feat(observability): Add metrics, logging, and sync-run core modules

Introduce the foundational observability layer for the sync pipeline:

- MetricsLayer: Custom tracing subscriber layer that captures span timing
  and structured fields, materializing them into a hierarchical
  Vec<StageTiming> tree for robot-mode performance data output
- logging: Dual-layer subscriber infrastructure with configurable stderr
  verbosity (-v/-vv/-vvv) and always-on JSON file logging with daily
  rotation and configurable retention (default 30 days)
- SyncRunRecorder: Compile-time enforced lifecycle recorder for sync_runs
  table (start -> succeed|fail), with correlation IDs and aggregate counts
- LoggingConfig: New config section for log_dir, retention_days, and
  file_logging toggle
- get_log_dir(): Path helper for log directory resolution
- is_permanent_api_error(): Distinguish retryable vs permanent API failures
  (only 404 is truly permanent; 403/auth errors may be environmental)

Database changes:
- Migration 013: Add resource_events_synced_for_updated_at watermark columns
  to issues and merge_requests tables for incremental resource event sync
- Migration 014: Enrich sync_runs with run_id correlation ID, aggregate
  counts (total_items_processed, total_errors), and run_id index
- Wrap file-based migrations in savepoints for rollback safety

Dependencies: Add uuid (run_id generation), tracing-appender (file logging)

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

migrations/013_resource_event_watermarks.sql

@@ -0,0 +1,10 @@
+-- Migration 013: Add resource event sync watermarks
+-- Mirrors the discussions_synced_for_updated_at pattern so that only entities
+-- whose updated_at exceeds the last resource event sync get re-enqueued.
+
+ALTER TABLE issues ADD COLUMN resource_events_synced_for_updated_at INTEGER;
+ALTER TABLE merge_requests ADD COLUMN resource_events_synced_for_updated_at INTEGER;
+
+-- Update schema version
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (13, strftime('%s', 'now') * 1000, 'Add resource event sync watermarks to issues and merge_requests');

migrations/014_sync_runs_enrichment.sql

@@ -0,0 +1,12 @@
+-- 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);
+
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (14, strftime('%s', 'now') * 1000, 'Sync runs enrichment for observability');