feat: Implement Gate 3 timeline pipeline and Gate 4 migration scaffolding

Complete 5 beads for the Phase B temporal intelligence feature:

- bd-1oo: Register migration 015 (commit SHAs, closes watermark) and
  create migration 016 (mr_file_changes table with 4 indexes for
  Gate 4 file-history)

- bd-20e: Define TimelineEvent model with 9 event type variants,
  EntityRef, ExpandedEntityRef, UnresolvedRef, and TimelineResult
  types. Ord impl for chronological sorting with stable tiebreak.

- bd-32q: Implement timeline seed phase - FTS5 keyword search to
  entity IDs with discussion-to-parent resolution, entity dedup,
  and evidence note extraction with snippet truncation.

- bd-ypa: Implement timeline expand phase - BFS cross-reference
  expansion over entity_references with bidirectional traversal,
  depth limiting, mention filtering, provenance tracking, and
  unresolved reference collection.

- bd-3as: Implement timeline event collection - gathers Created,
  StateChanged, LabelAdded/Removed, MilestoneSet/Removed, Merged,
  and NoteEvidence events. Merged dedup (state=merged -> Merged
  variant only). NULL label/milestone fallbacks. Chronological
  interleaving with since filter and limit.

38 new tests, all 445 tests pass. All quality gates clean.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

migrations/016_mr_file_changes.sql

@@ -0,0 +1,20 @@
+-- Migration 016: MR file changes table
+-- Powers file-history and trace commands (Gates 4-5)
+
+CREATE TABLE mr_file_changes (
+    id INTEGER PRIMARY KEY,
+    merge_request_id INTEGER NOT NULL REFERENCES merge_requests(id) ON DELETE CASCADE,
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    old_path TEXT,
+    new_path TEXT NOT NULL,
+    change_type TEXT NOT NULL CHECK (change_type IN ('added', 'modified', 'renamed', 'deleted')),
+    UNIQUE(merge_request_id, new_path)
+);
+
+CREATE INDEX idx_mfc_project_path ON mr_file_changes(project_id, new_path);
+CREATE INDEX idx_mfc_project_old_path ON mr_file_changes(project_id, old_path) WHERE old_path IS NOT NULL;
+CREATE INDEX idx_mfc_mr ON mr_file_changes(merge_request_id);
+CREATE INDEX idx_mfc_renamed ON mr_file_changes(project_id, change_type) WHERE change_type = 'renamed';
+
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (16, strftime('%s', 'now') * 1000, 'MR file changes table');