gobby 0.2.6__py3-none-any.whl → 0.2.8__py3-none-any.whl

gobby/storage/migrations.py

@@ -3,17 +3,27 @@
 This module handles schema migrations for the Gobby database.
 
 For new databases (version == 0):
-    The BASELINE_SCHEMA is applied directly, jumping to version 60.
+    By default (use_flattened_baseline=True), BASELINE_SCHEMA_V2 is applied,
+    jumping directly to version 75 with a clean schema definition.
 
-For existing databases (0 < version < 60):
-    Legacy migrations are imported from migrations_legacy.py and run incrementally.
+    To use the legacy path (use_flattened_baseline=False), the old BASELINE_SCHEMA
+    is applied at version 60, followed by incremental migrations.
+
+For existing databases (0 < version < 75):
+    Upgrade is not supported without legacy migrations (removed).
+
+For existing databases (version >= 75):
+    Any migrations in MIGRATIONS (v76+) are applied incrementally.
+
+Troubleshooting:
+    If you experience issues with new database creation, ensure you are starting
+    fresh or have a database version >= 60.
 
-For all databases:
-    Any migrations in MIGRATIONS (v61+) are applied after the baseline/legacy path.
 
 To add a new migration:
-    1. Add it to the MIGRATIONS list below with version = 61, 62, etc.
+    1. Add it to the MIGRATIONS list below with version = 76, 77, etc.
     2. Use SQL strings for schema changes, callables for data migrations.
+    3. Also add the migration to BASELINE_SCHEMA_V2 for future fresh installs.
 """
 
 import logging
@@ -23,22 +33,29 @@ from gobby.storage.database import LocalDatabase
 
 logger = logging.getLogger(__name__)
 
+
+class MigrationUnsupportedError(Exception):
+    """Raised when database version is too old to migrate."""
+
+    pass
+
+
 # Migration can be SQL string or a callable that takes LocalDatabase
 MigrationAction = str | Callable[[LocalDatabase], None]
 
-# Baseline version - the schema state after all legacy migrations
-BASELINE_VERSION = 60
+# Baseline version - the schema state at v78 (flattened)
+# This is applied for new databases directly
+BASELINE_VERSION = 78
 
-# Baseline schema - applied directly for new databases
-# This represents the final schema state after migrations 1-60
+# Baseline schema - flattened from v78 production state, includes hub tracking fields
+# This is applied for new databases directly
+# Generated by: sqlite3 ~/.gobby/gobby-hub.db .schema
 BASELINE_SCHEMA = """
--- Schema version tracking
 CREATE TABLE schema_version (
     version INTEGER PRIMARY KEY,
     applied_at TEXT NOT NULL DEFAULT (datetime('now'))
 );
 
--- Projects
 CREATE TABLE projects (
     id TEXT PRIMARY KEY,
     name TEXT NOT NULL UNIQUE,
@@ -57,7 +74,6 @@ VALUES ('00000000-0000-0000-0000-000000000000', '_orphaned', NULL, datetime('now
 INSERT INTO projects (id, name, repo_path, created_at, updated_at)
 VALUES ('00000000-0000-0000-0000-000000000001', '_migrated', NULL, datetime('now'), datetime('now'));
 
--- MCP Servers
 CREATE TABLE mcp_servers (
     id TEXT PRIMARY KEY,
     name TEXT NOT NULL,
@@ -78,7 +94,6 @@ CREATE INDEX idx_mcp_servers_project_id ON mcp_servers(project_id);
 CREATE INDEX idx_mcp_servers_enabled ON mcp_servers(enabled);
 CREATE UNIQUE INDEX idx_mcp_servers_name_project ON mcp_servers(name, project_id);
 
--- Tools
 CREATE TABLE tools (
     id TEXT PRIMARY KEY,
     mcp_server_id TEXT NOT NULL REFERENCES mcp_servers(id) ON DELETE CASCADE,
@@ -92,7 +107,6 @@ CREATE TABLE tools (
 CREATE INDEX idx_tools_server_id ON tools(mcp_server_id);
 CREATE INDEX idx_tools_name ON tools(name);
 
--- Tool embeddings for semantic search
 CREATE TABLE tool_embeddings (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     tool_id TEXT NOT NULL REFERENCES tools(id) ON DELETE CASCADE,
@@ -111,7 +125,6 @@ CREATE INDEX idx_tool_embeddings_server ON tool_embeddings(server_name);
 CREATE INDEX idx_tool_embeddings_project ON tool_embeddings(project_id);
 CREATE INDEX idx_tool_embeddings_hash ON tool_embeddings(text_hash);
 
--- Tool schema hashes for incremental re-indexing
 CREATE TABLE tool_schema_hashes (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     server_name TEXT NOT NULL,
@@ -127,7 +140,6 @@ CREATE INDEX idx_schema_hashes_server ON tool_schema_hashes(server_name);
 CREATE INDEX idx_schema_hashes_project ON tool_schema_hashes(project_id);
 CREATE INDEX idx_schema_hashes_verified ON tool_schema_hashes(last_verified_at);
 
--- Tool metrics
 CREATE TABLE tool_metrics (
     id TEXT PRIMARY KEY,
     project_id TEXT NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
@@ -149,7 +161,6 @@ CREATE INDEX idx_tool_metrics_tool ON tool_metrics(tool_name);
 CREATE INDEX idx_tool_metrics_call_count ON tool_metrics(call_count DESC);
 CREATE INDEX idx_tool_metrics_last_called ON tool_metrics(last_called_at);
 
--- Tool metrics daily aggregates
 CREATE TABLE tool_metrics_daily (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     project_id TEXT NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
@@ -168,7 +179,6 @@ CREATE INDEX idx_tool_metrics_daily_project ON tool_metrics_daily(project_id);
 CREATE INDEX idx_tool_metrics_daily_date ON tool_metrics_daily(date);
 CREATE INDEX idx_tool_metrics_daily_server ON tool_metrics_daily(server_name);
 
--- Agent runs
 CREATE TABLE agent_runs (
     id TEXT PRIMARY KEY,
     parent_session_id TEXT NOT NULL REFERENCES sessions(id),
@@ -192,7 +202,6 @@ CREATE INDEX idx_agent_runs_child_session ON agent_runs(child_session_id);
 CREATE INDEX idx_agent_runs_status ON agent_runs(status);
 CREATE INDEX idx_agent_runs_provider ON agent_runs(provider);
 
--- Sessions
 CREATE TABLE sessions (
     id TEXT PRIMARY KEY,
     external_id TEXT NOT NULL,
@@ -221,6 +230,8 @@ CREATE TABLE sessions (
     usage_total_cost_usd REAL DEFAULT 0.0,
     terminal_context TEXT,
     seq_num INTEGER,
+    model TEXT,
+    had_edits BOOLEAN DEFAULT 0,
     created_at TEXT NOT NULL DEFAULT (datetime('now')),
     updated_at TEXT NOT NULL DEFAULT (datetime('now'))
 );
@@ -235,10 +246,9 @@ CREATE INDEX idx_sessions_agent_depth ON sessions(agent_depth);
 CREATE INDEX idx_sessions_spawned_by ON sessions(spawned_by_agent_id);
 CREATE INDEX idx_sessions_workflow ON sessions(workflow_name);
 CREATE INDEX idx_sessions_agent_run ON sessions(agent_run_id);
-CREATE UNIQUE INDEX idx_sessions_seq_num ON sessions(seq_num);
+CREATE UNIQUE INDEX idx_sessions_seq_num ON sessions(project_id, seq_num);
 CREATE UNIQUE INDEX idx_sessions_unique ON sessions(external_id, machine_id, source, project_id);
 
--- Session messages
 CREATE TABLE session_messages (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -259,7 +269,6 @@ CREATE INDEX idx_session_messages_role ON session_messages(role);
 CREATE INDEX idx_session_messages_timestamp ON session_messages(timestamp);
 CREATE INDEX idx_session_messages_tool ON session_messages(tool_name);
 
--- Session message processing state
 CREATE TABLE session_message_state (
     session_id TEXT PRIMARY KEY REFERENCES sessions(id) ON DELETE CASCADE,
     last_byte_offset INTEGER DEFAULT 0,
@@ -269,7 +278,6 @@ CREATE TABLE session_message_state (
     updated_at TEXT NOT NULL DEFAULT (datetime('now'))
 );
 
--- Session artifacts with FTS
 CREATE TABLE session_artifacts (
     id TEXT PRIMARY KEY,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -286,7 +294,6 @@ CREATE INDEX idx_session_artifacts_type ON session_artifacts(artifact_type);
 CREATE INDEX idx_session_artifacts_created ON session_artifacts(created_at);
 CREATE VIRTUAL TABLE session_artifacts_fts USING fts5(id UNINDEXED, content);
 
--- Session stop signals for autonomous stop
 CREATE TABLE session_stop_signals (
     session_id TEXT PRIMARY KEY REFERENCES sessions(id) ON DELETE CASCADE,
     source TEXT NOT NULL,
@@ -297,7 +304,6 @@ CREATE TABLE session_stop_signals (
 CREATE INDEX idx_stop_signals_pending ON session_stop_signals(acknowledged_at)
     WHERE acknowledged_at IS NULL;
 
--- Loop progress for autonomous progress tracking
 CREATE TABLE loop_progress (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -311,7 +317,6 @@ CREATE INDEX idx_loop_progress_session ON loop_progress(session_id, recorded_at
 CREATE INDEX idx_loop_progress_high_value ON loop_progress(session_id, is_high_value, recorded_at DESC)
     WHERE is_high_value = 1;
 
--- Tasks
 CREATE TABLE tasks (
     id TEXT PRIMARY KEY,
     project_id TEXT NOT NULL REFERENCES projects(id),
@@ -374,7 +379,6 @@ CREATE INDEX idx_tasks_closed_session ON tasks(closed_in_session_id);
 CREATE UNIQUE INDEX idx_tasks_seq_num ON tasks(project_id, seq_num);
 CREATE INDEX idx_tasks_path_cache ON tasks(path_cache);
 
--- Task dependencies
 CREATE TABLE task_dependencies (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     task_id TEXT NOT NULL REFERENCES tasks(id) ON DELETE CASCADE,
@@ -386,7 +390,6 @@ CREATE TABLE task_dependencies (
 CREATE INDEX idx_deps_task ON task_dependencies(task_id);
 CREATE INDEX idx_deps_depends_on ON task_dependencies(depends_on);
 
--- Session-task linkages
 CREATE TABLE session_tasks (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -398,7 +401,6 @@ CREATE TABLE session_tasks (
 CREATE INDEX idx_session_tasks_session ON session_tasks(session_id);
 CREATE INDEX idx_session_tasks_task ON session_tasks(task_id);
 
--- Task validation history
 CREATE TABLE task_validation_history (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     task_id TEXT NOT NULL REFERENCES tasks(id) ON DELETE CASCADE,
@@ -413,7 +415,6 @@ CREATE TABLE task_validation_history (
 );
 CREATE INDEX idx_validation_history_task ON task_validation_history(task_id);
 
--- Task selection history for stuck detection
 CREATE TABLE task_selection_history (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -424,7 +425,6 @@ CREATE TABLE task_selection_history (
 CREATE INDEX idx_task_selection_session ON task_selection_history(session_id, selected_at DESC);
 CREATE INDEX idx_task_selection_task ON task_selection_history(session_id, task_id, selected_at DESC);
 
--- Workflow states
 CREATE TABLE workflow_states (
     session_id TEXT PRIMARY KEY,
     workflow_name TEXT NOT NULL,
@@ -445,7 +445,6 @@ CREATE TABLE workflow_states (
     FOREIGN KEY (session_id) REFERENCES sessions(id) ON DELETE CASCADE
 );
 
--- Workflow audit log
 CREATE TABLE workflow_audit_log (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL,
@@ -465,7 +464,6 @@ CREATE INDEX idx_audit_timestamp ON workflow_audit_log(timestamp);
 CREATE INDEX idx_audit_event_type ON workflow_audit_log(event_type);
 CREATE INDEX idx_audit_result ON workflow_audit_log(result);
 
--- Memories
 CREATE TABLE memories (
     id TEXT PRIMARY KEY,
     project_id TEXT REFERENCES projects(id),
@@ -485,7 +483,6 @@ CREATE INDEX idx_memories_project ON memories(project_id);
 CREATE INDEX idx_memories_type ON memories(memory_type);
 CREATE INDEX idx_memories_importance ON memories(importance DESC);
 
--- Session-memory linkages
 CREATE TABLE session_memories (
     id INTEGER PRIMARY KEY AUTOINCREMENT,
     session_id TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
@@ -497,7 +494,6 @@ CREATE TABLE session_memories (
 CREATE INDEX idx_session_memories_session ON session_memories(session_id);
 CREATE INDEX idx_session_memories_memory ON session_memories(memory_id);
 
--- Memory cross-references
 CREATE TABLE memory_crossrefs (
     source_id TEXT NOT NULL REFERENCES memories(id) ON DELETE CASCADE,
     target_id TEXT NOT NULL REFERENCES memories(id) ON DELETE CASCADE,
@@ -509,7 +505,6 @@ CREATE INDEX idx_crossrefs_source ON memory_crossrefs(source_id);
 CREATE INDEX idx_crossrefs_target ON memory_crossrefs(target_id);
 CREATE INDEX idx_crossrefs_similarity ON memory_crossrefs(similarity DESC);
 
--- Worktrees
 CREATE TABLE worktrees (
     id TEXT PRIMARY KEY,
     project_id TEXT NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
@@ -531,7 +526,6 @@ CREATE INDEX idx_worktrees_session ON worktrees(agent_session_id);
 CREATE UNIQUE INDEX idx_worktrees_branch ON worktrees(project_id, branch_name);
 CREATE UNIQUE INDEX idx_worktrees_path ON worktrees(worktree_path);
 
--- Merge resolutions
 CREATE TABLE merge_resolutions (
     id TEXT PRIMARY KEY,
     worktree_id TEXT NOT NULL REFERENCES worktrees(id) ON DELETE CASCADE,
@@ -547,7 +541,6 @@ CREATE INDEX idx_merge_resolutions_status ON merge_resolutions(status);
 CREATE INDEX idx_merge_resolutions_source_branch ON merge_resolutions(source_branch);
 CREATE INDEX idx_merge_resolutions_target_branch ON merge_resolutions(target_branch);
 
--- Merge conflicts
 CREATE TABLE merge_conflicts (
     id TEXT PRIMARY KEY,
     resolution_id TEXT NOT NULL REFERENCES merge_resolutions(id) ON DELETE CASCADE,
@@ -562,353 +555,167 @@ CREATE TABLE merge_conflicts (
 CREATE INDEX idx_merge_conflicts_resolution ON merge_conflicts(resolution_id);
 CREATE INDEX idx_merge_conflicts_file_path ON merge_conflicts(file_path);
 CREATE INDEX idx_merge_conflicts_status ON merge_conflicts(status);
-"""
-
-# Future migrations (v61+)
-# Add new migrations here. Do not modify the baseline schema above.
-
-
-def _migrate_test_strategy_to_category(db: LocalDatabase) -> None:
-    """Rename test_strategy column to category if it exists.
-
-    This is a no-op for fresh databases that already have category in the baseline schema.
-    Only runs the rename for databases upgraded from versions before the rename.
-    """
-    # Check if test_strategy column exists
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if row and "test_strategy" in row["sql"].lower():
-        db.execute("ALTER TABLE tasks RENAME COLUMN test_strategy TO category")
-        logger.info("Renamed test_strategy column to category")
-    else:
-        logger.debug("test_strategy column not found (fresh database), skipping rename")
-
-
-def _migrate_add_agent_name(db: LocalDatabase) -> None:
-    """Add agent_name column to tasks table for agent configuration."""
-    # Check if agent_name column already exists (fresh database)
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if row and "agent_name" not in row["sql"].lower():
-        db.execute("ALTER TABLE tasks ADD COLUMN agent_name TEXT")
-        logger.info("Added agent_name column to tasks table")
-    else:
-        logger.debug("agent_name column already exists, skipping")
-
-
-def _migrate_add_reference_doc(db: LocalDatabase) -> None:
-    """Add reference_doc column to tasks table for spec traceability."""
-    # Check if reference_doc column already exists (fresh database)
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if row and "reference_doc" not in row["sql"].lower():
-        db.execute("ALTER TABLE tasks ADD COLUMN reference_doc TEXT")
-        logger.info("Added reference_doc column to tasks table")
-    else:
-        logger.debug("reference_doc column already exists, skipping")
-
-
-def _migrate_add_boolean_columns(db: LocalDatabase) -> None:
-    """Add is_enriched and is_expanded columns to tasks table.
-
-    Note: is_tdd_applied was previously added here but is now deprecated and
-    removed in migration 74. This migration only adds is_enriched and is_expanded.
-    """
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if not row:
-        return
-
-    sql_lower = row["sql"].lower()
-
-    # Add each column if it doesn't exist
-    if "is_enriched" not in sql_lower:
-        db.execute("ALTER TABLE tasks ADD COLUMN is_enriched INTEGER DEFAULT 0")
-        logger.info("Added is_enriched column to tasks table")
-
-    if "is_expanded" not in sql_lower:
-        db.execute("ALTER TABLE tasks ADD COLUMN is_expanded INTEGER DEFAULT 0")
-        logger.info("Added is_expanded column to tasks table")
-
-
-def _migrate_add_review_columns(db: LocalDatabase) -> None:
-    """Add requires_user_review and accepted_by_user columns for review status support."""
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if not row:
-        return
-
-    sql_lower = row["sql"].lower()
-
-    if "requires_user_review" not in sql_lower:
-        db.execute("ALTER TABLE tasks ADD COLUMN requires_user_review INTEGER DEFAULT 0")
-        logger.info("Added requires_user_review column to tasks table")
-
-    if "accepted_by_user" not in sql_lower:
-        db.execute("ALTER TABLE tasks ADD COLUMN accepted_by_user INTEGER DEFAULT 0")
-        logger.info("Added accepted_by_user column to tasks table")
 
+CREATE TABLE inter_session_messages (
+    id TEXT PRIMARY KEY,
+    from_session TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+    to_session TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
+    content TEXT NOT NULL,
+    priority TEXT NOT NULL DEFAULT 'normal',
+    sent_at TEXT NOT NULL,
+    read_at TEXT
+);
+CREATE INDEX idx_inter_session_messages_from_session ON inter_session_messages(from_session);
+CREATE INDEX idx_inter_session_messages_to_session ON inter_session_messages(to_session);
+CREATE INDEX idx_inter_session_messages_unread ON inter_session_messages(to_session, read_at)
+    WHERE read_at IS NULL;
 
-def _migrate_drop_is_enriched(db: LocalDatabase) -> None:
-    """Drop deprecated is_enriched column from tasks table.
+CREATE TABLE skills (
+    id TEXT PRIMARY KEY,
+    name TEXT NOT NULL,
+    description TEXT NOT NULL,
+    content TEXT NOT NULL,
+    version TEXT,
+    license TEXT,
+    compatibility TEXT,
+    allowed_tools TEXT,
+    metadata TEXT,
+    source_path TEXT,
+    source_type TEXT,
+    source_ref TEXT,
+    hub_name TEXT,
+    hub_slug TEXT,
+    hub_version TEXT,
+    enabled INTEGER DEFAULT 1,
+    project_id TEXT REFERENCES projects(id) ON DELETE CASCADE,
+    created_at TEXT NOT NULL,
+    updated_at TEXT NOT NULL
+);
+CREATE INDEX idx_skills_name ON skills(name);
+CREATE INDEX idx_skills_project_id ON skills(project_id);
+CREATE INDEX idx_skills_enabled ON skills(enabled);
+CREATE UNIQUE INDEX idx_skills_name_project ON skills(name, project_id);
+CREATE UNIQUE INDEX idx_skills_name_global ON skills(name) WHERE project_id IS NULL;
 
-    The is_enriched flag is no longer used after the Task Expansion V3 simplification.
-    SQLite 3.35.0+ supports ALTER TABLE DROP COLUMN.
-    """
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if not row:
-        return
+CREATE TABLE clones (
+    id TEXT PRIMARY KEY,
+    project_id TEXT NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    branch_name TEXT NOT NULL,
+    clone_path TEXT NOT NULL,
+    base_branch TEXT DEFAULT 'main',
+    task_id TEXT REFERENCES tasks(id) ON DELETE SET NULL,
+    agent_session_id TEXT REFERENCES sessions(id) ON DELETE SET NULL,
+    status TEXT DEFAULT 'active',
+    remote_url TEXT,
+    last_sync_at TEXT,
+    cleanup_after TEXT,
+    created_at TEXT NOT NULL DEFAULT (datetime('now')),
+    updated_at TEXT NOT NULL DEFAULT (datetime('now'))
+);
+CREATE INDEX idx_clones_project ON clones(project_id);
+CREATE INDEX idx_clones_status ON clones(status);
+CREATE INDEX idx_clones_task ON clones(task_id);
+CREATE INDEX idx_clones_session ON clones(agent_session_id);
+CREATE UNIQUE INDEX idx_clones_path ON clones(clone_path);
+"""
 
-    if "is_enriched" in row["sql"].lower():
-        try:
-            db.execute("ALTER TABLE tasks DROP COLUMN is_enriched")
-            logger.info("Dropped is_enriched column from tasks table")
-        except Exception as e:
-            # SQLite < 3.35.0 doesn't support DROP COLUMN
-            # Column will remain but be unused - not a problem
-            logger.warning(f"Could not drop is_enriched column (SQLite < 3.35?): {e}")
+# Future migrations (v61+)
+# Add new migrations here. Do not modify the baseline schema above.
 
 
-def _migrate_add_inter_session_messages(db: LocalDatabase) -> None:
-    """Add inter_session_messages table for parent-child agent communication.
+def _migrate_session_seq_num_project_scoped(db: LocalDatabase) -> None:
+    """Change sessions.seq_num index from global to project-scoped.
 
-    This table enables asynchronous messaging between agent sessions,
-    allowing parent agents to send instructions to child agents and
-    receive status updates back.
+    This allows different projects to have independent session numbering (#1, #2, etc.)
+    matching how tasks already work.
     """
-    # Check if table already exists (fresh database with baseline)
+    # Check if the old global index exists
     row = db.fetchone(
-        "SELECT name FROM sqlite_master WHERE type='table' AND name='inter_session_messages'"
+        "SELECT sql FROM sqlite_master WHERE type='index' AND name='idx_sessions_seq_num'"
     )
-    if row:
-        logger.debug("inter_session_messages table already exists, skipping")
+    if not row:
+        logger.debug("idx_sessions_seq_num index does not exist, skipping")
         return
 
-    # Create the table
-    db.execute("""
-        CREATE TABLE inter_session_messages (
-            id TEXT PRIMARY KEY,
-            from_session TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
-            to_session TEXT NOT NULL REFERENCES sessions(id) ON DELETE CASCADE,
-            content TEXT NOT NULL,
-            priority TEXT NOT NULL DEFAULT 'normal',
-            sent_at TEXT NOT NULL,
-            read_at TEXT
-        )
-    """)
-
-    # Create indexes for efficient querying
-    db.execute(
-        "CREATE INDEX idx_inter_session_messages_from_session ON inter_session_messages(from_session)"
-    )
-    db.execute(
-        "CREATE INDEX idx_inter_session_messages_to_session ON inter_session_messages(to_session)"
-    )
-    db.execute(
-        "CREATE INDEX idx_inter_session_messages_unread ON inter_session_messages(to_session, read_at) "
-        "WHERE read_at IS NULL"
-    )
-
-    logger.info("Created inter_session_messages table with indexes")
-
-
-def _migrate_add_media_column(db: LocalDatabase) -> None:
-    """Add media column to memories table for multimodal support."""
-    # Check if media column already exists (fresh database from baseline)
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='memories'")
-    if row and "media" not in row["sql"].lower():
-        db.execute("ALTER TABLE memories ADD COLUMN media TEXT")
-        logger.info("Added media column to memories table")
-    else:
-        logger.debug("media column already exists, skipping")
-
-
-def _migrate_add_expansion_status(db: LocalDatabase) -> None:
-    """Add expansion_status column to tasks table for skill-based expansion."""
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if row and "expansion_status" not in row["sql"].lower():
-        db.execute("ALTER TABLE tasks ADD COLUMN expansion_status TEXT DEFAULT 'none'")
-        logger.info("Added expansion_status column to tasks table")
-    else:
-        logger.debug("expansion_status column already exists, skipping")
-
-
-def _migrate_add_skills_table(db: LocalDatabase) -> None:
-    """Add skills table for Agent Skills spec compliant skill storage.
-
-    Skills provide structured instructions for AI agents following the
-    Agent Skills specification (agentskills.io) with Gobby-specific extensions.
-    """
-    # Check if table already exists
-    row = db.fetchone("SELECT name FROM sqlite_master WHERE type='table' AND name='skills'")
-    if row:
-        logger.debug("skills table already exists, skipping")
+    # Check if it's already project-scoped (contains 'project_id')
+    if "project_id" in (row["sql"] or "").lower():
+        logger.debug("idx_sessions_seq_num is already project-scoped, skipping")
         return
 
-    # Create the skills table
-    db.execute("""
-        CREATE TABLE skills (
-            id TEXT PRIMARY KEY,
-            name TEXT NOT NULL,
-            description TEXT NOT NULL,
-            content TEXT NOT NULL,
-            version TEXT,
-            license TEXT,
-            compatibility TEXT,
-            allowed_tools TEXT,
-            metadata TEXT,
-            source_path TEXT,
-            source_type TEXT,
-            source_ref TEXT,
-            enabled INTEGER DEFAULT 1,
-            project_id TEXT REFERENCES projects(id) ON DELETE CASCADE,
-            created_at TEXT NOT NULL DEFAULT (datetime('now')),
-            updated_at TEXT NOT NULL DEFAULT (datetime('now'))
-        )
-    """)
-
-    # Create indexes
-    db.execute("CREATE INDEX idx_skills_name ON skills(name)")
-    db.execute("CREATE INDEX idx_skills_project_id ON skills(project_id)")
-    db.execute("CREATE INDEX idx_skills_enabled ON skills(enabled)")
-    # Unique constraint: name must be unique within a project scope
-    db.execute("CREATE UNIQUE INDEX idx_skills_name_project ON skills(name, project_id)")
-    # Partial unique index for global skills (project_id IS NULL)
-    # This enforces uniqueness for global skill names since NULL != NULL in SQL
-    db.execute(
-        "CREATE UNIQUE INDEX idx_skills_name_global ON skills(name) WHERE project_id IS NULL"
-    )
+    # Drop the old global index and create new project-scoped index atomically
+    with db.transaction() as conn:
+        conn.execute("DROP INDEX IF EXISTS idx_sessions_seq_num")
+        conn.execute("CREATE UNIQUE INDEX idx_sessions_seq_num ON sessions(project_id, seq_num)")
 
-    logger.info("Created skills table with indexes")
+    logger.info("Changed sessions.seq_num index from global to project-scoped")
 
 
-def _migrate_add_skills_global_unique_index(db: LocalDatabase) -> None:
-    """Add partial unique index for global skills (project_id IS NULL).
+def _migrate_backfill_session_seq_num_per_project(db: LocalDatabase) -> None:
+    """Re-backfill session seq_num values to be per-project.
 
-    This enforces uniqueness for global skill names since NULL != NULL in SQL.
-    The existing idx_skills_name_project only enforces uniqueness within a project scope.
+    This migration re-numbers sessions so each project has independent numbering
+    starting from 1. Required after changing the index to be project-scoped.
     """
-    # Check if index already exists (fresh database from v70+)
-    row = db.fetchone(
-        "SELECT name FROM sqlite_master WHERE type='index' AND name='idx_skills_name_global'"
-    )
-    if row:
-        logger.debug("idx_skills_name_global index already exists, skipping")
-        return
-
-    # Check if skills table exists (might not if on old version that never created it)
-    row = db.fetchone("SELECT name FROM sqlite_master WHERE type='table' AND name='skills'")
-    if not row:
-        logger.debug("skills table does not exist, skipping")
-        return
-
-    db.execute(
-        "CREATE UNIQUE INDEX idx_skills_name_global ON skills(name) WHERE project_id IS NULL"
+    # Get all sessions grouped by project, ordered by created_at
+    sessions = db.fetchall(
+        """
+        SELECT id, project_id FROM sessions
+        ORDER BY project_id, created_at ASC, id ASC
+        """
     )
-    logger.debug("Added idx_skills_name_global partial unique index to skills table")
 
-
-def _migrate_add_clones_table(db: LocalDatabase) -> None:
-    """Add clones table for local git clone management.
-
-    Clones are full repository copies, distinct from worktrees which share
-    a single .git directory. This enables parallel development across machines
-    or isolated environments.
-    """
-    # Check if table already exists
-    row = db.fetchone("SELECT name FROM sqlite_master WHERE type='table' AND name='clones'")
-    if row:
-        logger.debug("clones table already exists, skipping")
+    if not sessions:
+        logger.debug("No sessions to re-number")
         return
 
-    # Create the clones table
-    db.execute("""
-        CREATE TABLE clones (
-            id TEXT PRIMARY KEY,
-            project_id TEXT NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
-            branch_name TEXT NOT NULL,
-            clone_path TEXT NOT NULL,
-            base_branch TEXT DEFAULT 'main',
-            task_id TEXT REFERENCES tasks(id) ON DELETE SET NULL,
-            agent_session_id TEXT REFERENCES sessions(id) ON DELETE SET NULL,
-            status TEXT DEFAULT 'active',
-            remote_url TEXT,
-            last_sync_at TEXT,
-            cleanup_after TEXT,
-            created_at TEXT NOT NULL DEFAULT (datetime('now')),
-            updated_at TEXT NOT NULL DEFAULT (datetime('now'))
-        )
-    """)
-
-    # Create indexes
-    db.execute("CREATE INDEX idx_clones_project ON clones(project_id)")
-    db.execute("CREATE INDEX idx_clones_status ON clones(status)")
-    db.execute("CREATE INDEX idx_clones_task ON clones(task_id)")
-    db.execute("CREATE INDEX idx_clones_session ON clones(agent_session_id)")
-    db.execute("CREATE UNIQUE INDEX idx_clones_path ON clones(clone_path)")
+    # Wrap the entire re-numbering in a transaction for atomicity
+    with db.transaction() as conn:
+        # First, clear all seq_num values to avoid unique constraint violations
+        # when the existing seq_num order doesn't match created_at order
+        conn.execute("UPDATE sessions SET seq_num = NULL")
 
-    logger.debug("Created clones table with indexes")
+        # Assign seq_num per project
+        current_project: str | None = None
+        seq_num = 0
+        updated = 0
 
+        for session in sessions:
+            if session["project_id"] != current_project:
+                current_project = session["project_id"]
+                seq_num = 1
+            else:
+                seq_num += 1
 
-def _migrate_add_model_column(db: LocalDatabase) -> None:
-    """Add model column to sessions table for cost tracking by model.
+            conn.execute(
+                "UPDATE sessions SET seq_num = ? WHERE id = ?",
+                (seq_num, session["id"]),
+            )
+            updated += 1
 
-    This enables the TokenTracker to aggregate usage by model and apply
-    model-specific pricing for budget tracking.
-    """
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='sessions'")
-    if row and "model" not in row["sql"].lower():
-        db.execute("ALTER TABLE sessions ADD COLUMN model TEXT")
-        logger.info("Added model column to sessions table")
-    else:
-        logger.debug("model column already exists, skipping")
+    logger.info(f"Re-numbered {updated} sessions with per-project seq_num")
 
 
-def _migrate_drop_is_tdd_applied(db: LocalDatabase) -> None:
-    """Drop deprecated is_tdd_applied column from tasks table.
+def _migrate_add_hub_tracking_to_skills(db: LocalDatabase) -> None:
+    """Add hub tracking fields to skills table.
 
-    The is_tdd_applied flag is no longer used after removing the TDD sandwich pattern.
-    TDD instructions are now embedded directly in task descriptions for code/config categories.
-    SQLite 3.35.0+ supports ALTER TABLE DROP COLUMN.
+    Adds hub_name, hub_slug, and hub_version columns to track which hub
+    a skill was installed from.
     """
-    row = db.fetchone("SELECT sql FROM sqlite_master WHERE type='table' AND name='tasks'")
-    if not row:
-        return
+    with db.transaction() as conn:
+        conn.execute("ALTER TABLE skills ADD COLUMN hub_name TEXT")
+        conn.execute("ALTER TABLE skills ADD COLUMN hub_slug TEXT")
+        conn.execute("ALTER TABLE skills ADD COLUMN hub_version TEXT")
 
-    if "is_tdd_applied" in row["sql"].lower():
-        try:
-            db.execute("ALTER TABLE tasks DROP COLUMN is_tdd_applied")
-            logger.info("Dropped is_tdd_applied column from tasks table")
-        except Exception as e:
-            # SQLite < 3.35.0 doesn't support DROP COLUMN
-            # Column will remain but be unused - not a problem
-            logger.warning(f"Could not drop is_tdd_applied column (SQLite < 3.35?): {e}")
+    logger.info("Added hub tracking fields to skills table")
 
 
 MIGRATIONS: list[tuple[int, str, MigrationAction]] = [
-    # TDD Expansion Restructure: Rename test_strategy to category
-    (61, "Rename test_strategy to category", _migrate_test_strategy_to_category),
-    # TDD Expansion Restructure: Add agent_name column
-    (62, "Add agent_name column to tasks", _migrate_add_agent_name),
-    # TDD Expansion Restructure: Add reference_doc column
-    (63, "Add reference_doc column to tasks", _migrate_add_reference_doc),
-    # TDD Expansion Restructure: Add boolean columns for idempotent operations
-    (64, "Add boolean columns to tasks", _migrate_add_boolean_columns),
-    # Review status: Add columns for HITL review workflow
-    (65, "Add review columns to tasks", _migrate_add_review_columns),
-    # Task Expansion V3: Drop unused is_enriched column
-    (66, "Drop is_enriched column from tasks", _migrate_drop_is_enriched),
-    # Inter-session messaging: Add table for parent-child agent communication
-    (67, "Add inter_session_messages table", _migrate_add_inter_session_messages),
-    # Memory V3 Phase 2: Add media column for multimodal support
-    (68, "Add media column to memories", _migrate_add_media_column),
-    # Skill-based expansion: Add expansion_status column to tasks
-    (69, "Add expansion_status column to tasks", _migrate_add_expansion_status),
-    # Skills storage: Add skills table for Agent Skills spec
-    (70, "Add skills table", _migrate_add_skills_table),
-    # Skills: Add partial unique index for global skills
-    (71, "Add global skills unique index", _migrate_add_skills_global_unique_index),
-    # Local clones: Add table for git clone management
-    (72, "Add clones table", _migrate_add_clones_table),
-    # Token tracking: Add model column to sessions for cost tracking by model
-    (73, "Add model column to sessions", _migrate_add_model_column),
-    # TDD cleanup: Drop unused is_tdd_applied column from tasks
-    (74, "Drop is_tdd_applied column from tasks", _migrate_drop_is_tdd_applied),
+    # Project-scoped session refs: Change seq_num index from global to project-scoped
+    (76, "Make sessions.seq_num project-scoped", _migrate_session_seq_num_project_scoped),
+    # Project-scoped session refs: Re-backfill seq_num per project
+    (77, "Backfill sessions.seq_num per project", _migrate_backfill_session_seq_num_per_project),
+    # Hub tracking: Add hub_name, hub_slug, hub_version to skills table
+    (78, "Add hub tracking fields to skills", _migrate_add_hub_tracking_to_skills),
 ]
 
 
@@ -922,8 +729,8 @@ def get_current_version(db: LocalDatabase) -> int:
 
 
 def _apply_baseline(db: LocalDatabase) -> None:
-    """Apply baseline schema for new databases."""
-    logger.info("Applying baseline schema (v60)")
+    """Apply baseline schema for new databases (flattened at v75)."""
+    logger.info("Applying baseline schema (v75)")
 
     # Execute baseline schema
     for statement in BASELINE_SCHEMA.strip().split(";"):
@@ -995,13 +802,10 @@ def run_migrations(db: LocalDatabase) -> int:
     Run pending migrations.
 
     For new databases (version == 0):
-        Applies baseline schema directly, jumping to version 60.
-
-    For existing databases (0 < version < 60):
-        Imports and runs legacy migrations incrementally.
+        - Applies baseline schema (v75) directly.
 
-    For all databases:
-        Runs any new migrations (v61+) after baseline/legacy path.
+    For existing databases:
+        - Runs any new migrations from v76 onwards.
 
     Args:
         db: LocalDatabase instance
@@ -1013,20 +817,22 @@ def run_migrations(db: LocalDatabase) -> int:
     total_applied = 0
 
     if current_version == 0:
-        # New database: apply baseline schema directly
+        # New database with flattened baseline: apply schema directly
+        logger.info("Using flattened baseline for new database")
         _apply_baseline(db)
         total_applied = 1
         current_version = BASELINE_VERSION
     elif current_version < BASELINE_VERSION:
-        # Existing database needing legacy migrations
-        # Lazy import to avoid loading legacy code for new databases
-        from gobby.storage.migrations_legacy import LEGACY_MIGRATIONS
-
-        applied = _run_migration_list(db, current_version, LEGACY_MIGRATIONS)
-        total_applied += applied
-        current_version = get_current_version(db)
+        # Unsupported: Pre-v75 database without local migrations
+        # Since we removed legacy migrations, we can't upgrade.
+        msg = (
+            f"Database version {current_version} is older than baseline "
+            f"{BASELINE_VERSION}. Upgrade not supported without legacy migrations."
+        )
+        logger.error(msg)
+        raise MigrationUnsupportedError(msg)
 
-    # Run any new migrations (v61+)
+    # Run any new migrations (v76+)
     if MIGRATIONS:
         applied = _run_migration_list(db, current_version, MIGRATIONS)
         total_applied += applied