transform_issue function

VERIFY: `cargo test issue_transformer`

## Edge Cases

- GitLab timestamps are ISO 8601 with timezone - use chrono::DateTime::parse_from_rfc3339
- Description can be null in GitLab API - map to Option<String>
- Empty labels array is valid - return empty Vec
- Do NOT parse labels_details - it varies across GitLab versions

Implemented IssueRow, IssueWithLabels, transform_issue with 6 passing unit tests covering all edge cases


[CP0] Database setup with migrations and app lock

## Background

The database is the backbone of gitlab-inbox. SQLite with WAL mode for performance, foreign keys for integrity, and proper pragmas for reliability. Migrations allow schema evolution. App lock prevents concurrent sync corruption.

Reference: docs/prd/checkpoint-0.md sections "Database Schema", "SQLite Runtime Pragmas", "App Lock Mechanism"

## Approach

**src/core/db.ts:**
```typescript
import Database from 'better-sqlite3';
import { join, dirname } from 'node:path';
import { mkdirSync, readdirSync, readFileSync } from 'node:fs';
import { getDbPath } from './paths';
import { dbLogger } from './logger';

export function createConnection(dbPath: string): Database.Database {
  mkdirSync(dirname(dbPath), { recursive: true });
  const db = new Database(dbPath);

  // Production-grade pragmas
  db.pragma('journal_mode = WAL');
  db.pragma('synchronous = NORMAL');
  db.pragma('foreign_keys = ON');
  db.pragma('busy_timeout = 5000');
  db.pragma('temp_store = MEMORY');

  return db;
}

export function runMigrations(db: Database.Database, migrationsDir: string): void {
  // Create schema_version table if not exists
  // Read migration files sorted by version
  // Apply migrations not yet applied
  // Track in schema_version table
}
```

**migrations/001_initial.sql:**
Full schema with tables: schema_version, projects, sync_runs, app_locks, sync_cursors, raw_payloads

**src/core/lock.ts:**
AppLock class with:
- acquire(force?): acquires lock or throws DatabaseLockError
- release(): releases lock and stops heartbeat
- Heartbeat timer that updates heartbeat_at every N seconds
- Stale lock detection (heartbeat_at > staleLockMinutes ago)

## Acceptance Criteria

- [ ] createConnection() creates parent directories if missing
- [ ] WAL mode verified: `db.pragma('journal_mode')` returns 'wal'
- [ ] Foreign keys verified: `db.pragma('foreign_keys')` returns 1
- [ ] busy_timeout verified: `db.pragma('busy_timeout')` returns 5000
- [ ] 001_initial.sql creates all 6 tables
- [ ] schema_version shows version 1 after migration
- [ ] AppLock.acquire() succeeds for first caller
- [ ] AppLock.acquire() throws DatabaseLockError for second concurrent caller
- [ ] Stale lock (heartbeat > 10 min old) can be taken over
- [ ] tests/unit/db.test.ts passes (8 tests)
- [ ] tests/integration/app-lock.test.ts passes (6 tests)

## Files

CREATE:
- src/core/db.ts
- src/core/lock.ts
- migrations/001_initial.sql
- tests/unit/db.test.ts
- tests/integration/app-lock.test.ts

## TDD Loop

RED:
```typescript
// tests/unit/db.test.ts
describe('Database', () => {
  it('creates database file if not exists')
  it('applies migrations in order')
  it('sets WAL journal mode')
  it('enables foreign keys')
  it('sets busy_timeout=5000')
  it('sets synchronous=NORMAL')
  it('sets temp_store=MEMORY')
  it('tracks schema version')
})

// tests/integration/app-lock.test.ts
describe('App Lock', () => {
  it('acquires lock successfully')
  it('updates heartbeat during operation')
  it('detects stale lock and recovers')
  it('refuses concurrent acquisition')
  it('allows force override')
  it('releases lock on completion')
})
```

GREEN: Implement db.ts, lock.ts, 001_initial.sql

VERIFY:
```bash
npm run test -- tests/unit/db.test.ts
npm run test -- tests/integration/app-lock.test.ts
```

## Edge Cases

- Migration file with syntax error should rollback and throw MigrationError
- Lock heartbeat timer must be unref()'d to not block process exit
- Database file permissions - fail clearly if not writable
- Concurrent lock tests need separate database files


OBSERV Epic: Phase 5 - Rate Limit + Retry Instrumentation

Enhanced logging in GitLab HTTP client for rate limits and retries. Structured fields on retry/rate-limit events. StageTiming gets rate_limit_hits and retries counters.

Depends on: Phase 2 (spans for context)
Parallel with: Phase 3

Files: src/gitlab/client.rs, src/core/metrics.rs

Acceptance criteria (PRD Section 6.5):
- 429 events log at INFO with path, attempt, retry_after_secs, status_code
- Retry events log with path, attempt, error
- StageTiming includes rate_limit_hits and retries (omitted when zero)
- lore -v sync shows retry activity on stderr
- Rate limit counts included in metrics_json

All Phase 5 tasks complete: structured rate-limit logging (bd-12ae) and rate_limit_hits/retries counters in StageTiming (bd-3vqk)


OBSERV Epic: Phase 4 - Sync History Enrichment

Wire up sync_runs INSERT/UPDATE lifecycle (table exists but nothing writes to it), schema migration 014, enhanced sync-status with recent runs and metrics.

Depends on: Phase 3 (needs Vec<StageTiming> to store in metrics_json)
Unblocks: nothing (terminal phase)

Files: migrations/014_sync_runs_enrichment.sql (new), src/core/sync_run.rs (new), src/cli/commands/sync.rs, src/cli/commands/ingest.rs, src/cli/commands/sync_status.rs

Acceptance criteria (PRD Section 6.4):
- lore sync creates sync_runs row with status=running, updated to succeeded/failed
- sync_runs.run_id matches log files and robot JSON
- metrics_json contains serialized Vec<StageTiming>
- lore sync-status shows last 10 runs with metrics
- Failed syncs record error and partial metrics
- Migration 014 applies cleanly

Phase 4 complete: migration 014, SyncRunRecorder, wiring, sync-status enhancement


Implement search filters module

## Background
Search filters are applied post-retrieval to narrow results by source type, author, project, date, labels, and file paths. The filter module must preserve ranking order from the search pipeline (FTS/RRF scores). It uses SQLite's JSON1 extension (json_each) to pass ranked document IDs efficiently and maintain their original order.

## Approach
Create `src/search/filters.rs` per PRD Section 3.3. The full implementation is specified in the PRD including the SQL query.

**Key types:**
- `SearchFilters` struct with all filter fields + `has_any_filter()` + `clamp_limit()`
- `PathFilter` enum: `Prefix(String)` (trailing `/`) or `Exact(String)`

**Core function:**
```rust
pub fn apply_filters(
    conn: &Connection,
    document_ids: &[i64],
    filters: &SearchFilters,
) -> Result<Vec<i64>>
```

**SQL pattern (JSON1 for ordered ID passing):**
```sql
SELECT d.id
FROM json_each(?) AS j
JOIN documents d ON d.id = j.value
WHERE 1=1
  AND d.source_type = ?      -- if source_type filter set
  AND d.author_username = ?  -- if author filter set
  -- ... dynamic WHERE clauses
ORDER BY j.key               -- preserves ranking order
LIMIT ?
```

**Filter logic:**
- Labels: AND logic via `EXISTS (SELECT 1 FROM document_labels dl WHERE dl.document_id = d.id AND dl.label_name = ?)`
- Path prefix: `LIKE ? ESCAPE '\\'` with escaped wildcards
- Path exact: `= ?`
- Limit: clamped to [1, 100], default 20

## Acceptance Criteria
- [ ] source_type filter works (issue, merge_request, discussion)
- [ ] author filter: exact username match
- [ ] project_id filter: restricts to single project
- [ ] after filter: created_at >= value
- [ ] updated_after filter: updated_at >= value
- [ ] labels filter: AND logic (all specified labels must be present)
- [ ] path exact filter: matches exact path string
- [ ] path prefix filter: trailing `/` triggers LIKE with escaped wildcards
- [ ] Ranking order preserved (ORDER BY j.key from json_each)
- [ ] Limit clamped: 0 -> 20 (default), 200 -> 100 (max)
- [ ] Empty document_ids returns empty Vec
- [ ] Multiple filters compose correctly (all applied via AND)
- [ ] `cargo test filters` passes

## Files
- `src/search/filters.rs` — new file
- `src/search/mod.rs` — add `pub use filters::{SearchFilters, PathFilter, apply_filters};`

## TDD Loop
RED: Tests in `filters.rs` `#[cfg(test)] mod tests`:
- `test_no_filters` — all docs returned up to limit
- `test_source_type_filter` — only issues returned
- `test_author_filter` — exact match
- `test_labels_and_logic` — must have ALL specified labels
- `test_path_exact` — matches exact path
- `test_path_prefix` — trailing slash matches prefix
- `test_limit_clamping` — 0 -> 20, 200 -> 100
- `test_ranking_preserved` — output order matches input order
- `test_has_any_filter` — true when any filter set, false when default
GREEN: Implement apply_filters with dynamic SQL
VERIFY: `cargo test filters`

## Edge Cases
- Path containing SQL LIKE wildcards (`%`, `_`): must be escaped before LIKE
- Empty labels list: no label filter applied (not "must have zero labels")
- `has_any_filter()` returns false for default SearchFilters (no filters set)
- Large document_ids array (1000+): JSON1 handles efficiently

Completed: SearchFilters with has_any_filter/clamp_limit, PathFilter enum, apply_filters with dynamic SQL + json_each ordering, escape_like, 8 tests pass


[CP1] Final validation - tests, smoke tests, integrity checks

Run all tests and perform data integrity checks.

Validation steps:
1. Run all unit tests (vitest)
2. Run all integration tests
3. Run ESLint
4. Run TypeScript strict check
5. Manual smoke tests per PRD table
6. Data integrity SQL checks:
   - Issue count matches GitLab
   - Every issue has raw_payload
   - Labels in junction exist in labels table
   - sync_cursors has entry per project
   - Re-run fetches 0 new items
   - Discussion count > 0
   - Every discussion has >= 1 note
   - individual_note=true has exactly 1 note

Files: All CP1 files
Done when: All gate criteria from Definition of Done pass


Implement lore generate-docs CLI command

## Background
The generate-docs CLI command is the user-facing wrapper around the document regeneration pipeline. It has two modes: incremental (default, processes dirty_sources queue only) and full (seeds dirty_sources with ALL entities, then drains). Both modes use the same regenerator codepath to avoid logic divergence. Full mode uses keyset pagination (WHERE id > last_id) for seeding to avoid O(n^2) OFFSET degradation on large tables.

## Approach
Create `src/cli/commands/generate_docs.rs` per PRD Section 2.4.

**Core function:**
```rust
pub fn run_generate_docs(
    config: &Config,
    full: bool,
    project_filter: Option<&str>,
) -> Result<GenerateDocsResult>
```

**Full mode seeding (keyset pagination):**
```rust
const FULL_MODE_CHUNK_SIZE: usize = 2000;

// For each source type (issues, MRs, discussions):
let mut last_id: i64 = 0;
loop {
    let tx = conn.transaction()?;
    let inserted = tx.execute(
        "INSERT INTO dirty_sources (source_type, source_id, queued_at, ...)
         SELECT 'issue', id, ?, 0, NULL, NULL, NULL
         FROM issues WHERE id > ? ORDER BY id LIMIT ?
         ON CONFLICT(source_type, source_id) DO NOTHING",
        params![now_ms(), last_id, FULL_MODE_CHUNK_SIZE],
    )?;
    if inserted == 0 { tx.commit()?; break; }
    // Advance keyset cursor...
    tx.commit()?;
}
```

**After draining (full mode only):**
```sql
INSERT INTO documents_fts(documents_fts) VALUES('optimize')
```

**CLI args:**
```rust
#[derive(Args)]
pub struct GenerateDocsArgs {
    #[arg(long)]
    full: bool,
    #[arg(long)]
    project: Option<String>,
}
```

**Output:** Human-readable table + JSON robot mode.

## Acceptance Criteria
- [ ] Default mode (no --full): processes only existing dirty_sources entries
- [ ] --full mode: seeds dirty_sources with ALL issues, MRs, and discussions
- [ ] Full mode uses keyset pagination (WHERE id > last_id, not OFFSET)
- [ ] Full mode chunk size is 2000
- [ ] Full mode does FTS optimize after completion
- [ ] Both modes use regenerate_dirty_documents() (same codepath)
- [ ] Progress bar shown in human mode (via indicatif)
- [ ] JSON output in robot mode with GenerateDocsResult
- [ ] GenerateDocsResult has issues/mrs/discussions/total/truncated/skipped counts
- [ ] `cargo build` succeeds

## Files
- `src/cli/commands/generate_docs.rs` — new file
- `src/cli/commands/mod.rs` — add `pub mod generate_docs;`
- `src/cli/mod.rs` — add GenerateDocsArgs, wire up generate-docs subcommand
- `src/main.rs` — add generate-docs command handler

## TDD Loop
RED: Integration test with seeded DB
GREEN: Implement run_generate_docs with seeding + drain
VERIFY: `cargo build && cargo test generate_docs`

## Edge Cases
- Empty database (no issues/MRs/discussions): full mode seeds nothing, returns all-zero counts
- --project filter in full mode: only seed dirty_sources for entities in that project
- Interrupted full mode: dirty_sources entries persist (ON CONFLICT DO NOTHING), resume by re-running
- FTS optimize on empty FTS table: no-op (safe)

Implemented generate-docs command with incremental + full mode, keyset pagination seeding, FTS optimize, project filter, human + JSON output. Builds clean.


Epic: Gate C - Sync MVP

## Background
Gate C adds the sync orchestrator and queue infrastructure that makes the search pipeline incremental and self-maintaining. It introduces dirty source tracking (change detection during ingestion), the discussion fetch queue, and the unified lore sync command that orchestrates the full pipeline. Gate C also adds integrity checks and repair paths.

## Gate C Deliverables
1. Orchestrated lore sync command with incremental doc regen + re-embedding
2. Integrity checks + repair paths for FTS/embeddings consistency

## Bead Dependencies (execution order, after Gate A)
1. **bd-mem** — Shared backoff utility (no deps, shared with Gate B)
2. **bd-38q** — Dirty source tracking (blocked by bd-36p, bd-hrs, bd-mem)
3. **bd-1je** — Discussion queue (blocked by bd-hrs, bd-mem)
4. **bd-1i2** — Integrate dirty tracking into ingestion (blocked by bd-38q)
5. **bd-1x6** — Sync CLI (blocked by bd-38q, bd-1je, bd-1i2, bd-3qs, bd-2sx)

## Acceptance Criteria
- [ ] `lore sync` runs full pipeline: ingest -> generate-docs -> embed
- [ ] `lore sync --full` does full re-sync + regeneration
- [ ] `lore sync --no-embed` skips embedding stage
- [ ] Dirty tracking: upserted entities automatically marked for regeneration
- [ ] Queue draining: dirty_sources fully drained in bounded batch loop
- [ ] Backoff: failed items use exponential backoff with jitter
- [ ] `lore stats --check` detects inconsistencies
- [ ] `lore stats --repair` fixes FTS/embedding inconsistencies

All Gate C sub-beads complete: backoff utility, dirty tracking, discussion queue, ingestion integration, sync CLI, stats CLI


Add 'lore count events' command with robot mode

## Background
Need to verify event ingestion and report counts by type. The existing count command (src/cli/commands/count.rs) handles issues, mrs, discussions, notes with both human and robot output. This adds 'events' as a new count subcommand.

## Approach
Extend the existing count command in src/cli/commands/count.rs:

1. Add CountTarget::Events variant (or string match) in the count dispatcher
2. Query each event table with GROUP BY entity type:
```sql
SELECT
  CASE WHEN issue_id IS NOT NULL THEN 'issue' ELSE 'merge_request' END as entity_type,
  COUNT(*) as count
FROM resource_state_events
GROUP BY entity_type;
-- (repeat for label and milestone events)
```

3. Human output: table format
```
Event Type       Issues  MRs    Total
State events     1,234   567    1,801
Label events     2,345   890    3,235
Milestone events   456   123      579
Total            4,035   1,580  5,615
```

4. Robot JSON:
```json
{
  "ok": true,
  "data": {
    "state_events": {"issue": 1234, "merge_request": 567, "total": 1801},
    "label_events": {"issue": 2345, "merge_request": 890, "total": 3235},
    "milestone_events": {"issue": 456, "merge_request": 123, "total": 579},
    "total": 5615
  }
}
```

5. Register in CLI: add "events" to count's entity_type argument in src/cli/mod.rs

## Acceptance Criteria
- [ ] `lore count events` shows correct counts by event type and entity type
- [ ] Robot JSON matches the schema above
- [ ] Works with empty tables (all zeros)
- [ ] Does not error if migration 011 hasn't been applied (graceful degradation or "no event tables" message)

## Files
- src/cli/commands/count.rs (add events counting logic)
- src/cli/mod.rs (add "events" to count's accepted entity types)

## TDD Loop
RED: tests/count_tests.rs (or extend existing):
- `test_count_events_empty_tables` - verify all zeros on fresh DB
- `test_count_events_with_data` - seed state + label events, verify correct counts
- `test_count_events_robot_json` - verify JSON structure

GREEN: Add the events branch to count command

VERIFY: `cargo test count -- --nocapture`

## Edge Cases
- Tables don't exist if user hasn't run migrate — check table existence first or catch the error
- COUNT with GROUP BY returns no rows for empty tables — need to handle missing entity types as 0

Added 'events' to count CLI parser, run_count_events function, print_event_count (table format) and print_event_count_json (structured JSON). Wired into handle_count in main.rs.


OBSERV: Add rate_limit_hits and retries counters to StageTiming

## Background
MetricsLayer counts span timing but doesn't yet count rate-limit hits and retries. These counters complete the observability picture, showing HOW MUCH time was spent waiting vs. working.

## Approach
### src/core/metrics.rs - StageTiming struct

Add two new fields:
```rust
#[derive(Debug, Clone, Serialize)]
pub struct StageTiming {
    // ... existing fields ...
    #[serde(skip_serializing_if = "is_zero")]
    pub rate_limit_hits: usize,
    #[serde(skip_serializing_if = "is_zero")]
    pub retries: usize,
}
```

### src/core/metrics.rs - MetricsLayer

The structured log events from bd-12ae use info!() with specific fields (status_code=429, "Rate limited, retrying"). MetricsLayer needs to count these events within each span.

Add to SpanData:
```rust
struct SpanData {
    // ... existing fields ...
    rate_limit_hits: usize,
    retries: usize,
}
```

Add on_event() to MetricsLayer:
```rust
fn on_event(&self, event: &tracing::Event<'_>, ctx: Context<'_, S>) {
    // Check if event message contains rate-limit or retry indicators
    // Increment counters on the current span
    if let Some(span_ref) = ctx.event_span(event) {
        let id = span_ref.id();
        if let Some(data) = self.spans.lock().unwrap().get_mut(&id.into_u64()) {
            let mut visitor = EventVisitor::default();
            event.record(&mut visitor);

            if visitor.status_code == Some(429) {
                data.rate_limit_hits += 1;
            }
            if visitor.is_retry {
                data.retries += 1;
            }
        }
    }
}
```

The EventVisitor checks for status_code=429 and message containing "retrying" to classify events.

On span close, propagate counts to parent (bubble up):
```rust
fn on_close(&self, id: Id, _ctx: Context<'_, S>) {
    if let Some(data) = self.spans.lock().unwrap().remove(&id.into_u64()) {
        let timing = StageTiming {
            // ... existing fields ...
            rate_limit_hits: data.rate_limit_hits,
            retries: data.retries,
        };
        // ... push to completed
    }
}
```

## Acceptance Criteria
- [ ] StageTiming has rate_limit_hits and retries fields
- [ ] Fields omitted when zero in JSON serialization
- [ ] MetricsLayer counts 429 events as rate_limit_hits
- [ ] MetricsLayer counts retry events as retries
- [ ] Counts bubble up to parent spans in extract_timings()
- [ ] Rate limit counts appear in metrics_json stored in sync_runs
- [ ] cargo clippy --all-targets -- -D warnings passes

## Files
- src/core/metrics.rs (add fields to StageTiming, add on_event to MetricsLayer, add EventVisitor)

## TDD Loop
RED:
  - test_stage_timing_rate_limit_counts: simulate 3 rate-limit events, extract, assert rate_limit_hits=3
  - test_stage_timing_retry_counts: simulate 2 retries, extract, assert retries=2
  - test_rate_limit_fields_omitted_when_zero: StageTiming with zero counts, serialize, assert no keys
GREEN: Add fields to StageTiming, implement on_event in MetricsLayer
VERIFY: cargo test && cargo clippy --all-targets -- -D warnings

## Edge Cases
- Events outside any span: ctx.event_span() returns None. Skip counting. This shouldn't happen in practice since all GitLab calls happen within stage spans.
- Event classification: rely on structured fields (status_code=429) not message text. More reliable and less fragile.
- Count bubbling: parent stage should aggregate child counts. In extract_timings(), sum children's counts into parent.

Implemented rate_limit_hits and retries counters in StageTiming with skip_serializing_if for zero values


Write unit tests for core algorithms

## Background
Unit tests verify the core algorithms in isolation: document extraction formatting, FTS query sanitization, RRF scoring, content hashing, backoff curves, and filter helpers. These tests don't require a database or external services — they test pure functions and logic.

## Approach
Add #[cfg(test)] mod tests blocks to each module:

**1. src/documents/extractor.rs:**
- test_source_type_parse_all_aliases — every alias resolves correctly
- test_source_type_parse_unknown — returns None
- test_source_type_as_str_roundtrip — as_str matches parse input
- test_content_hash_deterministic — same input = same hash
- test_list_hash_order_independent — sorted before hashing
- test_list_hash_empty — empty vec produces consistent hash

**2. src/documents/truncation.rs:**
- test_truncation_edge_cases (per bd-18t TDD Loop)

**3. src/search/fts.rs:**
- test_to_fts_query_basic — "auth error" -> quoted tokens
- test_to_fts_query_prefix — "auth*" preserves prefix
- test_to_fts_query_special_chars — "C++" quoted correctly
- test_to_fts_query_dash — "-DWITH_SSL" quoted (not NOT operator)
- test_to_fts_query_internal_quotes — escaped by doubling
- test_to_fts_query_empty — empty string returns empty

**4. src/search/rrf.rs:**
- test_rrf_dual_list — docs in both lists score higher
- test_rrf_normalization — best score = 1.0
- test_rrf_empty — empty returns empty

**5. src/core/backoff.rs:**
- test_exponential_curve — delays double each attempt
- test_cap_at_one_hour — high attempt_count capped
- test_jitter_range — within [0.9, 1.1) factor

**6. src/search/filters.rs:**
- test_has_any_filter — true/false for various filter combos
- test_clamp_limit — 0->20, 200->100, 50->50
- test_path_filter_from_str — trailing slash = Prefix

**7. src/search/hybrid.rs (hydration round-trip):**
- test_single_round_trip_query — verify hydration SQL produces correct structure

## Acceptance Criteria
- [ ] All edge cases covered per PRD acceptance criteria
- [ ] Tests are unit tests (no DB, no network, no Ollama)
- [ ] `cargo test` passes with all new tests
- [ ] No test depends on execution order
- [ ] Tests cover: document extractor formats, truncation, RRF, hashing, FTS sanitization, backoff, filters

## Files
- In-module tests in: extractor.rs, truncation.rs, fts.rs, rrf.rs, backoff.rs, filters.rs, hybrid.rs

## TDD Loop
These tests ARE the TDD loop for their respective beads. Each implementation bead should write its tests first (RED), then implement (GREEN).
VERIFY: `cargo test`

## Edge Cases
- Tests with Unicode: include emoji, CJK characters in truncation tests
- Tests with empty strings: empty queries, empty content, empty labels
- Tests with boundary values: limit=0, limit=100, limit=101

All acceptance criteria tests already exist across modules. 276 tests passing (189 unit + 87 integration).


Add GitLab MR types to types.rs

## Background
GitLab API types for merge requests. These structs define how we deserialize GitLab API responses. Must handle deprecated field aliases for backward compatibility with older GitLab instances.

## Approach
Add new structs to `src/gitlab/types.rs`:
- `GitLabMergeRequest` - Main MR struct with all fields
- `GitLabReviewer` - Reviewer with optional approval state
- `GitLabReferences` - Short and full reference strings

Use serde `#[serde(alias = "...")]` for deprecated field fallbacks.

## Files
- `src/gitlab/types.rs` - Add new structs after existing GitLabIssue
- `tests/fixtures/gitlab_merge_request.json` - Test fixture

## Acceptance Criteria
- [ ] `GitLabMergeRequest` struct exists with all fields from PRD
- [ ] `detailed_merge_status` field exists (non-deprecated)
- [ ] `#[serde(alias = "merge_status")]` on `merge_status_legacy` for fallback
- [ ] `merge_user` field exists (non-deprecated)
- [ ] `merged_by` field exists for fallback
- [ ] `draft` and `work_in_progress` both exist (draft preferred, WIP fallback)
- [ ] `sha` field maps to `head_sha` in transformer
- [ ] `references: Option<GitLabReferences>` for short/full refs
- [ ] `state: String` supports "opened", "merged", "closed", "locked"
- [ ] Fixture deserializes without error
- [ ] `cargo test` passes

## TDD Loop
RED: Add test that deserializes fixture -> struct not found
GREEN: Add GitLabMergeRequest, GitLabReviewer, GitLabReferences structs
VERIFY: `cargo test gitlab_types`

## Struct Definitions (from PRD)
```rust
#[derive(Debug, Clone, Deserialize)]
pub struct GitLabMergeRequest {
    pub id: i64,
    pub iid: i64,
    pub project_id: i64,
    pub title: String,
    pub description: Option<String>,
    pub state: String,                // "opened" | "merged" | "closed" | "locked"
    #[serde(default)]
    pub draft: bool,
    #[serde(default)]
    pub work_in_progress: bool,       // Deprecated fallback
    pub source_branch: String,
    pub target_branch: String,
    pub sha: Option<String>,          // head_sha
    pub references: Option<GitLabReferences>,
    pub detailed_merge_status: Option<String>,
    #[serde(alias = "merge_status")]
    pub merge_status_legacy: Option<String>,
    pub created_at: String,
    pub updated_at: String,
    pub merged_at: Option<String>,
    pub closed_at: Option<String>,
    pub author: GitLabAuthor,
    pub merge_user: Option<GitLabAuthor>,
    pub merged_by: Option<GitLabAuthor>,
    #[serde(default)]
    pub labels: Vec<String>,
    #[serde(default)]
    pub assignees: Vec<GitLabAuthor>,
    #[serde(default)]
    pub reviewers: Vec<GitLabReviewer>,
    pub web_url: String,
}

#[derive(Debug, Clone, Deserialize)]
pub struct GitLabReferences {
    pub short: String,   // e.g. "\!123"
    pub full: String,    // e.g. "group/project\!123"
}

#[derive(Debug, Clone, Deserialize)]
pub struct GitLabReviewer {
    pub id: i64,
    pub username: String,
    pub name: String,
}
```

## Test Fixture (create tests/fixtures/gitlab_merge_request.json)
```json
{
  "id": 12345,
  "iid": 42,
  "project_id": 100,
  "title": "Add user authentication",
  "description": "Implements JWT auth flow",
  "state": "merged",
  "draft": false,
  "work_in_progress": false,
  "source_branch": "feature/auth",
  "target_branch": "main",
  "sha": "abc123def456",
  "references": { "short": "\!42", "full": "group/project\!42" },
  "detailed_merge_status": "mergeable",
  "merge_status": "can_be_merged",
  "created_at": "2024-01-15T10:00:00Z",
  "updated_at": "2024-01-20T14:30:00Z",
  "merged_at": "2024-01-20T14:30:00Z",
  "closed_at": null,
  "author": { "id": 1, "username": "johndoe", "name": "John Doe" },
  "merge_user": { "id": 2, "username": "janedoe", "name": "Jane Doe" },
  "merged_by": { "id": 2, "username": "janedoe", "name": "Jane Doe" },
  "labels": ["enhancement", "auth"],
  "assignees": [{ "id": 3, "username": "bob", "name": "Bob Smith" }],
  "reviewers": [{ "id": 4, "username": "alice", "name": "Alice Wong" }],
  "web_url": "https://gitlab.example.com/group/project/-/merge_requests/42"
}
```

## Edge Cases
- `locked` state is transitional (merge in progress) - rare but valid
- Some older instances may not return `detailed_merge_status`
- Some older instances may not return `merge_user` (use `merged_by` fallback)
- `work_in_progress` is deprecated but still returned by some instances

Added GitLabMergeRequest, GitLabReviewer, GitLabReferences structs. Updated GitLabNotePosition with position_type, line_range, and SHA triplet fields. All 23 type tests passing.


[CP1] Issue ingestion module

Fetch and store issues with cursor-based incremental sync.

## Module
src/ingestion/issues.rs

## Key Structs

### IngestIssuesResult
- fetched: usize
- upserted: usize
- labels_created: usize
- issues_needing_discussion_sync: Vec<IssueForDiscussionSync>

### IssueForDiscussionSync
- local_issue_id: i64
- iid: i64
- updated_at: i64

## Main Function
pub async fn ingest_issues(conn, client, config, project_id, gitlab_project_id) -> Result<IngestIssuesResult>

## Logic
1. Get current cursor from sync_cursors (updated_at_cursor, tie_breaker_id)
2. Paginate through issues updated after cursor with cursor_rewind_seconds
3. Apply local filtering for tuple cursor semantics:
   - Skip if issue.updated_at < cursor_updated_at
   - Skip if issue.updated_at == cursor_updated_at AND issue.id <= cursor_gitlab_id
4. For each issue passing filter:
   - Begin transaction
   - Store raw payload (compressed)
   - Transform and upsert issue
   - Clear existing label links (DELETE FROM issue_labels)
   - Extract and upsert labels
   - Link issue to labels via junction
   - Commit transaction
   - Track for discussion sync eligibility
5. Incremental cursor update every 100 issues
6. Final cursor update
7. Determine issues needing discussion sync: where updated_at > discussions_synced_for_updated_at

## Helper Functions
- get_cursor(conn, project_id) -> (Option<i64>, Option<i64>)
- get_discussions_synced_at(conn, issue_id) -> Option<i64>
- upsert_issue(conn, issue, payload_id) -> usize
- get_local_issue_id(conn, gitlab_id) -> i64
- clear_issue_labels(conn, issue_id)
- upsert_label(conn, label) -> bool
- get_label_id(conn, project_id, name) -> i64
- link_issue_label(conn, issue_id, label_id)
- update_cursor(conn, project_id, resource_type, updated_at, gitlab_id)

Files: src/ingestion/mod.rs, src/ingestion/issues.rs
Tests: tests/issue_ingestion_tests.rs
Done when: Issues, labels, issue_labels populated correctly with resumable cursor


Extract cross-references from resource_state_events

## Background
resource_state_events includes source_merge_request (with iid) for 'closed by MR' events. After state events are stored (Gate 1), post-processing extracts these into entity_references for the cross-reference graph.

## Approach
Create src/core/references.rs (new module) or add to events_db.rs:

```rust
/// Extract cross-references from stored state events and insert into entity_references.
/// Looks for state events with source_merge_request_id IS NOT NULL (meaning "closed by MR").
///
/// Directionality: source = MR (that caused the close), target = issue (that was closed)
pub fn extract_refs_from_state_events(
    conn: &Connection,
    project_id: i64,
) -> Result<usize>  // returns count of new references inserted
```

SQL logic:
```sql
INSERT OR IGNORE INTO entity_references (
    source_entity_type, source_entity_id,
    target_entity_type, target_entity_id,
    reference_type, source_method, created_at
)
SELECT
    'merge_request',
    mr.id,
    'issue',
    rse.issue_id,
    'closes',
    'api_state_event',
    rse.created_at
FROM resource_state_events rse
JOIN merge_requests mr ON mr.project_id = rse.project_id AND mr.iid = rse.source_merge_request_id
WHERE rse.source_merge_request_id IS NOT NULL
  AND rse.issue_id IS NOT NULL
  AND rse.project_id = ?1;
```

Key: source_merge_request_id stores the MR iid, so we JOIN on merge_requests.iid to get the local DB id.

Register in src/core/mod.rs: `pub mod references;`

Call this after drain_dependent_queue in the sync pipeline (after all state events are stored).

## Acceptance Criteria
- [ ] State events with source_merge_request_id produce 'closes' references
- [ ] Source = MR (resolved by iid), target = issue
- [ ] source_method = 'api_state_event'
- [ ] INSERT OR IGNORE prevents duplicates with api_closes_issues data
- [ ] Returns count of newly inserted references
- [ ] No-op when no state events have source_merge_request_id

## Files
- src/core/references.rs (new)
- src/core/mod.rs (add `pub mod references;`)
- src/cli/commands/sync.rs (call after drain step)

## TDD Loop
RED: tests/references_tests.rs:
- `test_extract_refs_from_state_events_basic` - seed a "closed" state event with source_merge_request_id, verify entity_reference created
- `test_extract_refs_dedup_with_closes_issues` - insert ref from closes_issues API first, verify state event extraction doesn't duplicate
- `test_extract_refs_no_source_mr` - state events without source_merge_request_id produce no refs

Setup: create_test_db with migrations 001-011, seed project + issue + MR + state events.

GREEN: Implement extract_refs_from_state_events

VERIFY: `cargo test references -- --nocapture`

## Edge Cases
- source_merge_request_id may reference an MR not synced locally (cross-project close) — the JOIN will produce no match, which is correct behavior (ref simply not created)
- Multiple state events can reference the same MR for the same issue (reopen + re-close) — INSERT OR IGNORE handles dedup
- The merge_requests table might not have the MR yet if sync is still running — call this after all dependent fetches complete


[CP1] gi sync-status enhancement

Enhance sync-status from CP0 stub to show issue cursors.

## Changes to src/cli/commands/sync_status.rs

Update the existing stub to show:
- Last run timestamp and duration
- Cursor positions per project (issues resource_type)
- Entity counts (issues, discussions, notes)

## Output Format
Last sync: 2026-01-25 10:30:00 (succeeded, 45s)

Cursors:
  group/project-one
    issues: 2026-01-25T10:25:00Z (gitlab_id: 12345678)

Counts:
  Issues: 1,234
  Discussions: 5,678
  Notes: 23,456 (4,567 system)

Files: src/cli/commands/sync_status.rs
Done when: Shows cursor positions and counts after ingestion


Implement 'lore trace' command with human and robot output

## Background

The trace command is Gate 5's capstone CLI. It answers 'Why was this code introduced?' by building file -> MR -> issue -> discussion chains.

**Spec reference:** `docs/phase-b-temporal-intelligence.md` Section 5.3.

## Codebase Context

- CLI pattern: same as file-history (Commands enum, handler in main.rs)
- trace.rs (bd-2n4): run_trace() returns TraceResult with chains
- Path parsing: support 'src/foo.rs:45' syntax (line number for future Tier 2)
- merge_requests.merged_at exists (migration 006) — use COALESCE(merged_at, updated_at) for ordering

## Approach

### 1. TraceArgs (`src/cli/mod.rs`):
```rust
#[derive(Parser)]
pub struct TraceArgs {
    pub path: String,                      // supports :line suffix
    #[arg(short = 'p', long)] pub project: Option<String>,
    #[arg(long)] pub discussions: bool,
    #[arg(long = "no-follow-renames")] pub no_follow_renames: bool,
    #[arg(short = 'n', long = "limit", default_value = "20")] pub limit: usize,
}
```

### 2. Path parsing:
```rust
fn parse_trace_path(input: &str) -> (String, Option<u32>) {
    if let Some((path, line)) = input.rsplit_once(':') {
        if let Ok(n) = line.parse::<u32>() { return (path.to_string(), Some(n)); }
    }
    (input.to_string(), None)
}
```
If line present: warn 'Line-level tracing requires Tier 2. Showing file-level results.'

### 3. Human output shows chains with MR -> issue -> discussion context

### 4. Robot JSON:
```json
{"ok": true, "data": {"path": "...", "resolved_paths": [...], "trace_chains": [...]}, "meta": {"tier": "api_only", "line_requested": null}}
```

## Acceptance Criteria

- [ ] `lore trace src/foo.rs` with human output
- [ ] `lore --robot trace src/foo.rs` with JSON
- [ ] :line suffix parses and emits Tier 2 warning
- [ ] -p, --discussions, --no-follow-renames, -n all work
- [ ] Rename-aware via resolve_rename_chain
- [ ] meta.tier = 'api_only'
- [ ] Added to VALID_COMMANDS and robot-docs
- [ ] `cargo check --all-targets` passes

## Files

- `src/cli/mod.rs` (TraceArgs + Commands::Trace)
- `src/cli/commands/trace.rs` (NEW)
- `src/cli/commands/mod.rs` (re-export)
- `src/main.rs` (handler + VALID_COMMANDS + robot-docs)

## TDD Loop

RED:
- `test_parse_trace_path_simple` - "src/foo.rs" -> (path, None)
- `test_parse_trace_path_with_line` - "src/foo.rs:42" -> (path, Some(42))
- `test_parse_trace_path_windows` - "C:/foo.rs" -> (path, None) — don't misparse drive letter

GREEN: Implement CLI wiring and handlers.

VERIFY: `cargo check --all-targets`

## Edge Cases

- Windows paths: don't misparse C: as line number
- No MR data: friendly message with suggestion to sync
- Very deep rename chain: bounded by resolve_rename_chain


Implement embedding pipeline with chunking

## Background
The embedding pipeline takes documents, chunks them (paragraph-boundary splitting with overlap), sends chunks to Ollama for embedding via async HTTP, and stores vectors in sqlite-vec + metadata. It uses keyset pagination, concurrent HTTP requests via FuturesUnordered, per-batch transactions, and dimension validation.

## Approach
Create \`src/embedding/pipeline.rs\` per PRD Section 4.4. **The pipeline is async.**

**Constants (per PRD):**
```rust
const BATCH_SIZE: usize = 32;           // texts per Ollama API call
const DB_PAGE_SIZE: usize = 500;        // keyset pagination page size
const EXPECTED_DIMS: usize = 768;       // nomic-embed-text dimensions
const CHUNK_MAX_CHARS: usize = 32_000;  // max chars per chunk
const CHUNK_OVERLAP_CHARS: usize = 500; // overlap between chunks
```

**Core async function:**
```rust
pub async fn embed_documents(
    conn: &Connection,
    client: &OllamaClient,
    selection: EmbedSelection,
    concurrency: usize,              // max in-flight HTTP requests
    progress_callback: Option<Box<dyn Fn(usize, usize)>>,
) -> Result<EmbedResult>
```

**EmbedSelection:** Pending | RetryFailed
**EmbedResult:** { embedded, failed, skipped }

**Algorithm (per PRD):**
1. count_pending_documents(conn, selection) for progress total
2. Keyset pagination loop: find_pending_documents(conn, DB_PAGE_SIZE, last_id, selection)
3. For each page:
   a. Begin transaction
   b. For each doc: clear_document_embeddings(&tx, doc.id), split_into_chunks(&doc.content)
   c. Build ChunkWork items with doc_hash + chunk_hash
   d. Commit clearing transaction
4. Batch ChunkWork texts into Ollama calls (BATCH_SIZE=32)
5. Use **FuturesUnordered** for concurrent HTTP, cap at \`concurrency\`
6. collect_writes() in per-batch transactions: validate dims (768), store LE bytes, write metadata
7. On error: record_embedding_error per chunk (not abort)
8. Advance keyset cursor

**ChunkWork struct:**
```rust
struct ChunkWork {
    doc_id: i64,
    chunk_index: usize,
    doc_hash: String,    // SHA-256 of FULL document (staleness detection)
    chunk_hash: String,  // SHA-256 of THIS chunk (provenance)
    text: String,
}
```

**Splitting:** split_into_chunks(content) -> Vec<(usize, String)>
- Documents <= CHUNK_MAX_CHARS: single chunk (index 0)
- Longer: split at paragraph boundaries (\\n\\n), fallback to sentence/word, with CHUNK_OVERLAP_CHARS overlap

**Storage:** embeddings as raw LE bytes, rowid = encode_rowid(doc_id, chunk_idx)
**Staleness detection:** uses document_hash (not chunk_hash) because it's document-level

Also create \`src/embedding/change_detector.rs\` (referenced in PRD module structure):
```rust
pub fn detect_embedding_changes(conn: &Connection) -> Result<Vec<PendingDocument>>;
```

## Acceptance Criteria
- [ ] Pipeline is async (uses FuturesUnordered for concurrent HTTP)
- [ ] concurrency parameter caps in-flight HTTP requests
- [ ] progress_callback reports (processed, total)
- [ ] New documents embedded, changed re-embedded, unchanged skipped
- [ ] clear_document_embeddings before re-embedding (range delete vec0 + metadata)
- [ ] Chunking at paragraph boundaries with 500-char overlap
- [ ] Short documents (<32k chars) produce exactly 1 chunk
- [ ] Embeddings stored as raw LE bytes in vec0
- [ ] Rowids encoded via encode_rowid(doc_id, chunk_index)
- [ ] Dimension validation: 768 floats per embedding (mismatch -> record error, not store)
- [ ] Per-batch transactions for writes
- [ ] Errors recorded in embedding_metadata per chunk (last_error, attempt_count)
- [ ] Keyset pagination (d.id > last_id, not OFFSET)
- [ ] Pending detection uses document_hash (not chunk_hash)
- [ ] \`cargo build\` succeeds

## Files
- \`src/embedding/pipeline.rs\` — new file (async)
- \`src/embedding/change_detector.rs\` — new file
- \`src/embedding/mod.rs\` — add \`pub mod pipeline; pub mod change_detector;\` + re-exports

## TDD Loop
RED: Unit tests for chunking:
- \`test_short_document_single_chunk\` — <32k produces [(0, full_content)]
- \`test_long_document_multiple_chunks\` — >32k splits at paragraph boundaries
- \`test_chunk_overlap\` — adjacent chunks share 500-char overlap
- \`test_no_paragraph_boundary\` — falls back to char boundary
Integration tests need Ollama or mock.
GREEN: Implement split_into_chunks, embed_documents (async)
VERIFY: \`cargo test pipeline\`

## Edge Cases
- Empty document content_text: skip (don't embed)
- No paragraph boundaries: split at CHUNK_MAX_CHARS with overlap
- Ollama error for one batch: record error per chunk, continue with next batch
- Dimension mismatch (model returns 512 instead of 768): record error, don't store corrupt data
- Document deleted between pagination and embedding: skip gracefully

Implemented embedding pipeline: chunking at paragraph boundaries with 500-char overlap, change detector (keyset pagination, hash-based staleness), async embed via Ollama with batch processing, dimension validation, per-chunk error recording, LE byte vector storage. 7 chunking tests pass. 289 total tests.


OBSERV: Create migration 014 for sync_runs enrichment

## Background
The sync_runs table (created in migration 001) has columns id, started_at, heartbeat_at, finished_at, status, command, error, metrics_json but NOTHING writes to it. This migration adds columns for the observability correlation ID and aggregate counts, enabling queryable sync history.

## Approach
Create migrations/014_sync_runs_enrichment.sql:

```sql
-- Migration 014: sync_runs enrichment for observability
-- Adds correlation ID and aggregate counts for queryable sync history

ALTER TABLE sync_runs ADD COLUMN run_id TEXT;
ALTER TABLE sync_runs ADD COLUMN total_items_processed INTEGER DEFAULT 0;
ALTER TABLE sync_runs ADD COLUMN total_errors INTEGER DEFAULT 0;

-- Index for correlation queries (find run by run_id from logs)
CREATE INDEX IF NOT EXISTS idx_sync_runs_run_id ON sync_runs(run_id);
```

Migration naming convention: check migrations/ directory. Current latest is 013_resource_event_watermarks.sql. Next is 014.

Note: SQLite ALTER TABLE ADD COLUMN is always safe -- it sets NULL for existing rows. DEFAULT 0 applies to new INSERTs only.

## Acceptance Criteria
- [ ] Migration 014 applies cleanly on a fresh DB (all migrations 001-014)
- [ ] Migration 014 applies cleanly on existing DB with 001-013 already applied
- [ ] sync_runs table has run_id TEXT column
- [ ] sync_runs table has total_items_processed INTEGER DEFAULT 0 column
- [ ] sync_runs table has total_errors INTEGER DEFAULT 0 column
- [ ] idx_sync_runs_run_id index exists
- [ ] Existing sync_runs rows (if any) have NULL run_id, 0 for counts
- [ ] cargo clippy --all-targets -- -D warnings passes (no code changes, but verify migration is picked up)

## Files
- migrations/014_sync_runs_enrichment.sql (new file)

## TDD Loop
RED:
  - test_migration_014_applies: apply all migrations on fresh in-memory DB, query sync_runs schema
  - test_migration_014_idempotent: CREATE INDEX IF NOT EXISTS makes re-run safe; ALTER TABLE ADD COLUMN is NOT idempotent in SQLite (will error). Consider: skip this test or use IF NOT EXISTS workaround
GREEN: Create migration file
VERIFY: cargo test && cargo clippy --all-targets -- -D warnings

## Edge Cases
- ALTER TABLE ADD COLUMN in SQLite: NOT idempotent. Running migration twice will error "duplicate column name." The migration system should prevent re-runs, but IF NOT EXISTS is not available for ALTER TABLE in SQLite. Rely on migration tracking.
- Migration numbering conflict: if another PR adds 014 first, renumber to 015. Check before merging.
- metrics_json already exists (from migration 001): we don't touch it. The new columns supplement it with queryable aggregates.

Created migration 014 adding run_id TEXT, total_items_processed INTEGER, total_errors INTEGER to sync_runs, with idx_sync_runs_run_id index


WHO: Overlap mode query (query_overlap)

## Background

Overlap mode answers "Who else has MRs/notes touching my files?" — helps identify potential reviewers, collaborators, or conflicting work at a path. Tracks author and reviewer roles separately for richer signal.

## Approach

### SQL: two static variants (prefix/exact) with reviewer + author UNION ALL

Both branches return: username, role, touch_count (COUNT DISTINCT m.id), last_seen_at, mr_refs (GROUP_CONCAT of project-qualified refs).

Key differences from Expert:
- No scoring formula — just touch_count ranking
- mr_refs collected for actionable output (group/project!iid format)
- Rust-side merge needed (can't fully aggregate in SQL due to HashSet dedup of mr_refs across branches)

### Reviewer branch includes:
- Self-review exclusion: `n.author_username != m.author_username`
- MR state filter: `m.state IN ('opened','merged')`
- Project-qualified refs: `GROUP_CONCAT(DISTINCT (p.path_with_namespace || '!' || m.iid))`

### Rust accumulator pattern:
```rust
struct OverlapAcc {
    username: String,
    author_touch_count: u32,
    review_touch_count: u32,
    touch_count: u32,
    last_seen_at: i64,
    mr_refs: HashSet<String>,  // O(1) dedup from the start
}
// Build HashMap<String, OverlapAcc> from rows
// Convert to Vec, sort, bound mr_refs
```

### Bounded mr_refs:
```rust
const MAX_MR_REFS_PER_USER: usize = 50;
let mr_refs_total = mr_refs.len() as u32;
let mr_refs_truncated = mr_refs.len() > MAX_MR_REFS_PER_USER;
```

### Deterministic sort: touch_count DESC, last_seen_at DESC, username ASC

### format_overlap_role():
```rust
fn format_overlap_role(user: &OverlapUser) -> &'static str {
    match (user.author_touch_count > 0, user.review_touch_count > 0) {
        (true, true) => "A+R", (true, false) => "A",
        (false, true) => "R", (false, false) => "-",
    }
}
```

### OverlapResult/OverlapUser structs include path_match ("exact"/"prefix"), truncated bool, per-user mr_refs_total + mr_refs_truncated

## Files

- `src/cli/commands/who.rs`

## TDD Loop

RED:
```
test_overlap_dual_roles — user is author of MR 1 and reviewer of MR 2 at same path; verify A+R role, both touch counts > 0, mr_refs contain "team/backend!"
test_overlap_multi_project_mr_refs — same iid 100 in two projects; verify both "team/backend!100" and "team/frontend!100" present
test_overlap_excludes_self_review_notes — author comments on own MR; review_touch_count must be 0
```

GREEN: Implement query_overlap with both SQL variants + accumulator
VERIFY: `cargo test -- overlap`

## Acceptance Criteria

- [ ] test_overlap_dual_roles passes (A+R role detection)
- [ ] test_overlap_multi_project_mr_refs passes (project-qualified refs unique)
- [ ] test_overlap_excludes_self_review_notes passes
- [ ] Default since window: 30d
- [ ] mr_refs sorted alphabetically for deterministic output
- [ ] touch_count uses coherent units (COUNT DISTINCT m.id on BOTH branches)

## Edge Cases

- Both branches count MRs (not DiffNotes) for coherent touch_count — mixing units produces misleading totals
- mr_refs from GROUP_CONCAT may contain duplicates across branches — HashSet handles dedup
- Project scoping on n.project_id (not m.project_id) for index alignment
- mr_refs sorted before output (HashSet iteration is nondeterministic)