engram-mcp-server 1.7.2 → 1.7.3

package/dist/constants.d.ts

@@ -20,7 +20,28 @@ export declare const FILE_LOCK_DEFAULT_TIMEOUT_MINUTES = 30;
 export declare const DEFAULT_RETENTION_DAYS = 90;
 export declare const MAX_BACKUP_COUNT = 10;
 export declare const EXCLUDED_DIRS: Set<string>;
+/**
+ * STRONG markers: unambiguous project boundaries. Found → return immediately.
+ * These never appear in IDE install directories or npm global dirs.
+ */
+export declare const STRONG_PROJECT_MARKERS: readonly [".git", ".engram"];
+/**
+ * SOFT markers: typically present in real projects but also in Electron/Node
+ * app install dirs. Only used after strong markers are exhausted, AND only if
+ * the candidate path passes the BLOCKED_PATH_PATTERNS check.
+ */
+export declare const SOFT_PROJECT_MARKERS: string[];
+/**
+ * Legacy combined list kept for any external callers.
+ * Prefer STRONG_PROJECT_MARKERS + SOFT_PROJECT_MARKERS directly.
+ */
 export declare const PROJECT_MARKERS: string[];
+/**
+ * Path-segment patterns that indicate an IDE install, npm global, or OS system
+ * directory. A soft-marker candidate whose normalised path matches any of these
+ * is rejected so we don't mistake an IDE's own install dir for a project root.
+ */
+export declare const BLOCKED_PATH_PATTERNS: RegExp[];
 export declare const NPM_REGISTRY_URL = "https://registry.npmjs.org/engram-mcp-server/latest";
 export declare const GITHUB_REPO = "keggan-std/Engram";
 export declare const GITHUB_RELEASES_URL = "https://github.com/keggan-std/Engram/releases";

package/dist/constants.d.ts.map

@@ -1 +1 @@
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package/dist/constants.js

@@ -54,8 +54,21 @@ export const EXCLUDED_DIRS = new Set([
     ".pub-cache",
 ]);
 // Project root markers — used to auto-detect project boundaries
-export const PROJECT_MARKERS = [
+// FLAW-1 FIX: two tiers prevent IDE install dirs from being picked up.
+/**
+ * STRONG markers: unambiguous project boundaries. Found → return immediately.
+ * These never appear in IDE install directories or npm global dirs.
+ */
+export const STRONG_PROJECT_MARKERS = [
     ".git",
+    ".engram", // already-initialised Engram project
+];
+/**
+ * SOFT markers: typically present in real projects but also in Electron/Node
+ * app install dirs. Only used after strong markers are exhausted, AND only if
+ * the candidate path passes the BLOCKED_PATH_PATTERNS check.
+ */
+export const SOFT_PROJECT_MARKERS = [
     "package.json",
     "build.gradle",
     "build.gradle.kts",
@@ -74,6 +87,39 @@ export const PROJECT_MARKERS = [
     "Gemfile",
     "composer.json",
 ];
+/**
+ * Legacy combined list kept for any external callers.
+ * Prefer STRONG_PROJECT_MARKERS + SOFT_PROJECT_MARKERS directly.
+ */
+export const PROJECT_MARKERS = [
+    ...STRONG_PROJECT_MARKERS,
+    ...SOFT_PROJECT_MARKERS,
+];
+/**
+ * Path-segment patterns that indicate an IDE install, npm global, or OS system
+ * directory. A soft-marker candidate whose normalised path matches any of these
+ * is rejected so we don't mistake an IDE's own install dir for a project root.
+ */
+export const BLOCKED_PATH_PATTERNS = [
+    // Windows IDE install / npm global locations
+    /[/\\]AppData[/\\]Local[/\\]Programs[/\\]/i,
+    /[/\\]AppData[/\\]Roaming[/\\]npm[/\\]/i,
+    /[/\\]AppData[/\\]Local[/\\]npm[/\\]/i,
+    // Windows system dirs
+    /^[A-Za-z]:[/\\]Program Files( \(x86\))?[/\\]/i,
+    /^[A-Za-z]:[/\\]Windows[/\\]/i,
+    // macOS application bundles and Homebrew
+    /\/Applications\/.+\.app\//,
+    /\/usr\/local\/(bin|lib|Cellar)\//,
+    /\/opt\/(homebrew|local)\//,
+    // Linux system dirs
+    /^\/usr\/(bin|lib|share|local)\//,
+    /^\/opt\//,
+    // npm / node global installs (all OSes)
+    /[/\\]node_modules[/\\]engram-mcp-server[/\\]/i,
+    /[/\\]lib[/\\]node_modules[/\\]/i,
+    /[/\\]node_modules\.bin[/\\]/i,
+];
 // Update check
 export const NPM_REGISTRY_URL = "https://registry.npmjs.org/engram-mcp-server/latest";
 export const GITHUB_REPO = "keggan-std/Engram";

package/dist/constants.js.map

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package/dist/database.d.ts

@@ -9,7 +9,7 @@ export interface Services {
     update: UpdateService;
     agentRules: AgentRulesService;
 }
-export declare function initDatabase(projectRoot: string): Promise<DatabaseType>;
+export declare function initDatabase(projectRoot: string): DatabaseType;
 export declare function getDb(): DatabaseType;
 export declare function getRepos(): Repositories;
 export declare function getServices(): Services;

package/dist/database.d.ts.map

@@ -1 +1 @@
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package/dist/database.js

@@ -17,25 +17,36 @@ let _dbPath = "";
 // ─── Initialization ──────────────────────────────────────────────────
 /**
  * Open the SQLite database, auto-recovering from WAL/SHM corruption.
- * If the WAL or SHM files cause SQLITE_CORRUPT, they are removed and the
- * main DB is reopened (which is almost always intact in WAL mode).
- * If the main DB itself is corrupt, it is renamed to a timestamped .corrupt
- * file and a fresh database is created.
+ *
+ * FLAW-2 FIX: busy_timeout is set immediately after open — BEFORE any other
+ * pragma — so concurrent access from multiple IDE windows waits up to 5 s
+ * instead of crashing with SQLITE_BUSY.
+ *
+ * FLAW-3 FIX: SQLITE_BUSY is no longer swallowed by the corruption-recovery
+ * path. A busy DB is not corrupt; the two conditions must not be conflated.
+ *
+ * If WAL/SHM files cause SQLITE_CORRUPT they are removed and the main DB is
+ * reopened (almost always intact in WAL mode). If the main DB itself is
+ * corrupt it is renamed to a timestamped .corrupt file and a fresh database
+ * is created.
  */
 function openDatabaseWithRecovery(dbPath) {
-    // First attempt
+    const CORRUPTION_CODES = new Set(["SQLITE_CORRUPT", "SQLITE_NOTADB"]);
+    // ── First attempt ──────────────────────────────────────────────────
     try {
         const db = new Database(dbPath);
-        db.pragma("journal_mode = WAL"); // quick smoke-test
+        db.pragma("busy_timeout = 5000"); // FLAW-2: set BEFORE any other pragma
+        db.pragma("journal_mode = WAL"); // smoke-test (waits up to 5 s if busy)
         db.pragma("journal_mode = DELETE"); // reset so caller sets it properly
         return db;
     }
     catch (err) {
-        const code = err.code;
-        if (code !== "SQLITE_CORRUPT" && code !== "SQLITE_NOTADB")
+        const code = err.code ?? "";
+        // FLAW-3: never enter corruption recovery for a locked-but-healthy DB
+        if (!CORRUPTION_CODES.has(code))
             throw err;
     }
-    // Try removing WAL/SHM — the main file is usually fine in WAL mode
+    // ── Try removing WAL/SHM ── main file is usually fine in WAL mode ──
     const walPath = dbPath + "-wal";
     const shmPath = dbPath + "-shm";
     const ts = new Date().toISOString().replace(/[:.]/g, "-");
@@ -49,37 +60,43 @@ function openDatabaseWithRecovery(dbPath) {
     }
     try {
         const db = new Database(dbPath);
+        db.pragma("busy_timeout = 5000"); // FLAW-2: set here too
         db.pragma("journal_mode = WAL");
         db.pragma("journal_mode = DELETE");
         console.error("[Engram] [WARN] Recovered from corrupt WAL/SHM — some recent changes may be lost.");
         return db;
     }
     catch (err) {
-        const code = err.code;
-        if (code !== "SQLITE_CORRUPT" && code !== "SQLITE_NOTADB")
+        const code = err.code ?? "";
+        if (!CORRUPTION_CODES.has(code))
             throw err;
     }
-    // Main DB is also corrupt — rename it and start fresh
+    // ── Main DB is also corrupt — rename and start fresh ───────────────
     try {
         fs.renameSync(dbPath, dbPath + `.corrupt.${ts}.bak`);
     }
     catch { /* best-effort */ }
     console.error("[Engram] [WARN] Main database was corrupt — renamed to backup, starting fresh.");
-    return new Database(dbPath);
+    const freshDb = new Database(dbPath);
+    freshDb.pragma("busy_timeout = 5000"); // FLAW-2: set on fresh DB too
+    return freshDb;
 }
-export async function initDatabase(projectRoot) {
+// FLAW-5 FIX: initDatabase is synchronous (better-sqlite3 is sync throughout).
+// The misleading async/Promise wrapper is removed — callers no longer need
+// to remember to await a function that never actually awaits anything.
+export function initDatabase(projectRoot) {
     _projectRoot = projectRoot;
     const dbDir = path.join(projectRoot, DB_DIR_NAME);
     fs.mkdirSync(dbDir, { recursive: true });
     ensureGitignore(projectRoot);
     _dbPath = path.join(dbDir, DB_FILE_NAME);
     _db = openDatabaseWithRecovery(_dbPath);
-    // Performance pragmas
+    // Performance pragmas (busy_timeout already set inside openDatabaseWithRecovery)
     _db.pragma("journal_mode = WAL");
     _db.pragma("foreign_keys = ON");
     _db.pragma("synchronous = NORMAL");
     _db.pragma("cache_size = -8000"); // 8MB cache
-    _db.pragma("busy_timeout = 5000");
+    _db.pragma("busy_timeout = 5000"); // re-affirm after WAL mode switch
     // Run versioned migrations
     runMigrations(_db);
     // Initialize repositories
@@ -146,7 +163,21 @@ export function backupDatabase(destPath) {
     return destPath;
 }
 // ─── Gitignore ───────────────────────────────────────────────────────
+// FLAW-6 / FLAW-13 FIX: Write a self-contained .engram/.gitignore ("*") that
+// protects the DB regardless of whether a root .gitignore exists or is writable.
+// Also append to root .gitignore when present, as a belt-and-suspenders measure.
 function ensureGitignore(projectRoot) {
+    // 1. Self-contained: .engram/.gitignore with wildcard — always works
+    try {
+        const dbDir = path.join(projectRoot, DB_DIR_NAME);
+        const innerIgnore = path.join(dbDir, ".gitignore");
+        if (!fs.existsSync(innerIgnore)) {
+            fs.mkdirSync(dbDir, { recursive: true });
+            fs.writeFileSync(innerIgnore, "# Engram AI agent memory — do not commit\n*\n!.gitignore\n", "utf-8");
+        }
+    }
+    catch { /* best-effort */ }
+    // 2. Belt-and-suspenders: append to root .gitignore if it exists
     const gitignorePath = path.join(projectRoot, ".gitignore");
     try {
         if (fs.existsSync(gitignorePath)) {

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package/dist/global-db.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"global-db.d.ts","sourceRoot":"","sources":["../src/global-db.ts"],"names":[],"mappings":"AAUA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAWtC,wBAAgB,WAAW,IAAI,YAAY,CAAC,OAAO,QAAQ,CAAC,GAAG,IAAI,CAmBlE;AAoCD,MAAM,WAAW,mBAAmB;IAChC,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC1B,IAAI,CAAC,EAAE,MAAM,EAAE,GAAG,IAAI,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;CACrB;AAED,wBAAgB,mBAAmB,CAAC,KAAK,EAAE,mBAAmB,GAAG,MAAM,GAAG,IAAI,CAiB7E;AAED,wBAAgB,qBAAqB,CAAC,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAY3H;AAED,MAAM,WAAW,iBAAiB;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,EAAE,MAAM,CAAC;IACrB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,GAAG,IAAI,CAAC;IACzB,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IACpB,SAAS,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,mBAAmB;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,EAAE,MAAM,CAAC;IACrB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;CACrB;AAED,wBAAgB,oBAAoB,CAAC,KAAK,CAAC,EAAE,MAAM,EAAE,KAAK,GAAE,MAAW,GAAG,iBAAiB,EAAE,CAqB5F;AAED,wBAAgB,sBAAsB,CAAC,KAAK,GAAE,MAAW,GAAG,mBAAmB,EAAE,CAUhF"}

package/dist/global-db.js

@@ -23,6 +23,9 @@ export function getGlobalDb() {
             fs.mkdirSync(GLOBAL_DB_DIR, { recursive: true });
         }
         const db = new Database(GLOBAL_DB_PATH);
+        // FLAW-7 FIX: set busy_timeout before any other pragma so concurrent
+        // multi-agent access waits instead of crashing with SQLITE_BUSY.
+        db.pragma("busy_timeout = 5000");
         db.pragma("journal_mode = WAL");
         db.pragma("foreign_keys = ON");
         initGlobalSchema(db);

package/dist/global-db.js.map

@@ -1 +1 @@
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package/dist/index.js

@@ -91,7 +91,7 @@ async function main() {
         args.includes("-v") ||
         args.includes("--install-hooks") ||
         args.includes("--remove-hooks")) {
-        runInstaller(args);
+        await runInstaller(args); // FLAW-12 FIX: runInstaller is async; was missing await
         return;
     }
     // ─── record-commit (git hook handler) ──────────────────────────────
@@ -102,7 +102,8 @@ async function main() {
     // Detect project root
     const projectRoot = findProjectRoot();
     log.info(`Project root: ${projectRoot}`);
-    // Initialize database
+    // Initialize database (synchronous — better-sqlite3 is sync throughout)
+    // FLAW-5 FIX: initDatabase is no longer async; no await needed
     initDatabase(projectRoot);
     log.info(`Database initialized at ${projectRoot}/.engram/memory.db`);
     // Create MCP server

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/installer/config-writer.d.ts

@@ -1,18 +1,38 @@
 import type { IdeDefinition } from "./ide-configs.js";
-/** Read the installed package version (used to stamp _engram_version in IDE configs). */
+/**
+ * FLAW-15 FIX: Read version from package.json relative to the dist output,
+ * but fall back to the SERVER_VERSION constant as the single source of truth.
+ * This is resilient to build output structure changes.
+ */
 export declare function getInstallerVersion(): string;
 /**
  * Generate the Engram server entry tailored to a specific IDE's requirements.
  * Includes _engram_version so the installer can detect upgrades and legacy installs.
  *
- * @param ide        IDE definition (controls type, cmd wrapper, etc.)
- * @param universal  When true, adds --mode=universal and --project-root to args.
- *                   Uses IDE-appropriate workspace variable when available.
+ * FLAW-4 FIX: When the IDE definition has a workspaceVar, it is injected as
+ * `--project-root=<var>`. At runtime the IDE expands the variable to the actual
+ * workspace path before spawning the server, so findProjectRoot() receives the
+ * correct root with no heuristics needed.
+ *
+ * @param ide        IDE definition (controls type, cmd wrapper, workspaceVar, etc.)
+ * @param universal  When true, adds --mode=universal to args.
  */
 export declare function makeEngramEntry(ide: IdeDefinition, universal?: boolean): Record<string, any>;
 /**
- * Read and parse a JSON config file. Returns null if file doesn't exist or is invalid.
+ * Read and parse a JSON config file.
+ * FLAW-8 FIX: distinguish between "file not found" and "file has invalid JSON".
+ * Returns:
+ *   null    — file does not exist (safe to create fresh)
+ *   object  — parsed successfully
+ * Throws ParseError (with .isParseError = true) when the file exists but
+ *   contains invalid JSON — callers should warn and bail rather than
+ *   silently overwriting the user's config.
  */
+export declare class ConfigParseError extends Error {
+    readonly filePath: string;
+    readonly cause: unknown;
+    constructor(filePath: string, cause: unknown);
+}
 export declare function readJson(filePath: string): Record<string, any> | null;
 /**
  * Write a JSON config file, creating parent directories if needed.
@@ -21,13 +41,14 @@ export declare function writeJson(filePath: string, data: any): void;
 export type InstallResult = "added" | "upgraded" | "exists" | "legacy-upgraded";
 /**
  * Add or update the Engram entry in a config file.
- * Uses the IDE's configKey ("mcpServers" or "servers") to write the correct JSON structure.
+ * FLAW-8 FIX: if the config file exists but has invalid JSON, back it up
+ * before overwriting so the user doesn't lose their other tool configs.
  *
  * Returns:
- *   "added"          — fresh install, no prior entry
- *   "exists"         — already installed at the same version, no changes made
- *   "upgraded"       — updated from an older tracked version to the current one
- *   "legacy-upgraded" — entry existed but had no _engram_version (pre-tracking era), now stamped
+ *   "added"           — fresh install, no prior entry
+ *   "exists"          — already installed at the same version, no changes made
+ *   "upgraded"        — updated from an older tracked version to the current one
+ *   "legacy-upgraded" — entry existed but had no _engram_version (pre-tracking era)
  */
 export declare function addToConfig(configPath: string, ide: IdeDefinition, universal?: boolean): InstallResult;
 /**

package/dist/installer/config-writer.d.ts.map

@@ -1 +1 @@
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package/dist/installer/config-writer.js

@@ -4,12 +4,24 @@
 import fs from "fs";
 import path from "path";
 import { fileURLToPath } from "url";
-/** Read the installed package version (used to stamp _engram_version in IDE configs). */
+/**
+ * FLAW-15 FIX: Read version from package.json relative to the dist output,
+ * but fall back to the SERVER_VERSION constant as the single source of truth.
+ * This is resilient to build output structure changes.
+ */
 export function getInstallerVersion() {
     try {
         const __dirname = path.dirname(fileURLToPath(import.meta.url));
-        const pkgPath = path.resolve(__dirname, "../../package.json");
-        return JSON.parse(fs.readFileSync(pkgPath, "utf-8")).version;
+        // Try dist/installer/ → ../../package.json (standard build layout)
+        for (const rel of ["../../package.json", "../../../package.json", "../../../../package.json"]) {
+            const pkgPath = path.resolve(__dirname, rel);
+            if (fs.existsSync(pkgPath)) {
+                const ver = JSON.parse(fs.readFileSync(pkgPath, "utf-8")).version;
+                if (ver)
+                    return ver;
+            }
+        }
+        return "unknown";
     }
     catch {
         return "unknown";
@@ -19,9 +31,13 @@ export function getInstallerVersion() {
  * Generate the Engram server entry tailored to a specific IDE's requirements.
  * Includes _engram_version so the installer can detect upgrades and legacy installs.
  *
- * @param ide        IDE definition (controls type, cmd wrapper, etc.)
- * @param universal  When true, adds --mode=universal and --project-root to args.
- *                   Uses IDE-appropriate workspace variable when available.
+ * FLAW-4 FIX: When the IDE definition has a workspaceVar, it is injected as
+ * `--project-root=<var>`. At runtime the IDE expands the variable to the actual
+ * workspace path before spawning the server, so findProjectRoot() receives the
+ * correct root with no heuristics needed.
+ *
+ * @param ide        IDE definition (controls type, cmd wrapper, workspaceVar, etc.)
+ * @param universal  When true, adds --mode=universal to args.
  */
 export function makeEngramEntry(ide, universal = false) {
     const entry = {};
@@ -34,6 +50,12 @@ export function makeEngramEntry(ide, universal = false) {
     if (universal) {
         baseArgs.push("--mode=universal");
     }
+    // FLAW-4 FIX: inject workspace root variable when the IDE supports it.
+    // The IDE expands this variable at spawn time (e.g. ${workspaceFolder} →
+    // /path/to/project) so the server always receives the correct project path.
+    if (ide.workspaceVar) {
+        baseArgs.push(`--project-root=${ide.workspaceVar}`);
+    }
     // Windows cmd /c wrapper for npx (npx is a .cmd on Windows)
     if (ide.requiresCmdWrapper) {
         entry.command = "cmd";
@@ -51,14 +73,34 @@ export function makeEngramEntry(ide, universal = false) {
     return entry;
 }
 /**
- * Read and parse a JSON config file. Returns null if file doesn't exist or is invalid.
+ * Read and parse a JSON config file.
+ * FLAW-8 FIX: distinguish between "file not found" and "file has invalid JSON".
+ * Returns:
+ *   null    — file does not exist (safe to create fresh)
+ *   object  — parsed successfully
+ * Throws ParseError (with .isParseError = true) when the file exists but
+ *   contains invalid JSON — callers should warn and bail rather than
+ *   silently overwriting the user's config.
  */
+export class ConfigParseError extends Error {
+    filePath;
+    cause;
+    constructor(filePath, cause) {
+        super(`Failed to parse JSON config at ${filePath}: ${cause}`);
+        this.filePath = filePath;
+        this.cause = cause;
+        this.name = "ConfigParseError";
+    }
+}
 export function readJson(filePath) {
+    if (!fs.existsSync(filePath))
+        return null; // file not found — safe to create
     try {
         return JSON.parse(fs.readFileSync(filePath, "utf-8"));
     }
-    catch {
-        return null;
+    catch (e) {
+        // File exists but is invalid JSON — signal this distinctly
+        throw new ConfigParseError(filePath, e);
     }
 }
 /**
@@ -70,16 +112,38 @@ export function writeJson(filePath, data) {
 }
 /**
  * Add or update the Engram entry in a config file.
- * Uses the IDE's configKey ("mcpServers" or "servers") to write the correct JSON structure.
+ * FLAW-8 FIX: if the config file exists but has invalid JSON, back it up
+ * before overwriting so the user doesn't lose their other tool configs.
  *
  * Returns:
- *   "added"          — fresh install, no prior entry
- *   "exists"         — already installed at the same version, no changes made
- *   "upgraded"       — updated from an older tracked version to the current one
- *   "legacy-upgraded" — entry existed but had no _engram_version (pre-tracking era), now stamped
+ *   "added"           — fresh install, no prior entry
+ *   "exists"          — already installed at the same version, no changes made
+ *   "upgraded"        — updated from an older tracked version to the current one
+ *   "legacy-upgraded" — entry existed but had no _engram_version (pre-tracking era)
  */
 export function addToConfig(configPath, ide, universal = false) {
-    let config = readJson(configPath) || {};
+    let config;
+    try {
+        config = readJson(configPath) ?? {};
+    }
+    catch (e) {
+        if (e instanceof ConfigParseError) {
+            // Backup the broken file then start fresh
+            const ts = new Date().toISOString().replace(/[:.]/g, "-");
+            const bakPath = configPath + `.invalid.${ts}.bak`;
+            try {
+                fs.copyFileSync(configPath, bakPath);
+            }
+            catch { /* best-effort */ }
+            console.warn(`[Engram] Config at ${configPath} contains invalid JSON.`);
+            console.warn(`         Backed up to: ${bakPath}`);
+            console.warn(`         Writing a fresh config with only the Engram entry.`);
+            config = {};
+        }
+        else {
+            throw e;
+        }
+    }
     const key = ide.configKey;
     if (!config[key])
         config[key] = {};

package/dist/installer/config-writer.js.map

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