code-auditor-mcp 3.4.14 → 3.4.16

package/dist/codeIndexDB.d.ts

@@ -4,8 +4,9 @@
  */
 import Database from 'better-sqlite3';
 import type { CompleteProjectTaskResult, CreateProjectTaskInput, ListProjectTasksOptions, ListProjectTasksTreeNode, ProjectTask, ProjectTaskDeleteMode } from './types/projectTask.js';
-import { EnhancedFunctionMetadata, FunctionMetadata, SearchResult, SearchOptions, SchemaDefinition, SchemaIndexMetadata, SchemaUsage } from './types.js';
+import { EnhancedFunctionMetadata, FunctionMetadata, DryFunctionIndexEntry, SearchResult, SearchOptions, SchemaDefinition, SchemaIndexMetadata, SchemaUsage } from './types.js';
 import { WhitelistEntry, WhitelistType, WhitelistStatus, WhitelistSuggestion } from './types/whitelist.js';
+export declare const DB_BUSY_TIMEOUT_MS = 30000;
 export declare class CodeIndexDB {
     private static instance;
     /** Subclasses (e.g. EnhancedCodeIndexDB) need access for extra tables without `as any`. */
@@ -38,6 +39,12 @@ export declare class CodeIndexDB {
     static getInstance(dbPath?: string, projectRoot?: string): CodeIndexDB;
     /** Reset the singleton — used by tests that need a fresh in-memory instance. */
     static resetInstance(): void;
+    /**
+     * The project root the current singleton was opened for (undefined when opened
+     * cwd-scoped). Detached-job readers use this to resolve the same DB the writer
+     * opened, without re-resolving against cwd and flipping the singleton away.
+     */
+    static get currentProject(): string | undefined;
     initialize(): Promise<void>;
     private initializeInternal;
     private runMigrations;
@@ -56,11 +63,33 @@ export declare class CodeIndexDB {
             error: string;
         }>;
     }>;
+    /**
+     * Upsert/remove one file's function rows. Runs inside the caller's
+     * transaction (no nested `db.transaction` here) so a batch sync can wrap many
+     * files in a single write transaction.
+     */
+    private syncFileIndexRow;
     syncFileIndex(filePath: string, currentFunctions: (FunctionMetadata | EnhancedFunctionMetadata)[]): Promise<{
         added: number;
         updated: number;
         removed: number;
     }>;
+    /**
+     * Batch variant of {@link syncFileIndex}: upsert many files in a single write
+     * transaction, then rebuild the dependency graph once (unscoped). The
+     * detached-audit path previously called {@link syncFileIndex} once per file —
+     * one transaction plus one dependency-graph rebuild per file, and the
+     * rebuild's un-scoped `SELECT` made that O(files × functions). Collapsing it
+     * to one transaction is Amendment B2.
+     */
+    syncFileIndexBatch(entries: Array<{
+        filePath: string;
+        currentFunctions: (FunctionMetadata | EnhancedFunctionMetadata)[];
+    }>): Promise<{
+        added: number;
+        updated: number;
+        removed: number;
+    }>;
     updateDependencyGraph(filePath?: string): Promise<void>;
     getTransitiveDependencies(functionName: string, maxDepth?: number): Promise<Array<{
         name: string;
@@ -77,6 +106,16 @@ export declare class CodeIndexDB {
     private rowToFunctionDoc;
     findDefinition(name: string, filePath?: string): Promise<EnhancedFunctionMetadata | null>;
     getAllFunctions(): Promise<EnhancedFunctionMetadata[]>;
+    /**
+     * Narrow variant for the scoped-DRY gate path (Spec 43 R4). Selects only the
+     * columns `buildFullFunctionHashmap` reads — name, file_path, start_line,
+     * line_number, body — so the hot `changed` path skips the wide JSON columns
+     * (`parameters`, `hooks`, `props`, `signature`, `metadata_json`,
+     * `content_hash`) and their per-row `JSON.parse` cost.
+     */
+    getAllFunctionsForDry(): Promise<DryFunctionIndexEntry[]>;
+    /** Row count of the `functions` table — for callers that only need `.length`. */
+    getFunctionCount(): Promise<number>;
     getStats(): Promise<{
         totalFunctions: number;
         languages: Record<string, number>;

package/dist/codeIndexDB.d.ts.map

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package/dist/codeIndexDB.js

@@ -17,6 +17,14 @@ import { QueryParser, compileToSQL } from './search/QueryParser.js';
 import { getPersistedStorageRoot, resolvePersistedIndexPath } from './dataPaths.js';
 import { ContextualError, getErrnoCode } from './mcpToolErrors.js';
 import { WhitelistType, WhitelistStatus } from './types/whitelist.js';
+// ── SQLite busy timeout ─────────────────────────────────────────────────
+// The database is shared across forked processes (a detached audit runner and
+// its shard workers). better-sqlite3's default busy timeout (~5s) is too short
+// for a running job's long completion transaction, so a queued job's lease
+// `BEGIN IMMEDIATE` (or the runner's own writes) would throw SQLITE_BUSY
+// ("database is locked") instead of waiting. A generous timeout makes
+// contention block gracefully; the lease loop also retries SQLITE_BUSY.
+export const DB_BUSY_TIMEOUT_MS = 30_000;
 // ── Content hash ────────────────────────────────────────────────────────
 function computeContentHash(body, signature) {
     const normalized = (body ?? '').replace(/\s+/g, ' ').trim() + '|' + (signature ?? '').trim();
@@ -233,7 +241,7 @@ export class CodeIndexDB {
     taskRepository = null;
     stmts = new Map();
     // ── Schema version ──────────────────────────────────────────────────
-    static SCHEMA_VERSION = 8;
+    static SCHEMA_VERSION = 11;
     constructor(dbPath = ':memory:') {
         this.dbPath = dbPath === ':memory:' ? dbPath : path.resolve(dbPath);
     }
@@ -279,6 +287,14 @@ export class CodeIndexDB {
         }
         CodeIndexDB.instance = null;
     }
+    /**
+     * The project root the current singleton was opened for (undefined when opened
+     * cwd-scoped). Detached-job readers use this to resolve the same DB the writer
+     * opened, without re-resolving against cwd and flipping the singleton away.
+     */
+    static get currentProject() {
+        return CodeIndexDB.currentProjectRoot;
+    }
     // ── Lifecycle ───────────────────────────────────────────────────────
     async initialize() {
         if (this.isInitialized)
@@ -333,7 +349,7 @@ export class CodeIndexDB {
         // Open SQLite database (with auto-recovery for corrupted files)
         let retried = false;
         try {
-            this.db = new Database(this.dbPath);
+            this.db = new Database(this.dbPath, { timeout: DB_BUSY_TIMEOUT_MS });
             this.db.pragma('journal_mode = WAL');
             this.db.pragma('foreign_keys = ON');
         }
@@ -346,7 +362,7 @@ export class CodeIndexDB {
                     await fs.unlink(this.dbPath);
                 }
                 catch { /* ignore */ }
-                this.db = new Database(this.dbPath);
+                this.db = new Database(this.dbPath, { timeout: DB_BUSY_TIMEOUT_MS });
                 this.db.pragma('journal_mode = WAL');
                 this.db.pragma('foreign_keys = ON');
             }
@@ -592,6 +608,85 @@ export class CodeIndexDB {
                 this.db.exec(`ALTER TABLE conventions ADD COLUMN export_kind TEXT`);
             }
         }
+        // Migration 8 → 9: Detached-run lifecycle + queryable coverage (Spec 41).
+        // `findings_ledger_runs` gains the job-lifecycle columns (status, timing,
+        // provenance, lease heartbeat, progress, stderr log); the one genuinely new
+        // table is `findings_ledger_coverage` (per-rule state + reason rows that
+        // `writeAuditToLedger` previously dropped).
+        if (currentVersion < 9) {
+            const runCols = this.db
+                .prepare(`PRAGMA table_info('findings_ledger_runs')`)
+                .all();
+            const hasRunCol = (name) => runCols.some((c) => c.name === name);
+            const newRunCols = [
+                ['status', "TEXT NOT NULL DEFAULT 'completed'"],
+                ['project_root', 'TEXT'],
+                ['started_at', 'TEXT'],
+                ['heartbeat_at', 'TEXT'],
+                ['finished_at', 'TEXT'],
+                ['error', 'TEXT'],
+                ['progress_json', 'TEXT'],
+                ['stderr_log', 'TEXT'],
+                ['content_hash', 'TEXT'],
+                ['files_count', 'INTEGER'],
+                ['file_manifest_json', 'TEXT'],
+            ];
+            for (const [name, decl] of newRunCols) {
+                if (!hasRunCol(name)) {
+                    this.db.exec(`ALTER TABLE findings_ledger_runs ADD COLUMN ${name} ${decl}`);
+                }
+            }
+            this.db.exec(`
+        CREATE TABLE IF NOT EXISTS findings_ledger_coverage (
+          run_id    TEXT NOT NULL REFERENCES findings_ledger_runs(run_id) ON DELETE CASCADE,
+          analyzer  TEXT NOT NULL,
+          rule_id   TEXT NOT NULL,
+          state     TEXT NOT NULL,
+          count     INTEGER NOT NULL DEFAULT 0,
+          reason    TEXT,
+          PRIMARY KEY (run_id, analyzer, rule_id)
+        );
+        CREATE INDEX IF NOT EXISTS idx_ledger_coverage_run ON findings_ledger_coverage(run_id);
+      `);
+        }
+        // Migration 9 → 10: PID-based lease liveness (Spec 41 Amendment B).
+        // The heartbeat is no longer the primary liveness signal for the common
+        // case (a healthy child whose synchronous `syncFileIndex` phase starves the
+        // event loop, so its heartbeat interval cannot fire). The child records its
+        // PID + process start time + hostname at lease claim; `reclaimStaleRunning`
+        // then skips any `running` row whose PID is still the same live process, and
+        // only reclaims when the process is genuinely gone (or on a foreign host,
+        // where the PID means nothing and the heartbeat stays the fallback).
+        if (currentVersion < 10) {
+            const runCols = this.db
+                .prepare(`PRAGMA table_info('findings_ledger_runs')`)
+                .all();
+            const hasRunCol = (name) => runCols.some((c) => c.name === name);
+            const newRunCols = [
+                ['runner_pid', 'INTEGER'],
+                ['runner_pid_started_at', 'TEXT'],
+                ['runner_host', 'TEXT'],
+            ];
+            for (const [name, decl] of newRunCols) {
+                if (!hasRunCol(name)) {
+                    this.db.exec(`ALTER TABLE findings_ledger_runs ADD COLUMN ${name} ${decl}`);
+                }
+            }
+        }
+        // Migration 10 → 11: unread stylesheet sources (Spec 42 R2).
+        // Records stylesheets whose dialect the style indexer cannot read, so
+        // styles/undefined-class can report notApplicable instead of asserting a
+        // class is undefined when it may live in one of these files.
+        if (currentVersion < 11) {
+            this.db.exec(`
+        CREATE TABLE IF NOT EXISTS style_unread_sources (
+          id         INTEGER PRIMARY KEY AUTOINCREMENT,
+          file_path  TEXT NOT NULL UNIQUE,
+          reason     TEXT NOT NULL,
+          created_at TEXT DEFAULT (datetime('now'))
+        );
+      `);
+        }
     }
     // ── SQLite schema ───────────────────────────────────────────────────
     createSchema() {
@@ -817,7 +912,21 @@ export class CodeIndexDB {
         target       TEXT NOT NULL,
         duration_ms  INTEGER NOT NULL DEFAULT 0,
         exit_status  INTEGER NOT NULL DEFAULT 0,
-        metadata_json TEXT DEFAULT '{}'
+        metadata_json TEXT DEFAULT '{}',
+        status        TEXT NOT NULL DEFAULT 'completed',
+        project_root  TEXT,
+        started_at    TEXT,
+        heartbeat_at  TEXT,
+        finished_at   TEXT,
+        error         TEXT,
+        progress_json TEXT,
+        stderr_log    TEXT,
+        content_hash  TEXT,
+        files_count   INTEGER,
+        file_manifest_json TEXT,
+        runner_pid           INTEGER,
+        runner_pid_started_at TEXT,
+        runner_host          TEXT
       );
       CREATE TABLE IF NOT EXISTS findings_ledger_findings (
         id           INTEGER PRIMARY KEY AUTOINCREMENT,
@@ -831,8 +940,18 @@ export class CodeIndexDB {
         symbol       TEXT DEFAULT '',
         fingerprint  TEXT NOT NULL
       );
+      CREATE TABLE IF NOT EXISTS findings_ledger_coverage (
+        run_id    TEXT NOT NULL REFERENCES findings_ledger_runs(run_id) ON DELETE CASCADE,
+        analyzer  TEXT NOT NULL,
+        rule_id   TEXT NOT NULL,
+        state     TEXT NOT NULL,
+        count     INTEGER NOT NULL DEFAULT 0,
+        reason    TEXT,
+        PRIMARY KEY (run_id, analyzer, rule_id)
+      );
       CREATE INDEX IF NOT EXISTS idx_ledger_runs_surface    ON findings_ledger_runs(surface);
       CREATE INDEX IF NOT EXISTS idx_ledger_runs_timestamp   ON findings_ledger_runs(timestamp);
+      CREATE INDEX IF NOT EXISTS idx_ledger_coverage_run     ON findings_ledger_coverage(run_id);
       CREATE INDEX IF NOT EXISTS idx_ledger_findings_run     ON findings_ledger_findings(run_id);
       CREATE INDEX IF NOT EXISTS idx_ledger_findings_fp      ON findings_ledger_findings(fingerprint);
       CREATE INDEX IF NOT EXISTS idx_ledger_findings_rule    ON findings_ledger_findings(analyzer, rule);
@@ -887,6 +1006,16 @@ export class CodeIndexDB {
       CREATE INDEX IF NOT EXISTS idx_style_class_usage_file   ON style_class_usage(file_path);
       CREATE INDEX IF NOT EXISTS idx_style_class_usage_unres  ON style_class_usage(unresolvable);
 
+      -- Spec 42 R2: Stylesheet sources the style indexer could not read.
+      -- When any rows exist, styles/undefined-class reports notApplicable
+      -- instead of asserting a class is undefined (it may live in one of these).
+      CREATE TABLE IF NOT EXISTS style_unread_sources (
+        id         INTEGER PRIMARY KEY AUTOINCREMENT,
+        file_path  TEXT NOT NULL UNIQUE,
+        reason     TEXT NOT NULL,
+        created_at TEXT DEFAULT (datetime('now'))
+      );
+
       -- Spec 12: Convention mining
       CREATE TABLE IF NOT EXISTS conventions (
         id INTEGER PRIMARY KEY AUTOINCREMENT,
@@ -1020,7 +1149,7 @@ export class CodeIndexDB {
             }
             // Rename old LokiJS file FIRST, then create fresh SQLite DB
             require('fs').renameSync(this.dbPath, bakPath);
-            const migDb = new Database(this.dbPath);
+            const migDb = new Database(this.dbPath, { timeout: DB_BUSY_TIMEOUT_MS });
             migDb.pragma('journal_mode = WAL');
             migDb.pragma('foreign_keys = ON');
             // User-authored tables only (function index gets rebuilt by sync).
@@ -1309,52 +1438,72 @@ export class CodeIndexDB {
             errors: errors
         };
     }
+    /**
+     * Upsert/remove one file's function rows. Runs inside the caller's
+     * transaction (no nested `db.transaction` here) so a batch sync can wrap many
+     * files in a single write transaction.
+     */
+    syncFileIndexRow(filePath, currentFunctions, stats) {
+        const existing = this.db.prepare('SELECT id, name, file_path, line_number FROM functions WHERE file_path = ?').all(filePath);
+        const createKey = (f) => `${f.name ?? f.name}:${f.filePath ?? f.file_path}:${f.lineNumber ?? f.line_number}`;
+        const currentMap = new Map(currentFunctions.map(f => [createKey(f), f]));
+        // Insert/update current functions
+        for (const func of currentFunctions) {
+            const exists = existing.find(e => e.name === func.name && e.line_number === func.lineNumber);
+            if (exists) {
+                const row = this.functionToRow(func);
+                const keys = Object.keys(row);
+                const sets = keys.filter(k => k !== 'name' && k !== 'file_path').map(k => `"${k}" = @${k}`);
+                const params = { ...row, _id: exists.id };
+                this.db.prepare(`UPDATE functions SET ${sets.join(', ')} WHERE id = @_id`).run(params);
+                stats.updated++;
+            }
+            else {
+                const row = this.functionToRow(func);
+                const keys = Object.keys(row);
+                const sql = `INSERT INTO functions ("${keys.join('", "')}") VALUES (${keys.map(k => '@' + k).join(', ')})`;
+                this.db.prepare(sql).run(row);
+                stats.added++;
+            }
+        }
+        // Remove stale functions
+        for (const e of existing) {
+            if (!currentMap.has(createKey(e))) {
+                this.db.prepare('DELETE FROM functions WHERE id = ?').run(e.id);
+                stats.removed++;
+            }
+        }
+    }
     async syncFileIndex(filePath, currentFunctions) {
         this.ensureInitialized();
         const stats = { added: 0, updated: 0, removed: 0 };
-        const txn = this.db.transaction(() => {
-            const existing = this.db.prepare('SELECT id, name, file_path, line_number FROM functions WHERE file_path = ?').all(filePath);
-            const createKey = (f) => `${f.name ?? f.name}:${f.filePath ?? f.file_path}:${f.lineNumber ?? f.line_number}`;
-            const currentMap = new Map(currentFunctions.map(f => [createKey(f), f]));
-            // Insert/update current functions
-            for (const func of currentFunctions) {
-                const exists = existing.find(e => e.name === func.name && e.line_number === func.lineNumber);
-                if (exists) {
-                    const row = this.functionToRow(func);
-                    const keys = Object.keys(row);
-                    const sets = keys.filter(k => k !== 'name' && k !== 'file_path').map(k => `"${k}" = @${k}`);
-                    const params = { ...row, _id: exists.id };
-                    this.db.prepare(`UPDATE functions SET ${sets.join(', ')} WHERE id = @_id`).run(params);
-                    stats.updated++;
-                }
-                else {
-                    const row = this.functionToRow(func);
-                    const keys = Object.keys(row);
-                    const sql = `INSERT INTO functions ("${keys.join('", "')}") VALUES (${keys.map(k => '@' + k).join(', ')})`;
-                    this.db.prepare(sql).run(row);
-                    stats.added++;
-                }
-            }
-            // Remove stale functions
-            for (const e of existing) {
-                if (!currentMap.has(createKey(e))) {
-                    this.db.prepare('DELETE FROM functions WHERE id = ?').run(e.id);
-                    stats.removed++;
-                }
-            }
-        });
-        txn();
+        this.db.transaction(() => this.syncFileIndexRow(filePath, currentFunctions, stats)).immediate();
         await this.updateDependencyGraph(filePath);
         return stats;
     }
+    /**
+     * Batch variant of {@link syncFileIndex}: upsert many files in a single write
+     * transaction, then rebuild the dependency graph once (unscoped). The
+     * detached-audit path previously called {@link syncFileIndex} once per file —
+     * one transaction plus one dependency-graph rebuild per file, and the
+     * rebuild's un-scoped `SELECT` made that O(files × functions). Collapsing it
+     * to one transaction is Amendment B2.
+     */
+    async syncFileIndexBatch(entries) {
+        this.ensureInitialized();
+        const stats = { added: 0, updated: 0, removed: 0 };
+        this.db.transaction(() => {
+            for (const { filePath, currentFunctions } of entries) {
+                this.syncFileIndexRow(filePath, currentFunctions, stats);
+            }
+        }).immediate();
+        await this.updateDependencyGraph();
+        return stats;
+    }
     // ── Dependency graph ────────────────────────────────────────────────
     async updateDependencyGraph(filePath) {
         this.ensureInitialized();
         const txn = this.db.transaction(() => {
-            // For functions in scope, rebuild their call edges
-            const functions = filePath
-                ? this.db.prepare('SELECT id, name, file_path FROM functions WHERE file_path = ?').all(filePath)
-                : this.db.prepare('SELECT id, name, file_path FROM functions').all();
             // Clear existing call edges for scoped functions
             if (filePath) {
                 this.db.prepare(`DELETE FROM function_calls WHERE caller_id IN (SELECT id FROM functions WHERE file_path = ?)`).run(filePath);
@@ -1369,12 +1518,14 @@ export class CodeIndexDB {
             else {
                 this.db.prepare('DELETE FROM function_dependencies').run();
             }
-            // Rebuild from metadata
+            // Rebuild edges from metadata. When scoped to one file, read only that
+            // file's functions — a per-file call previously re-read every function
+            // in the index, making the detached-audit loop O(files × functions).
             const allFns = filePath
-                ? this.db.prepare('SELECT id, name, file_path, metadata_json FROM functions').all()
+                ? this.db.prepare('SELECT id, name, file_path, metadata_json FROM functions WHERE file_path = ?').all(filePath)
                 : this.db.prepare('SELECT id, name, file_path, metadata_json FROM functions').all();
             const insertCall = this.db.prepare('INSERT OR IGNORE INTO function_calls (caller_id, callee_name) VALUES (?, ?)');
-            const insertDep = this.db.prepare('INSERT OR IGNORE INTO function_dependencies (function_id, dependency) VALUES (?, ?)');
+            const insertFnDep = this.db.prepare('INSERT OR IGNORE INTO function_dependencies (function_id, dependency) VALUES (?, ?)');
             for (const fn of allFns) {
                 const meta = tryParseJson(fn.metadata_json) ?? {};
                 if (meta.functionCalls) {
@@ -1382,11 +1533,6 @@ export class CodeIndexDB {
                         insertCall.run(fn.id, callee);
                     }
                 }
-            }
-            // Also rebuild dependency edges from the functions' import data
-            const insertFnDep = this.db.prepare('INSERT OR IGNORE INTO function_dependencies (function_id, dependency) VALUES (?, ?)');
-            for (const fn of allFns) {
-                const meta = tryParseJson(fn.metadata_json) ?? {};
                 // Add specifier-level dependencies (e.g., useState, useEffect)
                 const usedImports = meta.usedImports ?? [];
                 for (const imp of usedImports) {
@@ -1400,7 +1546,7 @@ export class CodeIndexDB {
                 }
             }
         });
-        txn();
+        txn.immediate();
     }
     async getTransitiveDependencies(functionName, maxDepth = 10) {
         this.ensureInitialized();
@@ -1641,6 +1787,32 @@ export class CodeIndexDB {
         const rows = this.db.prepare('SELECT * FROM functions').all();
         return rows.map((r) => this.rowToFunction(r));
     }
+    /**
+     * Narrow variant for the scoped-DRY gate path (Spec 43 R4). Selects only the
+     * columns `buildFullFunctionHashmap` reads — name, file_path, start_line,
+     * line_number, body — so the hot `changed` path skips the wide JSON columns
+     * (`parameters`, `hooks`, `props`, `signature`, `metadata_json`,
+     * `content_hash`) and their per-row `JSON.parse` cost.
+     */
+    async getAllFunctionsForDry() {
+        this.ensureInitialized();
+        const rows = this.db
+            .prepare('SELECT name, file_path, start_line, line_number, body FROM functions')
+            .all();
+        return rows.map((r) => ({
+            name: r.name,
+            filePath: r.file_path,
+            startLine: r.start_line ?? undefined,
+            lineNumber: r.line_number ?? undefined,
+            body: r.body ?? '',
+        }));
+    }
+    /** Row count of the `functions` table — for callers that only need `.length`. */
+    async getFunctionCount() {
+        this.ensureInitialized();
+        const row = this.db.prepare('SELECT COUNT(*) AS n FROM functions').get();
+        return row?.n ?? 0;
+    }
     async getStats() {
         this.ensureInitialized();
         const totalFunctions = this.db.prepare('SELECT COUNT(*) as cnt FROM functions').get().cnt;