diff --git a/packages/bootstrap/src/cli.mjs b/packages/bootstrap/src/cli.mjs
index 887ecd7..04442d3 100644
--- a/packages/bootstrap/src/cli.mjs
+++ b/packages/bootstrap/src/cli.mjs
@@ -21,10 +21,26 @@ import {
 } from './embedded-seaweedfs.mjs';
 import { resolveEmbeddedWorkerLaunch } from './embedded-worker.mjs';
 
+function findWorkspaceRoot(startDir = process.cwd()) {
+  let dir = startDir;
+  while (true) {
+    if (fs.existsSync(path.join(dir, 'pnpm-workspace.yaml'))) {
+      return dir;
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) {
+      break;
+    }
+    dir = parent;
+  }
+  return startDir;
+}
+
+const workspaceRoot = findWorkspaceRoot(process.cwd());
+
 function loadEnvFiles() {
-  const cwd = process.cwd();
-  const envPath = path.join(cwd, '.env');
-  const envLocalPath = path.join(cwd, '.env.local');
+  const envPath = path.join(workspaceRoot, '.env');
+  const envLocalPath = path.join(workspaceRoot, '.env.local');
 
   if (fs.existsSync(envPath)) {
     dotenv.config({ path: envPath });
@@ -111,7 +127,7 @@ function spawnMainCommand(command, env) {
 
 async function runDbMigrations(env) {
   console.log('Running database migrations...');
-  await runMigrations({ cwd: process.cwd(), env });
+  await runMigrations({ cwd: workspaceRoot, env });
 }
 
 function runStorageMigrations(env) {
@@ -278,7 +294,7 @@ async function main() {
     }
 
     if (useEmbeddedWeed) {
-      runtimeEnv.WEED_MINI_DIR = withDefault(runtimeEnv.WEED_MINI_DIR, 'docstore/seaweedfs');
+      runtimeEnv.WEED_MINI_DIR = withDefault(runtimeEnv.WEED_MINI_DIR, path.join(workspaceRoot, 'docstore/seaweedfs'));
       runtimeEnv.WEED_MINI_WAIT_SEC = withDefault(runtimeEnv.WEED_MINI_WAIT_SEC, '20');
       runtimeEnv.S3_BUCKET = withDefault(runtimeEnv.S3_BUCKET, 'openreader-documents');
       runtimeEnv.S3_REGION = withDefault(runtimeEnv.S3_REGION, 'us-east-1');
@@ -371,7 +387,7 @@ async function main() {
       runtimeEnv.COMPUTE_WORKER_HOST = withDefault(runtimeEnv.COMPUTE_WORKER_HOST, '127.0.0.1');
       runtimeEnv.COMPUTE_NATS_REPLICAS = withDefault(runtimeEnv.COMPUTE_NATS_REPLICAS, '1');
 
-      const natsStoreDir = withDefault(runtimeEnv.EMBEDDED_NATS_STORE_DIR, 'docstore/nats/jetstream');
+      const natsStoreDir = withDefault(runtimeEnv.EMBEDDED_NATS_STORE_DIR, path.join(workspaceRoot, 'docstore/nats/jetstream'));
       fs.mkdirSync(natsStoreDir, { recursive: true });
 
       console.log(`Starting embedded nats-server on 127.0.0.1:${embeddedNatsPort}...`);
diff --git a/packages/bootstrap/src/storage-migration.mjs b/packages/bootstrap/src/storage-migration.mjs
index e2f0c7d..53f159d 100644
--- a/packages/bootstrap/src/storage-migration.mjs
+++ b/packages/bootstrap/src/storage-migration.mjs
@@ -17,7 +17,23 @@ const { Pool } = require('pg');
 const BetterSqlite3 = require('better-sqlite3');
 const ffmpegStatic = require('ffmpeg-static');
 
-const DOCSTORE_DIR = path.join(process.cwd(), 'docstore');
+function findWorkspaceRoot(startDir = process.cwd()) {
+  let dir = startDir;
+  while (true) {
+    if (fs.existsSync(path.join(dir, 'pnpm-workspace.yaml'))) {
+      return dir;
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) {
+      break;
+    }
+    dir = parent;
+  }
+  return startDir;
+}
+
+const workspaceRoot = findWorkspaceRoot(process.cwd());
+const DOCSTORE_DIR = path.join(workspaceRoot, 'docstore');
 const DOCUMENTS_V1_DIR = path.join(DOCSTORE_DIR, 'documents_v1');
 const AUDIOBOOKS_V1_DIR = path.join(DOCSTORE_DIR, 'audiobooks_v1');
 const UNCLAIMED_USER_ID = 'unclaimed';
@@ -27,10 +43,15 @@ const SAFE_AUDIOBOOK_ID_REGEX = /^[a-zA-Z0-9._-]{1,128}$/;
 const DOCUMENT_ID_REGEX = /^[a-f0-9]{64}$/i;
 
 function loadEnvFiles() {
-  const envPath = path.join(process.cwd(), '.env');
-  const envLocalPath = path.join(process.cwd(), '.env.local');
-  if (fs.existsSync(envPath)) dotenv.config({ path: envPath });
-  if (fs.existsSync(envLocalPath)) dotenv.config({ path: envLocalPath, override: true });
+  const envPath = path.join(workspaceRoot, '.env');
+  const envLocalPath = path.join(workspaceRoot, '.env.local');
+
+  if (fs.existsSync(envPath)) {
+    dotenv.config({ path: envPath });
+  }
+  if (fs.existsSync(envLocalPath)) {
+    dotenv.config({ path: envLocalPath, override: true });
+  }
 }
 
 function parseBool(value, fallback = false) {
@@ -688,7 +709,7 @@ function openDatabase() {
     };
   }
 
-  const dbPath = path.join(process.cwd(), 'docstore', 'sqlite3.db');
+  const dbPath = path.join(DOCSTORE_DIR, 'sqlite3.db');
   fs.mkdirSync(path.dirname(dbPath), { recursive: true });
   const sqlite = new BetterSqlite3(dbPath);
   return {
diff --git a/packages/database/src/index.ts b/packages/database/src/index.ts
index a6e43ec..f20fd79 100644
--- a/packages/database/src/index.ts
+++ b/packages/database/src/index.ts
@@ -59,6 +59,21 @@ export function ensureSystemUserExists(userId: string) {
   }
 }
 
+function findWorkspaceRoot(startDir: string = process.cwd()): string {
+  let dir = startDir;
+  while (true) {
+    if (fs.existsSync(path.join(dir, 'pnpm-workspace.yaml'))) {
+      return dir;
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) {
+      break;
+    }
+    dir = parent;
+  }
+  return startDir;
+}
+
 function getDrizzleDB() {
   if (dbInstance) return dbInstance;
 
@@ -79,7 +94,8 @@ function getDrizzleDB() {
     const { drizzle: drizzleSqlite } = require('drizzle-orm/better-sqlite3');
     // eslint-disable-next-line @typescript-eslint/no-require-imports
     const Database = require('better-sqlite3');
-    const dbPath = path.join(process.cwd(), 'docstore', 'sqlite3.db');
+    const workspaceRoot = findWorkspaceRoot(process.cwd());
+    const dbPath = path.join(workspaceRoot, 'docstore', 'sqlite3.db');
     const dir = path.dirname(dbPath);
     if (!fs.existsSync(dir)) {
       fs.mkdirSync(dir, { recursive: true });
diff --git a/packages/database/src/migrate.mjs b/packages/database/src/migrate.mjs
index 8aba886..b022aad 100644
--- a/packages/database/src/migrate.mjs
+++ b/packages/database/src/migrate.mjs
@@ -13,8 +13,24 @@ function loadEnvFiles(cwd) {
   if (fs.existsSync(envLocalPath)) dotenv.config({ path: envLocalPath, override: true });
 }
 
+function findWorkspaceRoot(startDir = process.cwd()) {
+  let dir = startDir;
+  while (true) {
+    if (fs.existsSync(path.join(dir, 'pnpm-workspace.yaml'))) {
+      return dir;
+    }
+    const parent = path.dirname(dir);
+    if (parent === dir) {
+      break;
+    }
+    dir = parent;
+  }
+  return startDir;
+}
+
 export async function runMigrations({ cwd = process.cwd(), env = process.env } = {}) {
-  loadEnvFiles(cwd);
+  const workspaceRoot = findWorkspaceRoot(cwd);
+  loadEnvFiles(workspaceRoot);
 
   if (env.POSTGRES_URL?.trim()) {
     const [{ drizzle }, { migrate }, { Pool }] = await Promise.all([
@@ -33,7 +49,7 @@ export async function runMigrations({ cwd = process.cwd(), env = process.env } =
     return;
   }
 
-  const dbPath = path.join(cwd, 'docstore', 'sqlite3.db');
+  const dbPath = path.join(workspaceRoot, 'docstore', 'sqlite3.db');
   fs.mkdirSync(path.dirname(dbPath), { recursive: true });
   const [{ drizzle }, { migrate }, { default: BetterSqlite3 }] = await Promise.all([
     import('drizzle-orm/better-sqlite3'),
@@ -49,3 +65,4 @@ export async function runMigrations({ cwd = process.cwd(), env = process.env } =
     sqlite.close();
   }
 }
+