diff --git a/migrations/.gitkeep b/migrations/.gitkeep
new file mode 100644
index 0000000..e69de29
diff --git a/migrations/001_initial.sql b/migrations/001_initial.sql
new file mode 100644
index 0000000..f9a70f1
--- /dev/null
+++ b/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);
diff --git a/migrations/002_issues.sql b/migrations/002_issues.sql
new file mode 100644
index 0000000..6699edd
--- /dev/null
+++ b/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');
diff --git a/migrations/003_indexes.sql b/migrations/003_indexes.sql
new file mode 100644
index 0000000..d74b8cb
--- /dev/null
+++ b/migrations/003_indexes.sql
@@ -0,0 +1,12 @@
+-- Migration 003: Performance and Orphan Detection Indexes
+-- Adds indexes for efficient orphan detection queries
+
+-- Index for orphan detection: find issues/discussions not seen recently
+-- Used by cleanup routines to identify potentially stale data
+CREATE INDEX IF NOT EXISTS idx_issues_last_seen ON issues(last_seen_at);
+CREATE INDEX IF NOT EXISTS idx_discussions_last_seen ON discussions(last_seen_at);
+CREATE INDEX IF NOT EXISTS idx_notes_last_seen ON notes(last_seen_at);
+
+-- Update schema version
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (3, strftime('%s', 'now') * 1000, 'Performance and orphan detection indexes');
diff --git a/migrations/004_discussions_payload.sql b/migrations/004_discussions_payload.sql
new file mode 100644
index 0000000..a073a55
--- /dev/null
+++ b/migrations/004_discussions_payload.sql
@@ -0,0 +1,8 @@
+-- Migration 004: Add raw_payload_id to discussions
+-- The column was expected by code but missing from initial schema
+
+ALTER TABLE discussions ADD COLUMN raw_payload_id INTEGER REFERENCES raw_payloads(id);
+
+-- Update schema version
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (4, strftime('%s', 'now') * 1000, 'Add raw_payload_id to discussions');
diff --git a/migrations/005_assignees_milestone_duedate.sql b/migrations/005_assignees_milestone_duedate.sql
new file mode 100644
index 0000000..17aad98
--- /dev/null
+++ b/migrations/005_assignees_milestone_duedate.sql
@@ -0,0 +1,43 @@
+-- Migration 005: Add assignees, milestone, and due_date support
+-- Schema version: 5
+
+-- Add new columns to issues table
+ALTER TABLE issues ADD COLUMN due_date TEXT;           -- YYYY-MM-DD format, nullable
+ALTER TABLE issues ADD COLUMN milestone_id INTEGER;    -- Local milestone ID (FK to milestones.id)
+ALTER TABLE issues ADD COLUMN milestone_title TEXT;    -- Denormalized for quick display
+
+-- Milestones table (captures key fields for filtering and display)
+CREATE TABLE IF NOT EXISTS milestones (
+    id INTEGER PRIMARY KEY,
+    gitlab_id INTEGER NOT NULL,
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    iid INTEGER NOT NULL,                              -- Project-scoped milestone number
+    title TEXT NOT NULL,
+    description TEXT,
+    state TEXT,                                        -- 'active' or 'closed'
+    due_date TEXT,                                     -- YYYY-MM-DD
+    web_url TEXT,
+    UNIQUE(project_id, gitlab_id)
+);
+
+CREATE INDEX IF NOT EXISTS idx_milestones_project ON milestones(project_id);
+CREATE INDEX IF NOT EXISTS idx_milestones_state ON milestones(project_id, state);
+
+-- Issue assignees junction table (issues can have multiple assignees)
+CREATE TABLE IF NOT EXISTS issue_assignees (
+    issue_id INTEGER NOT NULL REFERENCES issues(id) ON DELETE CASCADE,
+    username TEXT NOT NULL,
+    PRIMARY KEY (issue_id, username)
+);
+
+CREATE INDEX IF NOT EXISTS idx_issue_assignees_username ON issue_assignees(username);
+
+-- Index for due_date filtering
+CREATE INDEX IF NOT EXISTS idx_issues_due_date ON issues(due_date);
+
+-- Index for milestone filtering
+CREATE INDEX IF NOT EXISTS idx_issues_milestone ON issues(milestone_id);
+
+-- Update schema version
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (5, strftime('%s', 'now') * 1000, 'Add assignees, milestone, and due_date support');