kotadb 2.2.0-next.20260204235102 → 2.2.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "kotadb",
-  "version": "2.2.0-next.20260204235102",
+  "version": "2.2.0",
   "description": "Local-only code intelligence tool for CLI agents. SQLite-backed repository indexing and code search via MCP.",
   "type": "module",
   "module": "src/index.ts",

package/src/api/queries.ts

@@ -1409,75 +1409,3 @@ export async function createDefaultOrganization(
 ): Promise<string> {
 	throw new Error('createDefaultOrganization() is not available in local-only mode - organizations are a cloud-only feature');
 }
-
-/**
- * Get index statistics for startup context display.
- * Queries counts of indexed files, symbols, references, and memory entries.
- * 
- * @param db - Database instance (for testability)
- * @returns Statistics object with counts by type
- */
-function getIndexStatisticsInternal(db: KotaDatabase): {
-	files: number;
-	symbols: number;
-	references: number;
-	decisions: number;
-	patterns: number;
-	failures: number;
-	repositories: number;
-} {
-	const stats = {
-		files: 0,
-		symbols: 0,
-		references: 0,
-		decisions: 0,
-		patterns: 0,
-		failures: 0,
-		repositories: 0,
-	};
-	
-	// Helper function to safely query count with fallback for missing tables
-	const safeCount = (tableName: string): number => {
-		try {
-			const result = db.queryOne<{ count: number }>(
-				`SELECT COUNT(*) as count FROM ${tableName}`
-			);
-			return result?.count || 0;
-		} catch (error) {
-			// Table doesn't exist yet (e.g., memory layer tables)
-			return 0;
-		}
-	};
-	
-	// Count indexed files
-	stats.files = safeCount('indexed_files');
-	
-	// Count indexed symbols
-	stats.symbols = safeCount('indexed_symbols');
-	
-	// Count references
-	stats.references = safeCount('indexed_references');
-	
-	// Count decisions (may not exist in all installations)
-	stats.decisions = safeCount('kota_decisions');
-	
-	// Count patterns (may not exist in all installations)
-	stats.patterns = safeCount('kota_patterns');
-	
-	// Count failures (may not exist in all installations)
-	stats.failures = safeCount('kota_failures');
-	
-	// Count repositories
-	stats.repositories = safeCount('repositories');
-	
-	return stats;
-}
-
-/**
- * Get index statistics for startup context display (public API).
- * 
- * @returns Statistics object with counts by type
- */
-export function getIndexStatistics(): ReturnType<typeof getIndexStatisticsInternal> {
-	return getIndexStatisticsInternal(getGlobalDatabase());
-}

package/src/db/migrations/004_memory_layer.sql

@@ -3,53 +3,181 @@
 -- Migration: 004_memory_layer
 -- Issue: Memory Layer for Agent Intelligence
 -- Author: Claude Code
--- Date: 2026-02-03 (UPDATED: 2026-02-04)
+-- Date: 2026-02-03
 --
--- This migration extends the memory layer with:
--- - decisions.status column (active, superseded, deprecated)
--- - agent_sessions table for tracking agent work
+-- This migration extends the memory layer tables with additional schema:
+-- - decisions: Add status column (active, superseded, deprecated)
+-- - failed_approaches: Alternative to failures with clearer naming
+-- - pattern_annotations: Enhanced patterns with evidence/confidence scoring
+-- - agent_sessions: Track agent work sessions
+-- - session_insights: Insights linked to sessions with file references
 --
 -- Note: The base sqlite-schema.sql already has decisions, failures, patterns,
--- and insights tables. This migration only adds what's missing.
+-- and insights tables. This migration adds enhanced versions and the missing
+-- agent_sessions table for complete session tracking.
 
 -- ============================================================================
 -- 1. Extend Decisions Table - Add status column
 -- ============================================================================
 -- Add status column to track decision lifecycle
--- Note: SQLite ALTER TABLE ADD COLUMN will fail if column exists,
--- which is the expected behavior (migration already applied)
 
 ALTER TABLE decisions ADD COLUMN status TEXT DEFAULT 'active';
 
+-- Add index for active decisions (most common query)
 CREATE INDEX IF NOT EXISTS idx_decisions_status ON decisions(status) WHERE status = 'active';
 
 -- ============================================================================
--- 2. Agent Sessions Table
+-- 2. Failed Approaches Table (alternative to failures with clearer naming)
+-- ============================================================================
+-- Tracks what didn't work to prevent repeating mistakes
+
+CREATE TABLE IF NOT EXISTS failed_approaches (
+    id TEXT PRIMARY KEY,                         -- uuid → TEXT
+    repository_id TEXT NOT NULL,                 -- Foreign key to repositories
+    title TEXT NOT NULL,                         -- Short description
+    problem TEXT NOT NULL,                       -- What problem was being solved
+    approach TEXT NOT NULL,                      -- What was tried
+    failure_reason TEXT NOT NULL,                -- Why it failed
+    related_files TEXT,                          -- JSON array of related file paths
+    created_at TEXT NOT NULL DEFAULT (datetime('now')),
+    
+    FOREIGN KEY (repository_id) REFERENCES repositories(id) ON DELETE CASCADE
+);
+
+-- Indexes for common queries
+CREATE INDEX IF NOT EXISTS idx_failed_approaches_repository_id ON failed_approaches(repository_id);
+CREATE INDEX IF NOT EXISTS idx_failed_approaches_created_at ON failed_approaches(created_at DESC);
+
+-- ============================================================================
+-- 3. Failed Approaches FTS5 Virtual Table
+-- ============================================================================
+-- External content FTS5 for searching failed approaches
+
+CREATE VIRTUAL TABLE IF NOT EXISTS failed_approaches_fts USING fts5(
+    title,
+    problem,
+    approach,
+    failure_reason,
+    content='failed_approaches',
+    content_rowid='rowid'
+);
+
+-- ============================================================================
+-- 4. Failed Approaches FTS5 Sync Triggers
+-- ============================================================================
+
+-- After INSERT: Add new failed approach to FTS index
+CREATE TRIGGER IF NOT EXISTS failed_approaches_fts_ai 
+AFTER INSERT ON failed_approaches 
+BEGIN
+    INSERT INTO failed_approaches_fts(rowid, title, problem, approach, failure_reason) 
+    VALUES (new.rowid, new.title, new.problem, new.approach, new.failure_reason);
+END;
+
+-- After DELETE: Remove failed approach from FTS index
+CREATE TRIGGER IF NOT EXISTS failed_approaches_fts_ad 
+AFTER DELETE ON failed_approaches 
+BEGIN
+    INSERT INTO failed_approaches_fts(failed_approaches_fts, rowid, title, problem, approach, failure_reason) 
+    VALUES ('delete', old.rowid, old.title, old.problem, old.approach, old.failure_reason);
+END;
+
+-- After UPDATE: Update failed approach in FTS index (delete old, insert new)
+CREATE TRIGGER IF NOT EXISTS failed_approaches_fts_au 
+AFTER UPDATE ON failed_approaches 
+BEGIN
+    INSERT INTO failed_approaches_fts(failed_approaches_fts, rowid, title, problem, approach, failure_reason) 
+    VALUES ('delete', old.rowid, old.title, old.problem, old.approach, old.failure_reason);
+    INSERT INTO failed_approaches_fts(rowid, title, problem, approach, failure_reason) 
+    VALUES (new.rowid, new.title, new.problem, new.approach, new.failure_reason);
+END;
+
+-- ============================================================================
+-- 5. Pattern Annotations Table
+-- ============================================================================
+-- Enhanced pattern detection with evidence counting and confidence scoring
+
+CREATE TABLE IF NOT EXISTS pattern_annotations (
+    id TEXT PRIMARY KEY,                         -- uuid → TEXT
+    repository_id TEXT NOT NULL,                 -- Foreign key to repositories
+    pattern_type TEXT NOT NULL,                  -- Pattern category (logging, error-handling, testing, etc.)
+    pattern_name TEXT NOT NULL,                  -- Pattern identifier
+    description TEXT NOT NULL,                   -- Human-readable description
+    example_code TEXT,                           -- Code example (optional)
+    evidence_count INTEGER NOT NULL DEFAULT 1,   -- Number of occurrences found
+    confidence REAL NOT NULL DEFAULT 1.0,        -- Confidence score (0.0-1.0)
+    created_at TEXT NOT NULL DEFAULT (datetime('now')),
+    
+    FOREIGN KEY (repository_id) REFERENCES repositories(id) ON DELETE CASCADE,
+    
+    CHECK (confidence >= 0.0 AND confidence <= 1.0),
+    CHECK (evidence_count >= 1)
+);
+
+-- Indexes for common queries
+CREATE INDEX IF NOT EXISTS idx_pattern_annotations_repository_id ON pattern_annotations(repository_id);
+CREATE INDEX IF NOT EXISTS idx_pattern_annotations_pattern_type ON pattern_annotations(pattern_type);
+CREATE INDEX IF NOT EXISTS idx_pattern_annotations_confidence ON pattern_annotations(confidence DESC);
+-- Composite index for high-confidence patterns by type
+CREATE INDEX IF NOT EXISTS idx_pattern_annotations_type_confidence 
+ON pattern_annotations(repository_id, pattern_type, confidence DESC);
+
+-- ============================================================================
+-- 6. Agent Sessions Table
 -- ============================================================================
 -- Tracks agent work sessions for learning and analysis
 
 CREATE TABLE IF NOT EXISTS agent_sessions (
-    id TEXT PRIMARY KEY,
-    repository_id TEXT NOT NULL,
-    agent_type TEXT,
-    task_summary TEXT,
-    outcome TEXT,
-    files_modified TEXT,
+    id TEXT PRIMARY KEY,                         -- uuid → TEXT
+    repository_id TEXT NOT NULL,                 -- Foreign key to repositories
+    agent_type TEXT,                             -- Type of agent (plan, build, improve, etc.)
+    task_summary TEXT,                           -- What the agent was working on
+    outcome TEXT,                                -- Session outcome
+    files_modified TEXT,                         -- JSON array of modified file paths
     started_at TEXT NOT NULL DEFAULT (datetime('now')),
-    ended_at TEXT,
+    ended_at TEXT,                               -- NULL if session is ongoing
     
     FOREIGN KEY (repository_id) REFERENCES repositories(id) ON DELETE CASCADE,
+    
     CHECK (outcome IS NULL OR outcome IN ('success', 'failure', 'partial'))
 );
 
+-- Indexes for common queries
 CREATE INDEX IF NOT EXISTS idx_agent_sessions_repository_id ON agent_sessions(repository_id);
 CREATE INDEX IF NOT EXISTS idx_agent_sessions_agent_type ON agent_sessions(agent_type) WHERE agent_type IS NOT NULL;
 CREATE INDEX IF NOT EXISTS idx_agent_sessions_outcome ON agent_sessions(outcome) WHERE outcome IS NOT NULL;
 CREATE INDEX IF NOT EXISTS idx_agent_sessions_started_at ON agent_sessions(started_at DESC);
+-- Partial index for ongoing sessions
 CREATE INDEX IF NOT EXISTS idx_agent_sessions_ongoing ON agent_sessions(repository_id) WHERE ended_at IS NULL;
 
 -- ============================================================================
--- 3. Record Migration
+-- 7. Session Insights Table
+-- ============================================================================
+-- Insights discovered during agent sessions with proper foreign keys
+
+CREATE TABLE IF NOT EXISTS session_insights (
+    id TEXT PRIMARY KEY,                         -- uuid → TEXT
+    session_id TEXT NOT NULL,                    -- Foreign key to agent_sessions
+    insight_type TEXT NOT NULL,                  -- Type of insight
+    content TEXT NOT NULL,                       -- The insight content
+    related_file_id TEXT,                        -- Optional reference to indexed_files
+    created_at TEXT NOT NULL DEFAULT (datetime('now')),
+    
+    FOREIGN KEY (session_id) REFERENCES agent_sessions(id) ON DELETE CASCADE,
+    FOREIGN KEY (related_file_id) REFERENCES indexed_files(id) ON DELETE SET NULL,
+    
+    CHECK (insight_type IN ('discovery', 'failure', 'workaround'))
+);
+
+-- Indexes for common queries
+CREATE INDEX IF NOT EXISTS idx_session_insights_session_id ON session_insights(session_id);
+CREATE INDEX IF NOT EXISTS idx_session_insights_insight_type ON session_insights(insight_type);
+CREATE INDEX IF NOT EXISTS idx_session_insights_related_file ON session_insights(related_file_id) 
+WHERE related_file_id IS NOT NULL;
+CREATE INDEX IF NOT EXISTS idx_session_insights_created_at ON session_insights(created_at DESC);
+
+-- ============================================================================
+-- 8. Record Migration
 -- ============================================================================
 
 INSERT OR IGNORE INTO schema_migrations (name) VALUES ('004_memory_layer');

package/src/db/sqlite/sqlite-client.ts

@@ -19,7 +19,6 @@ import { cpus } from "node:os";
 import { createLogger } from "@logging/logger.js";
 import { findProjectRoot } from "@config/project-root.js";
 import { ensureKotadbIgnored } from "@config/gitignore.js";
-import { runMigrations, updateExistingChecksums } from "./migration-runner.js";
 
 const logger = createLogger({ module: "sqlite-client" });
 
@@ -138,11 +137,8 @@ export class KotaDatabase {
 		this.configurePragmas();
 
 		// Auto-initialize schema if not already present (writer only)
-		// - New database: Apply full base schema
-		// - Existing database: Run pending migrations
 		if (!this.config.readonly && !this.config.skipSchemaInit) {
 			if (!this.tableExists("indexed_files")) {
-				// NEW DATABASE: Apply base schema
 				const schemaPath = join(__dirname, "../sqlite-schema.sql");
 				const schema = readFileSync(schemaPath, "utf-8");
 				this.exec(schema);
@@ -150,28 +146,7 @@ export class KotaDatabase {
 					path: this.config.path,
 				});
 			} else {
-				// EXISTING DATABASE: Run migrations
-				const migrationsDir = join(__dirname, "../migrations");
-				try {
-					const result = runMigrations(this, migrationsDir);
-					if (result.appliedCount > 0) {
-						logger.info("Applied pending migrations", {
-							count: result.appliedCount,
-							migrations: result.appliedMigrations,
-						});
-					}
-					// Update checksums for existing migrations (after checksum column added)
-					updateExistingChecksums(this, migrationsDir);
-					if (result.errors.length > 0) {
-						logger.error("Migration errors", { errors: result.errors });
-					}
-				} catch (error) {
-					logger.error("Migration runner failed", {
-						error: error instanceof Error ? error.message : String(error),
-					});
-					// Do not throw - allow database to continue operating with current schema
-					// This prevents startup failures due to migration issues
-				}
+				logger.debug("SQLite schema already initialized");
 			}
 		}
 

package/src/db/sqlite-schema.sql

@@ -462,54 +462,6 @@ BEGIN
     VALUES (new.rowid, new.content);
 END;
 
--- ============================================================================
--- 11. Workflow Contexts Table (Issue #144)
--- ============================================================================
--- Stores curated context data for each workflow phase
-
-CREATE TABLE IF NOT EXISTS workflow_contexts (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    workflow_id TEXT NOT NULL,
-    phase TEXT NOT NULL,
-    context_data TEXT NOT NULL,
-    created_at TEXT NOT NULL DEFAULT (datetime('now')),
-    updated_at TEXT NOT NULL DEFAULT (datetime('now')),
-    
-    UNIQUE(workflow_id, phase),
-    CHECK (phase IN ('analysis', 'plan', 'build', 'improve'))
-);
-
-CREATE INDEX IF NOT EXISTS idx_workflow_contexts_workflow_id 
-ON workflow_contexts(workflow_id);
-
-CREATE INDEX IF NOT EXISTS idx_workflow_contexts_created_at 
-ON workflow_contexts(created_at DESC);
-
--- ============================================================================
--- 12. Agent Sessions Table
--- ============================================================================
--- Tracks agent work sessions for learning and analysis
-
-CREATE TABLE IF NOT EXISTS agent_sessions (
-    id TEXT PRIMARY KEY,
-    repository_id TEXT NOT NULL,
-    agent_type TEXT,
-    task_summary TEXT,
-    outcome TEXT,
-    files_modified TEXT,
-    started_at TEXT NOT NULL DEFAULT (datetime('now')),
-    ended_at TEXT,
-    
-    FOREIGN KEY (repository_id) REFERENCES repositories(id) ON DELETE CASCADE,
-    CHECK (outcome IS NULL OR outcome IN ('success', 'failure', 'partial'))
-);
-
-CREATE INDEX IF NOT EXISTS idx_agent_sessions_repository_id ON agent_sessions(repository_id);
-CREATE INDEX IF NOT EXISTS idx_agent_sessions_agent_type ON agent_sessions(agent_type) WHERE agent_type IS NOT NULL;
-CREATE INDEX IF NOT EXISTS idx_agent_sessions_outcome ON agent_sessions(outcome) WHERE outcome IS NOT NULL;
-CREATE INDEX IF NOT EXISTS idx_agent_sessions_started_at ON agent_sessions(started_at DESC);
-CREATE INDEX IF NOT EXISTS idx_agent_sessions_ongoing ON agent_sessions(repository_id) WHERE ended_at IS NULL;
-
 -- Record memory layer migration
 INSERT OR IGNORE INTO schema_migrations (name) VALUES ('002_memory_layer_tables');
 

package/src/indexer/constants.ts

@@ -25,7 +25,6 @@ export const SUPPORTED_EXTENSIONS = [
 	".jsx",
 	".mjs",
 	".cjs",
-	".sql",
 ] as const;
 
 /**

package/src/indexer/parsers.ts

@@ -15,7 +15,6 @@ const SUPPORTED_EXTENSIONS = new Set<string>([
 	".cjs",
 	".mjs",
 	".json",
-	".sql",
 ]);
 
 const IGNORED_DIRECTORIES = new Set<string>([
@@ -162,8 +161,7 @@ export async function parseSourceFile(
 		return null;
 	}
 
-	// Skip dependency extraction for SQL files
-	const dependencies = extname(path) === ".sql" ? [] : extractDependencies(content);
+	const dependencies = extractDependencies(content);
 
 	return {
 		projectRoot: resolve(projectRoot),

package/src/mcp/server.ts

@@ -16,7 +16,6 @@ import { Sentry } from "../instrument.js";
 import {
 	ANALYZE_CHANGE_IMPACT_TOOL,
 	GENERATE_TASK_CONTEXT_TOOL,
-	GET_INDEX_STATISTICS_TOOL,
 	INDEX_REPOSITORY_TOOL,
 	LIST_RECENT_FILES_TOOL,
 	SEARCH_TOOL,
@@ -36,7 +35,6 @@ import {
 	// Execute functions
 	executeAnalyzeChangeImpact,
 	executeGenerateTaskContext,
-	executeGetIndexStatistics,
 	executeIndexRepository,
 	executeListRecentFiles,
 	executeSearch,

package/src/mcp/tools.ts

@@ -6,7 +6,6 @@
  */
 
 import {
-	getIndexStatistics,
 	listRecentFiles,
 	queryDependencies,
 	queryDependents,
@@ -354,21 +353,6 @@ export const ANALYZE_CHANGE_IMPACT_TOOL: ToolDefinition = {
 	},
 };
 
-/**
- * Tool: get_index_statistics
- */
-export const GET_INDEX_STATISTICS_TOOL: ToolDefinition = {
-	tier: "core",
-	name: "get_index_statistics",
-	description:
-		"Get statistics about indexed data (files, symbols, references, decisions, patterns, failures). Useful for understanding what data is available for search.",
-	inputSchema: {
-		type: "object",
-		properties: {},
-		required: [],
-	},
-};
-
 /**
  * Tool: validate_implementation_spec
  */
@@ -786,7 +770,6 @@ export function getToolDefinitions(): ToolDefinition[] {
 		LIST_RECENT_FILES_TOOL,
 		SEARCH_DEPENDENCIES_TOOL,
 		ANALYZE_CHANGE_IMPACT_TOOL,
-		GET_INDEX_STATISTICS_TOOL,
 		VALIDATE_IMPLEMENTATION_SPEC_TOOL,
 		SYNC_EXPORT_TOOL,
 		SYNC_IMPORT_TOOL,
@@ -975,121 +958,11 @@ async function searchSymbols(
 	}));
 }
 
-/**
- * Generate contextual tips based on search query and parameters.
- * Uses static pattern matching (no NLP) to detect suboptimal usage patterns.
- * 
- * Tip frequency: MODERATE - show tips frequently including "nice to know" suggestions.
- * 
- * @param query - Search query string
- * @param scopes - Search scopes used
- * @param filters - Normalized filters applied
- * @param scopeResults - Results by scope
- * @returns Array of tip strings (empty if search is optimal)
- */
-function generateSearchTips(
-	query: string,
-	scopes: string[],
-	filters: NormalizedFilters,
-	scopeResults: Record<string, unknown[]>
-): string[] {
-	const tips: string[] = [];
-	const queryLower = query.toLowerCase();
-	
-	// Pattern 1: Query contains structural keywords but not using symbols scope
-	const structuralKeywords = ['function', 'class', 'interface', 'type', 'method', 'component'];
-	const hasStructuralKeyword = structuralKeywords.some(kw => queryLower.includes(kw));
-	
-	if (hasStructuralKeyword && !scopes.includes('symbols')) {
-		const matchedKeyword = structuralKeywords.find(kw => queryLower.includes(kw)) || 'function';
-		tips.push(
-			`You searched for "${query}" in code. Try scope: ['symbols'] with filters: {symbol_kind: ['${matchedKeyword}']} for precise structural discovery.`
-		);
-	}
-	
-	// Pattern 2: Query looks like a file path but using code search
-	const looksLikeFilePath = /^[\w\-./]+\.(ts|tsx|js|jsx|py|rs|go|java)$/i.test(query);
-	if (looksLikeFilePath && scopes.includes('code')) {
-		tips.push(
-			`Query "${query}" looks like a file path. Consider using search_dependencies tool to find files that depend on this file or its dependencies.`
-		);
-	}
-	
-	// Pattern 3: Symbol search without exported_only filter
-	if (scopes.includes('symbols') && filters.exported_only === undefined) {
-		const symbolCount = scopeResults['symbols']?.length || 0;
-		if (symbolCount > 10) {
-			tips.push(
-				`Found ${symbolCount} symbols. Add filters: {exported_only: true} to narrow to public API only.`
-			);
-		}
-	}
-	
-	// Pattern 4: No repository filter with large result set
-	if (!filters.repositoryId) {
-		const totalResults = Object.values(scopeResults).reduce((sum, arr) => sum + arr.length, 0);
-		if (totalResults > 20) {
-			tips.push(
-				`Found ${totalResults} results across all repositories. Add filters: {repository: "owner/repo"} to narrow to a specific repository.`
-			);
-		}
-	}
-	
-	// Pattern 5: Code search without glob/language filters
-	if (scopes.includes('code') && !filters.glob && !filters.language) {
-		const codeCount = scopeResults['code']?.length || 0;
-		if (codeCount > 15) {
-			tips.push(
-				`Found ${codeCount} code results. Try filters: {glob: "**/*.ts"} or {language: "typescript"} to narrow file types.`
-			);
-		}
-	}
-	
-	// Pattern 6: Suggest decisions scope for "why" questions
-	if (/\b(why|reason|decision|chose|choice)\b/i.test(query) && !scopes.includes('decisions')) {
-		tips.push(
-			`Query contains "why/reason/decision". Try scope: ['decisions'] to search architectural decisions and rationale.`
-		);
-	}
-	
-	// Pattern 7: Suggest patterns scope for "how" questions
-	if (/\b(how|pattern|best practice|convention)\b/i.test(query) && !scopes.includes('patterns')) {
-		tips.push(
-			`Query asks "how to". Try scope: ['patterns'] to search coding patterns and conventions from this codebase.`
-		);
-	}
-	
-	// Pattern 8: Suggest failures scope for error-related queries
-	if (/\b(error|bug|fail|issue|problem|fix)\b/i.test(query) && !scopes.includes('failures')) {
-		tips.push(
-			`Query mentions errors/issues. Try scope: ['failures'] to learn from past mistakes and avoid repeated failures.`
-		);
-	}
-	
-	// Pattern 9: Single scope when multi-scope could be useful
-	if (scopes.length === 1 && scopes[0] === 'code') {
-		tips.push(
-			`Tip: You can search multiple scopes simultaneously. Try scope: ['code', 'symbols'] for broader discovery.`
-		);
-	}
-	
-	// Pattern 10: Suggest compact format for large result sets
-	const totalResults = Object.values(scopeResults).reduce((sum, arr) => sum + arr.length, 0);
-	if (totalResults > 30 && !tips.some(t => t.includes('output: "compact"'))) {
-		tips.push(
-			`Returning ${totalResults} full results. Use output: "compact" for summary view or output: "paths" for file paths only.`
-		);
-	}
-	
-	return tips;
-}
-
 function formatSearchResults(
 	query: string,
 	scopes: string[],
 	scopeResults: Record<string, unknown[]>,
-	format: string,
-	filters: NormalizedFilters
+	format: string
 ): Record<string, unknown> {
 	const response: Record<string, unknown> = {
 		query,
@@ -1134,13 +1007,6 @@ function formatSearchResults(
 		(response.counts as Record<string, unknown>).total = ((response.counts as Record<string, unknown>).total as number) + items.length;
 	}
 
-	
-	// Generate and add tips if applicable
-	const tips = generateSearchTips(query, scopes, filters, scopeResults);
-	if (tips.length > 0) {
-		response.tips = tips;
-	}
-	
 	return response;
 }
 
@@ -1276,7 +1142,7 @@ export async function executeSearch(
 	await Promise.all(searchPromises);
 
 	// Format output
-	const response = formatSearchResults(p.query as string, scopes, results, output, filters);
+	const response = formatSearchResults(p.query as string, scopes, results, output);
 
 	logger.info("Unified search completed", {
 		query: p.query,
@@ -1768,26 +1634,6 @@ export async function executeAnalyzeChangeImpact(
 	return result;
 }
 
-/**
- * Execute get_index_statistics tool
- */
-export async function executeGetIndexStatistics(
-	params: unknown,
-	requestId: string | number,
-	userId: string,
-): Promise<unknown> {
-	// No parameters to validate
-	
-	logger.info("Getting index statistics", { request_id: String(requestId), user_id: userId });
-	
-	const stats = getIndexStatistics();
-	
-	return {
-		...stats,
-		summary: `${stats.symbols.toLocaleString()} symbols, ${stats.files.toLocaleString()} files, ${stats.repositories} repositories indexed`,
-	};
-}
-
 /**
 
 /**

package/src/db/migrations/005_workflow_contexts.sql

@@ -1,41 +0,0 @@
--- SQLite Migration: Workflow Context Accumulation
---
--- Migration: 005_workflow_contexts
--- Issue: #144 - ADW context accumulation for inter-phase handoffs
--- Author: Claude Code
--- Date: 2026-02-04
---
--- This migration adds workflow context storage for ADW automation,
--- enabling context accumulation between workflow phases (analysis -> plan -> build -> improve).
--- Context is stored in the main KotaDB database for future MCP tool integration.
-
--- ============================================================================
--- 1. Workflow Contexts Table
--- ============================================================================
--- Stores curated context data for each workflow phase
-
-CREATE TABLE IF NOT EXISTS workflow_contexts (
-    id INTEGER PRIMARY KEY AUTOINCREMENT,
-    workflow_id TEXT NOT NULL,           -- 'adw-123-20260204T120000'
-    phase TEXT NOT NULL,                 -- 'analysis' | 'plan' | 'build' | 'improve'
-    context_data TEXT NOT NULL,          -- JSON blob
-    created_at TEXT NOT NULL DEFAULT (datetime('now')),
-    updated_at TEXT NOT NULL DEFAULT (datetime('now')),
-    
-    UNIQUE(workflow_id, phase),
-    CHECK (phase IN ('analysis', 'plan', 'build', 'improve'))
-);
-
--- Index for workflow-scoped queries (primary access pattern)
-CREATE INDEX IF NOT EXISTS idx_workflow_contexts_workflow_id 
-ON workflow_contexts(workflow_id);
-
--- Index for time-based queries (debugging/monitoring)
-CREATE INDEX IF NOT EXISTS idx_workflow_contexts_created_at 
-ON workflow_contexts(created_at DESC);
-
--- ============================================================================
--- 2. Record Migration
--- ============================================================================
-
-INSERT OR IGNORE INTO schema_migrations (name) VALUES ('005_workflow_contexts');

package/src/db/migrations/006_add_migration_checksums.sql

@@ -1,15 +0,0 @@
--- SQLite Migration: Add Checksum Tracking to Schema Migrations
---
--- Migration: 006_add_migration_checksums
--- Issue: #166 - Migration infrastructure
--- Author: Claude Code
--- Date: 2026-02-04
---
--- Adds checksum column to schema_migrations table for drift detection.
--- Existing migrations will have NULL checksums (validation skipped).
-
-ALTER TABLE schema_migrations ADD COLUMN checksum TEXT;
-
-CREATE INDEX IF NOT EXISTS idx_schema_migrations_name ON schema_migrations(name);
-
-INSERT OR IGNORE INTO schema_migrations (name) VALUES ('006_add_migration_checksums');

package/src/db/sqlite/migration-runner.ts

@@ -1,335 +0,0 @@
-/**
- * Migration runner for KotaDB SQLite schema management.
- *
- * Features:
- * - Scans migrations directory for .sql files
- * - Applies pending migrations in order
- * - Validates checksums for drift detection
- * - Transactional execution with automatic rollback
- *
- * @module @db/sqlite/migration-runner
- */
-
-import { readdirSync, readFileSync, existsSync } from "node:fs";
-import { join } from "node:path";
-import { createHash } from "node:crypto";
-import type { KotaDatabase } from "./sqlite-client.js";
-import { createLogger } from "@logging/logger.js";
-
-const logger = createLogger({ module: "migration-runner" });
-
-/**
- * Parsed migration file information
- */
-export interface Migration {
-	filename: string;
-	name: string;
-	number: number;
-	path: string;
-	content: string;
-	checksum: string;
-}
-
-/**
- * Migration record from the database
- */
-export interface AppliedMigration {
-	name: string;
-	applied_at: string;
-	checksum?: string | null;
-}
-
-/**
- * Result of a migration run
- */
-export interface MigrationResult {
-	appliedCount: number;
-	driftDetected: boolean;
-	appliedMigrations: string[];
-	errors: string[];
-}
-
-/**
- * Parse migration filename to extract number and name.
- * Format: {number}_{name}.sql
- *
- * @param filename - Migration filename (e.g., "004_memory_layer.sql")
- * @returns Parsed number and name, or null if invalid format
- */
-export function parseMigrationFilename(
-	filename: string
-): { number: number; name: string } | null {
-	const match = filename.match(/^(\d+)_(.+)\.sql$/);
-	if (!match) return null;
-
-	const numStr = match[1];
-	const name = match[2];
-	if (!numStr || !name) return null;
-
-	return { number: parseInt(numStr, 10), name: `${numStr}_${name}` };
-}
-
-/**
- * Compute SHA-256 checksum of migration content.
- *
- * @param content - Migration SQL content
- * @returns Hex-encoded SHA-256 hash
- */
-export function computeChecksum(content: string): string {
-	return createHash("sha256").update(content, "utf-8").digest("hex");
-}
-
-/**
- * Scan migrations directory and return sorted list of migrations.
- *
- * @param migrationsDir - Path to migrations directory
- * @returns Array of migrations sorted by number
- */
-export function scanMigrations(migrationsDir: string): Migration[] {
-	if (!existsSync(migrationsDir)) {
-		logger.warn("Migrations directory does not exist", { path: migrationsDir });
-		return [];
-	}
-
-	const files = readdirSync(migrationsDir)
-		.filter((f) => f.endsWith(".sql"))
-		.sort(); // Alphabetical sort ensures numeric order for 001, 002, etc.
-
-	const migrations: Migration[] = [];
-
-	for (const filename of files) {
-		const parsed = parseMigrationFilename(filename);
-		if (!parsed) {
-			logger.warn("Invalid migration filename (skipping)", { filename });
-			continue;
-		}
-
-		const path = join(migrationsDir, filename);
-		const content = readFileSync(path, "utf-8");
-		const checksum = computeChecksum(content);
-
-		migrations.push({
-			filename,
-			name: parsed.name,
-			number: parsed.number,
-			path,
-			content,
-			checksum,
-		});
-	}
-
-	// Sort by number (redundant if naming is correct, but ensures correctness)
-	migrations.sort((a, b) => a.number - b.number);
-
-	return migrations;
-}
-
-/**
- * Get list of applied migrations from schema_migrations table.
- *
- * @param db - Database instance
- * @returns Map of migration name to applied migration record
- */
-export function getAppliedMigrations(
-	db: KotaDatabase
-): Map<string, AppliedMigration> {
-	// Ensure schema_migrations table exists
-	if (!db.tableExists("schema_migrations")) {
-		logger.warn("schema_migrations table does not exist");
-		return new Map();
-	}
-
-	// Check if checksum column exists
-	const columns = db.query<{ name: string }>(
-		"SELECT name FROM pragma_table_info('schema_migrations')"
-	);
-	const hasChecksum = columns.some((c) => c.name === "checksum");
-
-	// Query with or without checksum column
-	const query = hasChecksum
-		? "SELECT name, applied_at, checksum FROM schema_migrations ORDER BY id"
-		: "SELECT name, applied_at, NULL as checksum FROM schema_migrations ORDER BY id";
-
-	const rows = db.query<AppliedMigration>(query);
-
-	return new Map(rows.map((r) => [r.name, r]));
-}
-
-/**
- * Apply a single migration within a transaction.
- *
- * @param db - Database instance
- * @param migration - Migration to apply
- */
-export function applyMigration(db: KotaDatabase, migration: Migration): void {
-	logger.info("Applying migration", { name: migration.name });
-
-	db.immediateTransaction(() => {
-		// Execute migration SQL
-		db.exec(migration.content);
-
-		// Check if checksum column exists for INSERT
-		const columns = db.query<{ name: string }>(
-			"SELECT name FROM pragma_table_info('schema_migrations')"
-		);
-		const hasChecksum = columns.some((c) => c.name === "checksum");
-
-		// Record migration (with checksum if column exists)
-		if (hasChecksum) {
-			db.run(
-				"INSERT OR REPLACE INTO schema_migrations (name, checksum, applied_at) VALUES (?, ?, datetime('now'))",
-				[migration.name, migration.checksum]
-			);
-		} else {
-			// Migration file already contains INSERT OR IGNORE for name
-			// Just ensure the record exists
-			db.run(
-				"INSERT OR IGNORE INTO schema_migrations (name, applied_at) VALUES (?, datetime('now'))",
-				[migration.name]
-			);
-		}
-	});
-
-	logger.info("Migration applied successfully", { name: migration.name });
-}
-
-/**
- * Validate checksum for already-applied migration (drift detection).
- *
- * @param migration - Migration file info
- * @param applied - Applied migration record
- * @returns True if checksum matches or no checksum stored
- */
-export function validateChecksum(
-	migration: Migration,
-	applied: AppliedMigration
-): boolean {
-	if (!applied.checksum) {
-		// Old migrations may not have checksum - skip validation
-		logger.debug("No checksum stored for migration (skipping validation)", {
-			name: migration.name,
-		});
-		return true;
-	}
-
-	if (migration.checksum !== applied.checksum) {
-		logger.warn("Migration checksum mismatch (DRIFT DETECTED)", {
-			name: migration.name,
-			expected: applied.checksum,
-			actual: migration.checksum,
-			message:
-				"Migration file was modified after being applied. This may indicate schema drift.",
-		});
-		return false;
-	}
-
-	return true;
-}
-
-/**
- * Run all pending migrations.
- *
- * @param db - Database instance
- * @param migrationsDir - Path to migrations directory
- * @returns Migration result with count and status
- */
-export function runMigrations(
-	db: KotaDatabase,
-	migrationsDir: string
-): MigrationResult {
-	logger.info("Starting migration runner", { migrationsDir });
-
-	const result: MigrationResult = {
-		appliedCount: 0,
-		driftDetected: false,
-		appliedMigrations: [],
-		errors: [],
-	};
-
-	// Scan filesystem for migration files
-	const availableMigrations = scanMigrations(migrationsDir);
-	logger.debug("Found migration files", { count: availableMigrations.length });
-
-	// Get applied migrations from database
-	const appliedMigrations = getAppliedMigrations(db);
-	logger.debug("Found applied migrations", { count: appliedMigrations.size });
-
-	for (const migration of availableMigrations) {
-		const applied = appliedMigrations.get(migration.name);
-
-		if (applied) {
-			// Migration already applied - validate checksum
-			const valid = validateChecksum(migration, applied);
-			if (!valid) {
-				result.driftDetected = true;
-			}
-		} else {
-			// Migration not yet applied - apply it
-			try {
-				applyMigration(db, migration);
-				result.appliedCount++;
-				result.appliedMigrations.push(migration.name);
-			} catch (error) {
-				const errorMessage =
-					error instanceof Error ? error.message : String(error);
-				logger.error("Migration failed", {
-					name: migration.name,
-					error: errorMessage,
-				});
-				result.errors.push(`Migration ${migration.name} failed: ${errorMessage}`);
-				// Stop applying further migrations on failure
-				break;
-			}
-		}
-	}
-
-	if (result.driftDetected) {
-		logger.warn(
-			"Schema drift detected. Some migration files have been modified after being applied."
-		);
-	}
-
-	logger.info("Migration runner completed", {
-		appliedCount: result.appliedCount,
-		driftDetected: result.driftDetected,
-	});
-
-	return result;
-}
-
-/**
- * Update checksums for all existing migrations.
- * Useful after adding checksum column to update records.
- *
- * @param db - Database instance
- * @param migrationsDir - Path to migrations directory
- * @returns Number of records updated
- */
-export function updateExistingChecksums(
-	db: KotaDatabase,
-	migrationsDir: string
-): number {
-	const migrations = scanMigrations(migrationsDir);
-	const applied = getAppliedMigrations(db);
-	let updatedCount = 0;
-
-	for (const migration of migrations) {
-		const record = applied.get(migration.name);
-		if (record && !record.checksum) {
-			db.run("UPDATE schema_migrations SET checksum = ? WHERE name = ?", [
-				migration.checksum,
-				migration.name,
-			]);
-			updatedCount++;
-			logger.debug("Updated checksum for migration", { name: migration.name });
-		}
-	}
-
-	if (updatedCount > 0) {
-		logger.info("Updated checksums for existing migrations", {
-			count: updatedCount,
-		});
-	}
-
-	return updatedCount;
-}