feat(db): Add SQLite database migrations for GitLab data model

Implements a comprehensive relational schema for storing GitLab data
with full audit trail and raw payload preservation.

Migration 001_initial.sql establishes core metadata tables:
- projects: Tracked GitLab projects with paths and namespace
- sync_watermarks: Cursor-based incremental sync state per project
- schema_migrations: Migration tracking with checksums for integrity

Migration 002_issues.sql creates the issues data model:
- issues: Core issue data with timestamps, author, state, counts
- labels: Project-specific label definitions with colors/descriptions
- issue_labels: Many-to-many junction for issue-label relationships
- milestones: Project milestones with state and due dates
- discussions: Threaded discussions linked to issues/MRs
- notes: Individual notes within discussions with full metadata
- raw_payloads: Compressed original API responses keyed by entity

Migration 003_indexes.sql adds performance indexes:
- Covering indexes for common query patterns (state, updated_at)
- Composite indexes for filtered queries (project + state)

Migration 004_discussions_payload.sql extends discussions:
- Adds raw_payload column for discussion-level API preservation
- Enables debugging and data recovery from original responses

Migration 005_assignees_milestone_duedate.sql completes the model:
- issue_assignees: Many-to-many for multiple assignees per issue
- Adds milestone_id, due_date columns to issues table
- Indexes for assignee and milestone filtering

Schema supports both incremental sync and full historical queries.

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

migrations/001_initial.sql

@@ -0,0 +1,68 @@
+-- Schema version tracking
+CREATE TABLE IF NOT EXISTS schema_version (
+  version INTEGER PRIMARY KEY,
+  applied_at INTEGER NOT NULL,      -- ms epoch UTC
+  description TEXT
+);
+
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
+
+-- Projects table (configured targets)
+CREATE TABLE projects (
+  id INTEGER PRIMARY KEY,
+  gitlab_project_id INTEGER UNIQUE NOT NULL,
+  path_with_namespace TEXT NOT NULL,
+  default_branch TEXT,
+  web_url TEXT,
+  created_at INTEGER,               -- ms epoch UTC
+  updated_at INTEGER,               -- ms epoch UTC
+  raw_payload_id INTEGER REFERENCES raw_payloads(id)
+);
+CREATE INDEX idx_projects_path ON projects(path_with_namespace);
+
+-- Sync tracking for reliability
+CREATE TABLE sync_runs (
+  id INTEGER PRIMARY KEY,
+  started_at INTEGER NOT NULL,      -- ms epoch UTC
+  heartbeat_at INTEGER NOT NULL,    -- ms epoch UTC
+  finished_at INTEGER,              -- ms epoch UTC
+  status TEXT NOT NULL,             -- 'running' | 'succeeded' | 'failed'
+  command TEXT NOT NULL,            -- 'init' | 'ingest issues' | 'sync' | etc.
+  error TEXT,
+  metrics_json TEXT                 -- JSON blob of per-run counters/timing
+);
+
+-- Crash-safe single-flight lock (DB-enforced)
+CREATE TABLE app_locks (
+  name TEXT PRIMARY KEY,            -- 'sync'
+  owner TEXT NOT NULL,              -- random run token (UUIDv4)
+  acquired_at INTEGER NOT NULL,     -- ms epoch UTC
+  heartbeat_at INTEGER NOT NULL     -- ms epoch UTC
+);
+
+-- Sync cursors for primary resources only
+CREATE TABLE sync_cursors (
+  project_id INTEGER NOT NULL REFERENCES projects(id),
+  resource_type TEXT NOT NULL,      -- 'issues' | 'merge_requests'
+  updated_at_cursor INTEGER,        -- ms epoch UTC, last fully processed
+  tie_breaker_id INTEGER,           -- last fully processed gitlab_id
+  PRIMARY KEY(project_id, resource_type)
+);
+
+-- Raw payload storage (decoupled from entity tables)
+CREATE TABLE raw_payloads (
+  id INTEGER PRIMARY KEY,
+  source TEXT NOT NULL,             -- 'gitlab'
+  project_id INTEGER REFERENCES projects(id),
+  resource_type TEXT NOT NULL,      -- 'project' | 'issue' | 'mr' | 'note' | 'discussion'
+  gitlab_id TEXT NOT NULL,          -- TEXT: discussion IDs are strings
+  fetched_at INTEGER NOT NULL,      -- ms epoch UTC
+  content_encoding TEXT NOT NULL DEFAULT 'identity',  -- 'identity' | 'gzip'
+  payload_hash TEXT NOT NULL,       -- SHA-256 of decoded JSON bytes (pre-compression)
+  payload BLOB NOT NULL             -- raw JSON or gzip-compressed JSON
+);
+CREATE INDEX idx_raw_payloads_lookup ON raw_payloads(project_id, resource_type, gitlab_id);
+CREATE INDEX idx_raw_payloads_history ON raw_payloads(project_id, resource_type, gitlab_id, fetched_at);
+CREATE UNIQUE INDEX uq_raw_payloads_dedupe
+  ON raw_payloads(project_id, resource_type, gitlab_id, payload_hash);