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/002_issues.sql

@@ -0,0 +1,105 @@
+-- Migration 002: Issue Ingestion Tables
+-- Applies on top of 001_initial.sql
+
+-- Issues table
+CREATE TABLE issues (
+    id INTEGER PRIMARY KEY,
+    gitlab_id INTEGER UNIQUE NOT NULL,
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    iid INTEGER NOT NULL,
+    title TEXT,
+    description TEXT,
+    state TEXT NOT NULL CHECK (state IN ('opened', 'closed')),
+    author_username TEXT,
+    created_at INTEGER NOT NULL,           -- ms epoch UTC
+    updated_at INTEGER NOT NULL,           -- ms epoch UTC
+    last_seen_at INTEGER NOT NULL,         -- updated on every upsert
+    discussions_synced_for_updated_at INTEGER, -- watermark for dependent sync
+    web_url TEXT,
+    raw_payload_id INTEGER REFERENCES raw_payloads(id)
+);
+
+CREATE INDEX idx_issues_project_updated ON issues(project_id, updated_at);
+CREATE INDEX idx_issues_author ON issues(author_username);
+CREATE UNIQUE INDEX uq_issues_project_iid ON issues(project_id, iid);
+
+-- Labels table (name-only for CP1)
+CREATE TABLE labels (
+    id INTEGER PRIMARY KEY,
+    gitlab_id INTEGER,                      -- optional, for future Labels API
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    name TEXT NOT NULL,
+    color TEXT,
+    description TEXT
+);
+
+CREATE UNIQUE INDEX uq_labels_project_name ON labels(project_id, name);
+CREATE INDEX idx_labels_name ON labels(name);
+
+-- Issue-label junction (DELETE before INSERT for stale removal)
+CREATE TABLE issue_labels (
+    issue_id INTEGER NOT NULL REFERENCES issues(id) ON DELETE CASCADE,
+    label_id INTEGER NOT NULL REFERENCES labels(id) ON DELETE CASCADE,
+    PRIMARY KEY(issue_id, label_id)
+);
+
+CREATE INDEX idx_issue_labels_label ON issue_labels(label_id);
+
+-- Discussion threads for issues (MR discussions added in CP2)
+CREATE TABLE discussions (
+    id INTEGER PRIMARY KEY,
+    gitlab_discussion_id TEXT NOT NULL,     -- GitLab string ID (e.g., "6a9c1750b37d...")
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    issue_id INTEGER REFERENCES issues(id) ON DELETE CASCADE,
+    merge_request_id INTEGER,               -- FK added in CP2 via ALTER TABLE
+    noteable_type TEXT NOT NULL CHECK (noteable_type IN ('Issue', 'MergeRequest')),
+    individual_note INTEGER NOT NULL DEFAULT 0,  -- 0=threaded, 1=standalone
+    first_note_at INTEGER,                  -- min(note.created_at) for ordering
+    last_note_at INTEGER,                   -- max(note.created_at) for "recently active"
+    last_seen_at INTEGER NOT NULL,          -- updated on every upsert
+    resolvable INTEGER NOT NULL DEFAULT 0,  -- MR discussions can be resolved
+    resolved INTEGER NOT NULL DEFAULT 0,
+    CHECK (
+        (noteable_type = 'Issue' AND issue_id IS NOT NULL AND merge_request_id IS NULL) OR
+        (noteable_type = 'MergeRequest' AND merge_request_id IS NOT NULL AND issue_id IS NULL)
+    )
+);
+
+CREATE UNIQUE INDEX uq_discussions_project_discussion_id ON discussions(project_id, gitlab_discussion_id);
+CREATE INDEX idx_discussions_issue ON discussions(issue_id);
+CREATE INDEX idx_discussions_mr ON discussions(merge_request_id);
+CREATE INDEX idx_discussions_last_note ON discussions(last_note_at);
+
+-- Notes belong to discussions
+CREATE TABLE notes (
+    id INTEGER PRIMARY KEY,
+    gitlab_id INTEGER UNIQUE NOT NULL,
+    discussion_id INTEGER NOT NULL REFERENCES discussions(id) ON DELETE CASCADE,
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    note_type TEXT,                         -- 'DiscussionNote' | 'DiffNote' | null
+    is_system INTEGER NOT NULL DEFAULT 0,   -- 1 for system-generated notes
+    author_username TEXT,
+    body TEXT,
+    created_at INTEGER NOT NULL,            -- ms epoch
+    updated_at INTEGER NOT NULL,            -- ms epoch
+    last_seen_at INTEGER NOT NULL,          -- updated on every upsert
+    position INTEGER,                       -- 0-indexed array order from API
+    resolvable INTEGER NOT NULL DEFAULT 0,
+    resolved INTEGER NOT NULL DEFAULT 0,
+    resolved_by TEXT,
+    resolved_at INTEGER,
+    -- DiffNote position metadata (populated for MR DiffNotes in CP2)
+    position_old_path TEXT,
+    position_new_path TEXT,
+    position_old_line INTEGER,
+    position_new_line INTEGER,
+    raw_payload_id INTEGER REFERENCES raw_payloads(id)
+);
+
+CREATE INDEX idx_notes_discussion ON notes(discussion_id);
+CREATE INDEX idx_notes_author ON notes(author_username);
+CREATE INDEX idx_notes_system ON notes(is_system);
+
+-- Update schema version
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (2, strftime('%s', 'now') * 1000, 'Issue ingestion tables');