amalgm 0.1.57 → 0.1.58

package/lib/cli.js

@@ -13,6 +13,7 @@ const {
   AMALGM_DIR,
   AMALGM_BRANCH,
   AMALGM_HOME,
+  AMALGM_RUNTIME_STATE_DIR,
   DEFAULT_APP_URL,
   DEVICE_FILE,
   LOG_DIR,
@@ -44,6 +45,7 @@ const {
   runtimeServiceProcesses,
   supervisorProcesses,
 } = require('./process-cleanup');
+const { migrateLegacyUserState } = require('./state-migration');
 const {
   runtimePortsForStatus,
   runtimeServiceNames,
@@ -138,6 +140,7 @@ function ensureDir(dir, mode = 0o700) {
 function ensureBaseDirs() {
   ensureDir(AMALGM_DIR, 0o700);
   ensureDir(LOG_DIR, 0o700);
+  migrateLegacyUserState();
 }
 
 function readJson(file, fallback = null) {
@@ -203,6 +206,7 @@ const SAFE_DAEMON_ENV_KEYS = [
   'AMALGM_NATIVE_NODE_MODULES',
   'AMALGM_RUNTIME_INSTANCE_ID',
   'AMALGM_RUNTIME_LABEL',
+  'AMALGM_RUNTIME_STATE_DIR',
   'AMALGM_RUNTIME_USER_ID',
   'AMALGM_SKIP_NATIVE_INSTALL',
   'CHAT_SERVER_PORT',
@@ -232,6 +236,8 @@ function daemonEnv(localOnly) {
     if (process.env[key]) env[key] = process.env[key];
   }
   env.AMALGM_DIR = AMALGM_DIR;
+  env.AMALGM_HOME = AMALGM_HOME;
+  env.AMALGM_RUNTIME_STATE_DIR = AMALGM_RUNTIME_STATE_DIR;
   env.AMALGM_RUNTIME_INSTANCE_ID = AMALGM_RUNTIME_INSTANCE_ID;
   env.AMALGM_RUNTIME_LABEL = AMALGM_RUNTIME_LABEL;
   env.AMALGM_BRANCH = AMALGM_BRANCH;
@@ -1073,6 +1079,7 @@ async function status() {
   console.log(`Label: ${AMALGM_RUNTIME_LABEL} (${AMALGM_BRANCH})`);
   console.log(`User scope: ${AMALGM_RUNTIME_USER_SCOPE}`);
   console.log(`State: ${AMALGM_DIR}`);
+  console.log(`Runtime state: ${AMALGM_RUNTIME_STATE_DIR}`);
   if (runtimeState?.gateway_url) console.log(`Gateway: ${runtimeState.gateway_url}`);
   if (lastShutdown?.signal || lastShutdown?.reason) {
     console.log(
@@ -1235,6 +1242,7 @@ async function doctor() {
   console.log(`Label: ${AMALGM_RUNTIME_LABEL} (${AMALGM_BRANCH})`);
   console.log(`User scope: ${AMALGM_RUNTIME_USER_SCOPE}`);
   console.log(`State: ${AMALGM_DIR}`);
+  console.log(`Runtime state: ${AMALGM_RUNTIME_STATE_DIR}`);
   for (const check of checks) {
     console.log(`${check.level.padEnd(4)} ${check.name.padEnd(18)} ${check.detail}`);
   }

package/lib/paths.js

@@ -10,6 +10,7 @@ const {
   runtimeBranchForLabel,
   runtimeInstanceIdForDir,
   scopedAmalgmDir,
+  scopedRuntimeDir,
 } = require('./runtime-identity');
 
 const PACKAGE_VERSION = require('../package.json').version;
@@ -26,28 +27,32 @@ const AMALGM_RUNTIME_USER_SCOPE = resolveRuntimeUserScope(
 const AMALGM_DIR = process.env.AMALGM_DIR
   ? path.resolve(process.env.AMALGM_DIR)
   : scopedAmalgmDir(AMALGM_HOME, AMALGM_RUNTIME_USER_SCOPE, AMALGM_RUNTIME_LABEL);
+const AMALGM_RUNTIME_STATE_DIR = process.env.AMALGM_RUNTIME_STATE_DIR
+  ? path.resolve(process.env.AMALGM_RUNTIME_STATE_DIR)
+  : scopedRuntimeDir(AMALGM_HOME, AMALGM_RUNTIME_USER_SCOPE, AMALGM_RUNTIME_LABEL);
 const AMALGM_RUNTIME_INSTANCE_ID = process.env.AMALGM_RUNTIME_INSTANCE_ID
-  || runtimeInstanceIdForDir(AMALGM_DIR);
+  || runtimeInstanceIdForDir(AMALGM_RUNTIME_STATE_DIR);
 // Physical machine identity is intentionally shared across runtime labels.
-// Runtime credentials/state below remain scoped by user + label.
+// User data below is scoped by user; live runtime files are scoped by label.
 const DEVICE_FILE = path.join(AMALGM_HOME, 'device.json');
 const COMPUTER_FILE = path.join(AMALGM_DIR, 'computer.json');
 const AUTH_FILE = path.join(AMALGM_DIR, 'auth.json');
-const RUNTIME_TOKEN_FILE = path.join(AMALGM_DIR, 'runtime-token.json');
-const PID_FILE = path.join(AMALGM_DIR, 'amalgm.pid');
-const RUNTIME_STATE_FILE = path.join(AMALGM_DIR, 'runtime-state.json');
-const LOG_DIR = path.join(AMALGM_DIR, 'logs');
-const SERVICE_DIR = path.join(AMALGM_DIR, 'service');
-const SERVICE_PID_FILE = path.join(AMALGM_DIR, 'amalgm-service.pid');
-const SERVICE_STATE_FILE = path.join(AMALGM_DIR, 'service-state.json');
-const SERVICE_STOP_FILE = path.join(AMALGM_DIR, 'amalgm-service.stop');
-const SHUTDOWN_REASON_FILE = path.join(AMALGM_DIR, 'shutdown-reason.json');
+const RUNTIME_TOKEN_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'runtime-token.json');
+const PID_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'amalgm.pid');
+const RUNTIME_STATE_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'runtime-state.json');
+const LOG_DIR = path.join(AMALGM_RUNTIME_STATE_DIR, 'logs');
+const SERVICE_DIR = path.join(AMALGM_RUNTIME_STATE_DIR, 'service');
+const SERVICE_PID_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'amalgm-service.pid');
+const SERVICE_STATE_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'service-state.json');
+const SERVICE_STOP_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'amalgm-service.stop');
+const SHUTDOWN_REASON_FILE = path.join(AMALGM_RUNTIME_STATE_DIR, 'shutdown-reason.json');
 const DEFAULT_APP_URL = process.env.AMALGM_APP_URL || 'https://amalgm.ai';
 
 module.exports = {
   AMALGM_BRANCH,
   AMALGM_DIR,
   AMALGM_HOME,
+  AMALGM_RUNTIME_STATE_DIR,
   AMALGM_RUNTIME_INSTANCE_ID,
   AMALGM_RUNTIME_LABEL,
   AMALGM_RUNTIME_USER_SCOPE,

package/lib/runtime-identity.js

@@ -88,11 +88,19 @@ function discoverLegacyUserScope(homeDir, label = '') {
     const usersDir = path.join(homeDir, 'users');
     for (const entry of fs.readdirSync(usersDir, { withFileTypes: true })) {
       if (!entry.isDirectory()) continue;
-      const scopedDir = path.join(usersDir, entry.name, runtimeLabel);
-      const scopedRecord = readJson(path.join(scopedDir, 'computer.json'), null);
+      const userDir = path.join(usersDir, entry.name);
+      const userRecord = readJson(path.join(userDir, 'computer.json'), null);
+      const fromUserRecord = userIdFromRecord(userRecord);
+      if (fromUserRecord) return fromUserRecord;
+      const userAuth = readJson(path.join(userDir, 'auth.json'), null);
+      const fromUserAuth = userIdFromRecord(userAuth);
+      if (fromUserAuth) return fromUserAuth;
+
+      const oldScopedDir = path.join(userDir, runtimeLabel);
+      const scopedRecord = readJson(path.join(oldScopedDir, 'computer.json'), null);
       const fromScopedRecord = userIdFromRecord(scopedRecord);
       if (fromScopedRecord) return fromScopedRecord;
-      const scopedAuth = readJson(path.join(scopedDir, 'auth.json'), null);
+      const scopedAuth = readJson(path.join(oldScopedDir, 'auth.json'), null);
       const fromScopedAuth = userIdFromRecord(scopedAuth);
       if (fromScopedAuth) return fromScopedAuth;
     }
@@ -117,7 +125,12 @@ function defaultAmalgmHome(env = process.env) {
 }
 
 function scopedAmalgmDir(homeDir, userScope, label) {
-  return path.join(homeDir, 'users', sanitizeScopeSegment(userScope), assertRuntimeLabel(label));
+  assertRuntimeLabel(label);
+  return path.join(homeDir, 'users', sanitizeScopeSegment(userScope));
+}
+
+function scopedRuntimeDir(homeDir, userScope, label) {
+  return path.join(scopedAmalgmDir(homeDir, userScope, label), 'runtimes', assertRuntimeLabel(label));
 }
 
 function runtimeInstanceIdForDir(dir) {
@@ -142,4 +155,5 @@ module.exports = {
   runtimeLabelFromVersion,
   sanitizeScopeSegment,
   scopedAmalgmDir,
+  scopedRuntimeDir,
 };

package/lib/service.js

@@ -7,12 +7,14 @@ const { spawn, spawnSync } = require('child_process');
 
 const {
   AMALGM_DIR,
+  AMALGM_HOME,
   AMALGM_BRANCH,
   LOG_DIR,
   PACKAGE_ROOT,
   PID_FILE,
   AMALGM_RUNTIME_INSTANCE_ID,
   AMALGM_RUNTIME_LABEL,
+  AMALGM_RUNTIME_STATE_DIR,
   AMALGM_RUNTIME_USER_SCOPE,
   SERVICE_DIR,
   SERVICE_PID_FILE,
@@ -43,6 +45,7 @@ const SERVICE_ENV_KEYS = [
   'AMALGM_HOME',
   'AMALGM_RUNTIME_INSTANCE_ID',
   'AMALGM_RUNTIME_LABEL',
+  'AMALGM_RUNTIME_STATE_DIR',
   'AMALGM_RUNTIME_USER_ID',
   'AMALGM_NATIVE_NODE_MODULES',
   'AMALGM_PROJECTS_DIR',
@@ -235,6 +238,8 @@ function detectServiceBackend(mode = 'auto') {
 function buildServiceEnv(localOnly) {
   const env = {
     AMALGM_DIR,
+    AMALGM_HOME,
+    AMALGM_RUNTIME_STATE_DIR,
     AMALGM_RUNTIME_INSTANCE_ID,
     AMALGM_RUNTIME_LABEL,
     AMALGM_BRANCH,
@@ -261,6 +266,8 @@ function writePortableScript(localOnly) {
     '#!/bin/sh',
     'set -u',
     `AMALGM_DIR=${shellQuote(AMALGM_DIR)}`,
+    `AMALGM_HOME=${shellQuote(AMALGM_HOME)}`,
+    `AMALGM_RUNTIME_STATE_DIR=${shellQuote(AMALGM_RUNTIME_STATE_DIR)}`,
     `LOG_DIR=${shellQuote(LOG_DIR)}`,
     `PID_FILE=${shellQuote(SERVICE_PID_FILE)}`,
     `WORKER_PID_FILE=${shellQuote(PID_FILE)}`,

package/lib/state-migration.js

@@ -0,0 +1,110 @@
+'use strict';
+
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+
+const {
+  AMALGM_DIR,
+  AMALGM_HOME,
+} = require('./paths');
+
+const MARKER_FILE = path.join(AMALGM_DIR, '.user-state-migrated.json');
+
+const DATA_FILES = [
+  'amalgm.db',
+  'apps.json',
+  'artifacts.json',
+  'agents.json',
+  'tasks.json',
+  'event-triggers.json',
+  'workflows.json',
+  'mcp-connections.json',
+  'computer.json',
+  'auth.json',
+  '.amalgm-credentials',
+];
+
+const DATA_DIRS = [
+  'apps',
+  'browser',
+  'browser-sessions',
+  'contexts',
+  'harness-configs',
+  'memories',
+  '.memories',
+  'task-runs',
+  'toolbox',
+  'uploads',
+];
+
+function readJson(file, fallback = null) {
+  try {
+    return JSON.parse(fs.readFileSync(file, 'utf8'));
+  } catch {
+    return fallback;
+  }
+}
+
+function writeJson(file, data) {
+  fs.mkdirSync(path.dirname(file), { recursive: true, mode: 0o700 });
+  fs.writeFileSync(file, `${JSON.stringify(data, null, 2)}\n`, { mode: 0o600 });
+}
+
+function copyFileIfUseful(source, target) {
+  if (!fs.existsSync(source)) return false;
+
+  const targetExists = fs.existsSync(target);
+  if (targetExists && path.basename(source) === 'amalgm.db') {
+    const sourceSize = fs.statSync(source).size;
+    const targetSize = fs.statSync(target).size;
+    if (targetSize > 64 * 1024 || sourceSize <= targetSize) return false;
+  } else if (targetExists && fs.statSync(target).size > 64) {
+    return false;
+  }
+
+  fs.mkdirSync(path.dirname(target), { recursive: true, mode: 0o700 });
+  fs.copyFileSync(source, target);
+  return true;
+}
+
+function copyDirIfMissing(source, target) {
+  if (!fs.existsSync(source) || fs.existsSync(target)) return false;
+  fs.mkdirSync(path.dirname(target), { recursive: true, mode: 0o700 });
+  fs.cpSync(source, target, { recursive: true, force: false, errorOnExist: true });
+  return true;
+}
+
+function migrateLegacyUserState() {
+  if (path.resolve(AMALGM_DIR) === path.resolve(AMALGM_HOME)) return { migrated: false, reason: 'legacy-root' };
+  if (path.resolve(AMALGM_DIR).startsWith(path.resolve(os.tmpdir()))) return { migrated: false, reason: 'temp-dir' };
+  if (readJson(MARKER_FILE, null)) return { migrated: false, reason: 'already-migrated' };
+
+  fs.mkdirSync(AMALGM_DIR, { recursive: true, mode: 0o700 });
+
+  const copied = [];
+  for (const fileName of DATA_FILES) {
+    const source = path.join(AMALGM_HOME, fileName);
+    const target = path.join(AMALGM_DIR, fileName);
+    if (copyFileIfUseful(source, target)) copied.push(fileName);
+  }
+
+  for (const dirName of DATA_DIRS) {
+    const source = path.join(AMALGM_HOME, dirName);
+    const target = path.join(AMALGM_DIR, dirName);
+    if (copyDirIfMissing(source, target)) copied.push(`${dirName}/`);
+  }
+
+  writeJson(MARKER_FILE, {
+    migrated_at: new Date().toISOString(),
+    source: AMALGM_HOME,
+    target: AMALGM_DIR,
+    copied,
+  });
+
+  return { migrated: copied.length > 0, copied };
+}
+
+module.exports = {
+  migrateLegacyUserState,
+};

package/lib/supervisor.js

@@ -11,10 +11,12 @@ const net = require('net');
 const {
   AMALGM_DIR,
   AMALGM_BRANCH,
+  AMALGM_HOME,
   LOG_DIR,
   PID_FILE,
   AMALGM_RUNTIME_INSTANCE_ID,
   AMALGM_RUNTIME_LABEL,
+  AMALGM_RUNTIME_STATE_DIR,
   AMALGM_RUNTIME_USER_SCOPE,
   RUNTIME_DIR,
   RUNTIME_STATE_FILE,
@@ -221,6 +223,11 @@ function baseRuntimeEnv(record, ports, options = {}) {
     AMALGM_AUTH_BACKUP_ENABLED: process.env.AMALGM_AUTH_BACKUP_ENABLED || 'false',
     AMALGM_CREATE_AUTH_WATCH_DIRS: process.env.AMALGM_CREATE_AUTH_WATCH_DIRS || 'false',
     AMALGM_DIR,
+    AMALGM_HOME,
+    AMALGM_RUNTIME_STATE_DIR,
+    AMALGM_RUNTIME_STATE_FILE: RUNTIME_STATE_FILE,
+    AMALGM_RUNTIME_TOKEN_FILE: RUNTIME_TOKEN_FILE,
+    AMALGM_LOG_DIR: LOG_DIR,
     AMALGM_RUNTIME_DIR: RUNTIME_DIR,
     AMALGM_WORKSPACES_DIR: workspaceRoot,
     AMALGM_PROJECTS_DIR: workspaceRoot,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "amalgm",
-  "version": "0.1.57",
+  "version": "0.1.58",
   "description": "Amalgm local computer runtime: login, MCP, chat, events, previews, and tunnels.",
   "license": "UNLICENSED",
   "private": false,
@@ -17,7 +17,7 @@
     "sync-runtime": "node ../../scripts/sync-npm-package-runtime.mjs",
     "prepack": "node ../../scripts/sync-npm-package-runtime.mjs",
     "pack:dry": "npm pack --dry-run",
-    "check": "node --check bin/amalgm.js && node --check lib/auth-store.js && node --check lib/cli.js && node --check lib/paths.js && node --check lib/process-cleanup.js && node --check lib/runtime-identity.js && node --check lib/runtime-manifest.js && node --check lib/service.js && node --check lib/supervisor.js && node --check lib/tunnel-chat.js && node --check lib/tunnel-events.js && node --check runtime/lib/runtime-manifest.js && node --check runtime/scripts/runtime-auth.js && node --check runtime/scripts/proxy-token-store.js && node --check runtime/scripts/local-gateway.js && node --check runtime/scripts/port-monitor.js && node --check runtime/scripts/chat-server.js && node --check runtime/scripts/chat-server/index.js && node --check runtime/scripts/chat-server/config.js && node --check runtime/scripts/chat-core/tooling/native-binaries.js && node --check runtime/scripts/chat-core/tooling/package-import.js && node --check runtime/scripts/amalgm-mcp/index.js && node --check runtime/scripts/amalgm-mcp/config.js"
+    "check": "node --check bin/amalgm.js && node --check lib/auth-store.js && node --check lib/cli.js && node --check lib/paths.js && node --check lib/process-cleanup.js && node --check lib/runtime-identity.js && node --check lib/runtime-manifest.js && node --check lib/service.js && node --check lib/state-migration.js && node --check lib/supervisor.js && node --check lib/tunnel-chat.js && node --check lib/tunnel-events.js && node --check runtime/lib/runtime-manifest.js && node --check runtime/scripts/runtime-auth.js && node --check runtime/scripts/proxy-token-store.js && node --check runtime/scripts/local-gateway.js && node --check runtime/scripts/port-monitor.js && node --check runtime/scripts/chat-server.js && node --check runtime/scripts/chat-server/index.js && node --check runtime/scripts/chat-server/config.js && node --check runtime/scripts/chat-core/tooling/native-binaries.js && node --check runtime/scripts/chat-core/tooling/package-import.js && node --check runtime/scripts/amalgm-mcp/index.js && node --check runtime/scripts/amalgm-mcp/config.js && node --check runtime/scripts/lib/project-paths.js && node --check runtime/scripts/lib/runtime-paths.js"
   },
   "engines": {
     "node": ">=20"

package/runtime/scripts/amalgm-mcp/apps/store.js

@@ -17,6 +17,7 @@ const {
 } = require('../config');
 const { ensureDir, readJson, writeJsonAtomic } = require('../lib/storage');
 const { appendStateEvent } = require('../state/events');
+const { canonicalProjectPath } = require('../../lib/project-paths');
 
 function ensureAppsDirs() {
   ensureDir(APPS_DIR);
@@ -55,6 +56,7 @@ function normalizeApp(app) {
   return {
     ...app,
     kind: 'app',
+    ...(app.cwd ? { cwd: canonicalProjectPath(app.cwd) } : {}),
     appRef,
     app_ref: appRef,
     appUrl: publicUrl,

package/runtime/scripts/amalgm-mcp/automations/store.js

@@ -8,6 +8,7 @@ const { appendStateEvent, insertStateEvent, publishStateEvent } = require('../st
 const { normalizeTaskSchedule } = require('../tasks/schedule-normalization');
 const { compileWorkflowText, splitEventRef } = require('../workflows/compiler');
 const { getWebhookUrl } = require('../events/webhook-url');
+const { canonicalProjectPath } = require('../../lib/project-paths');
 const { validateCellReferences } = require('./cell-references');
 const { validateWorkflowToolActions } = require('./tool-actions');
 
@@ -127,7 +128,7 @@ function normalizeWorkflowRecord(input = {}, existing = null) {
     name: cleanString(input.name) || existing?.name || 'Untitled workflow',
     description: input.description ?? existing?.description ?? '',
     enabled: input.enabled ?? existing?.enabled ?? true,
-    projectPath: input.projectPath ?? existing?.projectPath ?? null,
+    projectPath: canonicalProjectPath(input.projectPath ?? existing?.projectPath ?? null) || null,
     workflowText,
     workflowIr,
     compilerErrors,
@@ -166,7 +167,7 @@ function rowToWorkflow(row) {
     name: row.name,
     description: row.description || '',
     enabled: row.enabled === 1,
-    projectPath: row.project_path || null,
+    projectPath: canonicalProjectPath(row.project_path) || null,
     workflowText: row.workflow_text || parsed.workflowText,
     workflowIr: parseJson(row.workflow_ir_json, parsed.workflowIr || null),
     compilerErrors: parseJson(row.compiler_errors_json, parsed.compilerErrors || null),
@@ -276,7 +277,7 @@ function normalizeTriggerRecord(input = {}, automation, existing = null) {
     name: cleanString(input.name) || existing?.name || automation.name || 'Automation trigger',
     description: input.description ?? existing?.description ?? '',
     enabled: input.enabled ?? existing?.enabled ?? automation.enabled !== false,
-    projectPath: input.projectPath ?? existing?.projectPath ?? automation.projectPath ?? null,
+    projectPath: canonicalProjectPath(input.projectPath ?? existing?.projectPath ?? automation.projectPath ?? null) || null,
     createdAt: isoOrNull(input.createdAt) || existing?.createdAt || timestamp,
     updatedAt: existing ? timestamp : (isoOrNull(input.updatedAt) || null),
     lastFiredAt: isoOrNull(input.lastFiredAt) || existing?.lastFiredAt || null,
@@ -429,7 +430,7 @@ function rowToAutomationBase(row) {
     name: row.name,
     description: row.description || '',
     enabled: row.enabled === 1,
-    projectPath: row.project_path || null,
+    projectPath: canonicalProjectPath(row.project_path) || null,
     workflowId: row.workflow_id,
     createdAt: row.created_at,
     updatedAt: row.updated_at,
@@ -856,7 +857,7 @@ function rowToAutomationRun(row) {
     status: row.status,
     startedAt: row.started_at || parsed.startedAt || null,
     finishedAt: row.finished_at || parsed.finishedAt || null,
-    projectPath: row.project_path || parsed.projectPath || null,
+    projectPath: canonicalProjectPath(row.project_path || parsed.projectPath) || null,
     error: row.error || parsed.error || null,
     createdAt: row.created_at,
     updatedAt: row.updated_at,

package/runtime/scripts/amalgm-mcp/config.js

@@ -6,6 +6,7 @@
  * Same pattern as scripts/credential-adapter.js.
  */
 
+const fs = require('fs');
 const path = require('path');
 const os = require('os');
 
@@ -13,6 +14,7 @@ const PORT = parseInt(process.env.AMALGM_MCP_PORT || '8083', 10);
 const MCP_PROTOCOL_VERSION = '2024-11-05';
 
 const AMALGM_DIR = process.env.AMALGM_DIR || path.join(os.homedir(), '.amalgm');
+const AMALGM_HOME = process.env.AMALGM_HOME || path.join(os.homedir(), '.amalgm');
 
 // Storage file/dir layout under AMALGM_DIR.
 const STORAGE_DIR = AMALGM_DIR; // tasks.json etc. live directly under ~/.amalgm
@@ -90,10 +92,41 @@ const APP_ROUTE_SYNC_INTERVAL_MS = parseInt(
   10,
 );
 
+function copyIfUseful(source, target) {
+  if (!fs.existsSync(source)) return;
+  if (fs.existsSync(target) && fs.statSync(target).size > 64 * 1024) return;
+  fs.mkdirSync(path.dirname(target), { recursive: true, mode: 0o700 });
+  fs.copyFileSync(source, target);
+}
+
+function migrateLegacyUserState() {
+  if (path.resolve(AMALGM_DIR) === path.resolve(AMALGM_HOME)) return;
+  if (path.resolve(AMALGM_DIR).startsWith(path.resolve(os.tmpdir()))) return;
+  const marker = path.join(AMALGM_DIR, '.runtime-legacy-state-migrated.json');
+  if (fs.existsSync(marker)) return;
+  fs.mkdirSync(AMALGM_DIR, { recursive: true, mode: 0o700 });
+  for (const fileName of [
+    'amalgm.db',
+    'apps.json',
+    'artifacts.json',
+    'agents.json',
+    'tasks.json',
+    'event-triggers.json',
+    'workflows.json',
+    'mcp-connections.json',
+  ]) {
+    copyIfUseful(path.join(AMALGM_HOME, fileName), path.join(AMALGM_DIR, fileName));
+  }
+  fs.writeFileSync(marker, `${JSON.stringify({ migrated_at: new Date().toISOString(), source: AMALGM_HOME }, null, 2)}\n`);
+}
+
+migrateLegacyUserState();
+
 module.exports = {
   PORT,
   MCP_PROTOCOL_VERSION,
   AMALGM_DIR,
+  AMALGM_HOME,
   STORAGE_DIR,
   LOCAL_DB_FILE,
   TASKS_FILE,

package/runtime/scripts/amalgm-mcp/lib/prefs.js

@@ -7,6 +7,7 @@
 
 const { openLocalDb } = require('../state/db');
 const { insertStateEvent, publishStateEvent } = require('../state/events');
+const { canonicalProjectPath } = require('../../lib/project-paths');
 
 const DEFAULT_SELECTED_MODELS = {
   claude_code: 'anthropic/claude-opus-4.7',
@@ -382,7 +383,7 @@ function normalizePreferences(input) {
     last_used: {
       harness: lastUsedHarness,
       model: lastUsedModel,
-      cwd: cleanString(rawLastUsed.cwd ?? raw.last_cwd ?? raw.selected_cwd),
+      cwd: canonicalProjectPath(cleanString(rawLastUsed.cwd ?? raw.last_cwd ?? raw.selected_cwd)),
     },
     usage,
     recent_prefs: recentPrefs,

package/runtime/scripts/amalgm-mcp/workspace/store.js

@@ -6,6 +6,10 @@ const path = require('path');
 const { AMALGM_COMPUTER_ID } = require('../config');
 const { openLocalDb } = require('../state/db');
 const { insertStateEvent, publishStateEvent } = require('../state/events');
+const {
+  canonicalProjectPath,
+  isLegacyManagedWorkspacePath,
+} = require('../../lib/project-paths');
 
 function cleanString(value) {
   return typeof value === 'string' && value.trim() ? value.trim() : '';
@@ -65,17 +69,18 @@ function normalizeWorkspaceRecord(input, options = {}) {
     throw new Error('Workspace path must be an absolute local path');
   }
 
-  const resolvedPath = path.resolve(localPath);
+  const legacyManagedPath = isLegacyManagedWorkspacePath(localPath);
+  const resolvedPath = canonicalProjectPath(localPath);
   const computerId = stableComputerId(input.computerId || input.computer_id || options.computerId);
   const uri = cleanString(input.uri) || workspaceUriForPath(resolvedPath, computerId);
   const id = cleanString(input.id) || workspaceIdForUri(uri);
   const createdAt = cleanString(input.createdAt || input.created_at) || nowIso();
   const updatedAt = nowIso();
   const managed = input.managed !== undefined
-    ? Boolean(input.managed)
+    ? Boolean(input.managed) && !legacyManagedPath
     : isManagedWorkspacePath(resolvedPath, options.workspaceRoot);
   const status = cleanString(input.status) || (fs.existsSync(resolvedPath) ? 'ready' : 'missing');
-  const source = cleanString(input.source) || (managed ? 'managed' : 'computer');
+  const source = legacyManagedPath ? 'computer' : (cleanString(input.source) || (managed ? 'managed' : 'computer'));
   const name = cleanString(input.name) || basename(resolvedPath);
 
   return {
@@ -102,18 +107,20 @@ function normalizeWorkspaceRecord(input, options = {}) {
 function rowToWorkspace(row) {
   if (!row) return null;
   const parsed = parseJson(row.workspace_json, {});
+  const resolvedPath = row.path ? canonicalProjectPath(row.path) : row.path;
+  const legacyManagedPath = row.path ? isLegacyManagedWorkspacePath(row.path) : false;
   return {
     ...parsed,
     id: row.id,
     name: row.name,
     uri: row.uri,
-    path: row.path,
-    localPath: row.path,
+    path: resolvedPath,
+    localPath: resolvedPath,
     locationType: row.location_type,
     computerId: row.computer_id || parsed.computerId || null,
-    source: row.source,
-    managed: row.managed === 1,
-    status: row.status,
+    source: legacyManagedPath ? 'computer' : row.source,
+    managed: legacyManagedPath ? false : row.managed === 1,
+    status: resolvedPath && fs.existsSync(resolvedPath) ? 'ready' : row.status,
     createdAt: row.created_at,
     updatedAt: row.updated_at,
   };

package/runtime/scripts/chat-core/contract.js

@@ -4,6 +4,7 @@ const fs = require('fs');
 const os = require('os');
 const path = require('path');
 const { AMALGM_DIR, DEFAULT_CWD, PROXY_BASE_URL, PROXY_TOKEN } = require('../chat-server/config');
+const { canonicalProjectPath } = require('../lib/project-paths');
 const { authEnvelope, coerceAuth, fingerprint } = require('./auth');
 const { runtimePort } = require('../../lib/runtime-manifest');
 
@@ -241,15 +242,23 @@ function existingDirectory(candidate) {
   }
 }
 
+function safeProcessCwd() {
+  try {
+    return process.cwd();
+  } catch {
+    return null;
+  }
+}
+
 function resolveCwd(rawCwd, options = {}) {
-  const fallback = existingDirectory(expandHome(options.cwd))
-    || existingDirectory(expandHome(DEFAULT_CWD))
-    || existingDirectory(process.cwd())
+  const fallback = existingDirectory(canonicalProjectPath(expandHome(options.cwd)))
+    || existingDirectory(canonicalProjectPath(expandHome(DEFAULT_CWD)))
+    || existingDirectory(safeProcessCwd())
     || os.homedir();
   const expanded = expandHome(rawCwd);
   if (!expanded) return fallback;
   const absolute = path.isAbsolute(expanded) ? expanded : path.resolve(fallback, expanded);
-  return existingDirectory(absolute) || fallback;
+  return existingDirectory(canonicalProjectPath(absolute)) || fallback;
 }
 
 function nullableString(value) {

package/runtime/scripts/lib/project-paths.js

@@ -0,0 +1,72 @@
+'use strict';
+
+const fs = require('fs');
+const os = require('os');
+const path = require('path');
+
+function cleanString(value) {
+  return typeof value === 'string' && value.trim() ? value.trim() : '';
+}
+
+function expandHome(value) {
+  const input = cleanString(value);
+  if (!input) return '';
+  if (input === '~') return os.homedir();
+  if (input.startsWith('~/')) return path.join(os.homedir(), input.slice(2));
+  return input;
+}
+
+function isWithin(root, target) {
+  const relative = path.relative(root, target);
+  return relative === '' || (!!relative && !relative.startsWith('..') && !path.isAbsolute(relative));
+}
+
+function legacyWorkspaceRoots() {
+  const home = process.env.AMALGM_HOME || path.join(os.homedir(), '.amalgm');
+  return [
+    process.env.AMALGM_LEGACY_WORKSPACES_DIR,
+    path.join(home, 'workspaces'),
+    path.join(home, 'projects'),
+  ]
+    .filter(Boolean)
+    .map((entry) => path.resolve(expandHome(entry)));
+}
+
+function legacyManagedRelativePath(localPath) {
+  const resolved = path.resolve(expandHome(localPath));
+  const currentRoot = cleanString(process.env.AMALGM_WORKSPACES_DIR || process.env.AMALGM_PROJECTS_DIR);
+
+  for (const root of legacyWorkspaceRoots()) {
+    if (currentRoot && path.resolve(root) === path.resolve(expandHome(currentRoot))) continue;
+    if (!isWithin(root, resolved)) continue;
+    const relative = path.relative(root, resolved);
+    return relative && !relative.startsWith('..') ? relative : '';
+  }
+
+  return '';
+}
+
+function canonicalProjectPath(value) {
+  const expanded = expandHome(value);
+  if (!expanded) return '';
+  const absolute = path.isAbsolute(expanded) ? path.resolve(expanded) : path.resolve(expanded);
+  const legacyRelative = legacyManagedRelativePath(absolute);
+
+  if (legacyRelative) {
+    const homeCandidate = path.join(os.homedir(), legacyRelative);
+    if (fs.existsSync(homeCandidate)) return path.resolve(homeCandidate);
+  }
+
+  return absolute;
+}
+
+function isLegacyManagedWorkspacePath(value) {
+  return Boolean(cleanString(value) && legacyManagedRelativePath(value));
+}
+
+module.exports = {
+  canonicalProjectPath,
+  cleanString,
+  expandHome,
+  isLegacyManagedWorkspacePath,
+};

package/runtime/scripts/lib/runtime-paths.js

@@ -0,0 +1,47 @@
+'use strict';
+
+const os = require('os');
+const path = require('path');
+
+function normalizeRuntimeLabel(value) {
+  const raw = String(value || '').trim().toLowerCase();
+  if (['preview', 'canary', 'native-chat', 'staging'].includes(raw)) return 'preview';
+  if (['local', 'dev', 'development'].includes(raw)) return 'local';
+  return 'main';
+}
+
+function amalgmDir() {
+  return process.env.AMALGM_DIR || path.join(os.homedir(), '.amalgm');
+}
+
+function runtimeLabel() {
+  return normalizeRuntimeLabel(process.env.AMALGM_RUNTIME_LABEL || process.env.AMALGM_BRANCH);
+}
+
+function runtimeStateDir() {
+  return (
+    process.env.AMALGM_RUNTIME_STATE_DIR
+    || path.join(amalgmDir(), 'runtimes', runtimeLabel())
+  );
+}
+
+function runtimeStateFile() {
+  return process.env.AMALGM_RUNTIME_STATE_FILE || path.join(runtimeStateDir(), 'runtime-state.json');
+}
+
+function runtimeTokenFile() {
+  return process.env.AMALGM_RUNTIME_TOKEN_FILE || path.join(runtimeStateDir(), 'runtime-token.json');
+}
+
+function runtimeLogDir() {
+  return process.env.AMALGM_LOG_DIR || path.join(runtimeStateDir(), 'logs');
+}
+
+module.exports = {
+  amalgmDir,
+  runtimeLabel,
+  runtimeLogDir,
+  runtimeStateDir,
+  runtimeStateFile,
+  runtimeTokenFile,
+};

package/runtime/scripts/local-gateway.js

@@ -5,7 +5,7 @@
  *
  * One discoverable loopback entrypoint for the local Amalgm runtime. The
  * individual services still run as separate processes, but clients only need
- * to find this gateway port from ~/.amalgm/runtime-state.json.
+ * to find this gateway port from the label-scoped runtime-state.json.
  */
 
 const crypto = require('crypto');
@@ -23,6 +23,10 @@ const {
   runtimeAuthHeaders,
 } = require('./runtime-auth');
 const { runtimePort } = require('../lib/runtime-manifest');
+const {
+  runtimeLogDir,
+  runtimeStateFile,
+} = require('./lib/runtime-paths');
 
 function loadPty() {
   const candidates = [
@@ -45,10 +49,10 @@ function loadPty() {
 const pty = loadPty();
 
 const AMALGM_DIR = process.env.AMALGM_DIR || path.join(os.homedir(), '.amalgm');
-const STATE_FILE = path.join(AMALGM_DIR, 'runtime-state.json');
+const STATE_FILE = runtimeStateFile();
 const APPS_FILE = path.join(AMALGM_DIR, 'apps.json');
 const LEGACY_ARTIFACTS_FILE = path.join(AMALGM_DIR, 'artifacts.json');
-const LOG_DIR = path.join(AMALGM_DIR, 'logs');
+const LOG_DIR = runtimeLogDir();
 const BIND_HOST = process.env.AMALGM_BIND_HOST || '127.0.0.1';
 const OWNER = process.env.AMALGM_RUNTIME_SOURCE || 'local';
 const RUNTIME_LABEL = process.env.AMALGM_RUNTIME_LABEL || 'main';