@bastani/atomic 0.9.25-alpha.2 → 0.9.25-alpha.4

package/dist/builtin/mcp/native-client-licenses/LICENSES/modelcontextprotocol-typescript-sdk.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Anthropic, PBC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/builtin/mcp/native-client-licenses/NOTICE

@@ -0,0 +1,30 @@
+This directory vendors packages/mcp/src from earendil-works/pi at commit
+8ce69e9d2b171d173fe4b6b2b6256f1f4411e69d:
+https://github.com/earendil-works/pi/tree/8ce69e9d2b171d173fe4b6b2b6256f1f4411e69d/packages/mcp
+
+Relative TypeScript imports use .js extensions for Atomic's compiled package.
+Atomic patches OAuth discovery to refresh changed authorization-server metadata.
+Upstream's license is reproduced below. The additional MCP TypeScript SDK
+notice is retained in LICENSES/modelcontextprotocol-typescript-sdk.txt.
+
+MIT License
+
+Copyright (c) 2025 Mario Zechner
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/builtin/mcp/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@bastani/mcp",
-  "version": "0.9.25-alpha.2",
+  "version": "0.9.25-alpha.4",
   "private": true,
-  "description": "Atomic extension that adapts MCP (Model Context Protocol) servers into the coding agent. Fork of: https://github.com/nicobailon/pi-mcp-adapter",
+  "description": "Atomic's pi-compatible MCP integration for server connections, OAuth, tools, resources, and terminal management.",
   "contributors": [
     "Norin Lavaee",
     "Alex Lavaee"
@@ -18,8 +18,7 @@
     ".": "./index.ts"
   },
   "files": [
-    "*.ts",
-    "app-bridge.bundle.js",
+    "index.ts",
     "README.md",
     "OAUTH.md",
     "CHANGELOG.md",
@@ -31,31 +30,11 @@
     ]
   },
   "peerDependencies": {
-    "@bastani/atomic": "*",
-    "@bastani/pi-ai": "*",
-    "@earendil-works/pi-tui": "^0.99.1",
-    "zod": "^3.25.0 || ^4.0.0",
-    "typebox": "*"
+    "@bastani/atomic": "*"
   },
   "peerDependenciesMeta": {
     "@bastani/atomic": {
       "optional": true
-    },
-    "@bastani/pi-ai": {
-      "optional": true
-    },
-    "@earendil-works/pi-tui": {
-      "optional": true
     }
-  },
-  "dependencies": {
-    "@modelcontextprotocol/ext-apps": "^1.7.5",
-    "@modelcontextprotocol/sdk": "^1.30.0",
-    "open": "^11.0.1",
-    "proper-lockfile": "4.1.2",
-    "zod": "^3.25.0 || ^4.0.0"
-  },
-  "devDependencies": {
-    "@types/proper-lockfile": "4.1.4"
   }
 }

package/dist/builtin/subagents/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/subagents",
-  "version": "0.9.25-alpha.2",
+  "version": "0.9.25-alpha.4",
   "private": true,
   "description": "Atomic extension for delegating tasks to subagents with parallel execution. Fork of: https://github.com/nicobailon/pi-subagents",
   "contributors": [
@@ -35,8 +35,8 @@
   "peerDependencies": {
     "@bastani/atomic": "*",
     "@bastani/pi-ai": "*",
-    "@earendil-works/pi-agent-core": "^0.99.1",
-    "@earendil-works/pi-tui": "^0.99.1",
+    "@earendil-works/pi-agent-core": "^0.99.2",
+    "@earendil-works/pi-tui": "^0.99.2",
     "typebox": "*"
   },
   "peerDependenciesMeta": {

package/dist/builtin/web-access/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/web-access",
-  "version": "0.9.25-alpha.2",
+  "version": "0.9.25-alpha.4",
   "private": true,
   "description": "Atomic extension for web search, URL fetching, GitHub repo cloning, PDF/video extraction. Fork of: https://github.com/nicobailon/pi-web-access",
   "contributors": [
@@ -31,7 +31,7 @@
   },
   "peerDependencies": {
     "@bastani/atomic": "*",
-    "@earendil-works/pi-tui": "^0.99.1"
+    "@earendil-works/pi-tui": "^0.99.2"
   },
   "peerDependenciesMeta": {
     "@bastani/atomic": {

package/dist/builtin/workflows/CHANGELOG.md

@@ -6,6 +6,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ## [Unreleased]
 
+## [0.9.25-alpha.3] - 2026-09-30
+
+### Added
+
+- `pause`, `quit` and `resume` results from the `workflow` tool now carry a machine-readable `code` (`run_not_found`, `not_resumable`, `owned_elsewhere`, `database_unavailable`, `stage_not_found`, `stage_ambiguous`, `stage_resume_unsupported` or `control_failed`) when the request could not be carried out, so SDK hosts using `session.workflows` receive typed errors. Resuming a run that is executing in another live Atomic process now reports `owned_elsewhere` instead of `not_resumable`. Pausing or quitting, by full run id, a run owned by another session or executing in another live Atomic process now reports `owned_elsewhere` instead of `Run not found`. Pausing or resuming a stage that does not exist or matches several stages, and resuming a single stage of a durable run, now report `stage_not_found`, `stage_ambiguous` or `stage_resume_unsupported` instead of an uncoded no-op ([#3377](https://github.com/bastani-inc/atomic/issues/3377)).
+
+### Fixed
+
+- `pause` and `quit` with `all: true` no longer report success when some runs could not be stopped. The result is `partial` only when that call stopped at least one run and others are still active, and a `noop` with `control_failed` when active runs could not be stopped and the call stopped none, even if other runs were already paused. Either result lists each failed run id and reason in the message and in a `failedRuns` list. Runs that are already paused or already ended are not failures, and a batch with nothing left to stop is a benign `noop`. `/workflow pause --all` now names runs that failed to pause instead of reporting them as paused or as "No in-flight runs to pause", and reports an error when it stopped no run. Any failure while inspecting the database to pause or quit an unknown full run id now returns a structured `database_unavailable` result instead of throwing or a generic `control_failed` ([#3377](https://github.com/bastani-inc/atomic/issues/3377)).
+- On a heavily loaded machine, a workflow run could fail with a bare `Query read timeout` while Atomic verified its managed PostgreSQL connection, even though the database was healthy. Health queries now get more time (3 s) on every path, and both the check of a borrowed connection and Atomic's periodic background health check repeat once after a timeout. If the timeout persists, the run fails with a resumable database-unavailable error instead of `Query read timeout`, and other running workflows' database connections are not closed and PostgreSQL is not restarted. A refused or terminated connection, a server shutdown, or a changed database identity is still treated as an outage.
+- Fixed a workflow run resumed right after it was paused failing with `Workflow database admission timed out`. A pause or resume now waits for the control write already in flight instead of cancelling it mid-write, which could leave the run's database claim stuck and stall every later pause, resume, or quit on that run until the admission timeout ([#3377](https://github.com/bastani-inc/atomic/issues/3377)).
+
 ## [0.9.25-alpha.1] - 2026-09-29
 
 ### Added

package/dist/builtin/workflows/builtin/{chunk-e1254zvd.js → chunk-kfsnh3w7.js}

@@ -6308,6 +6308,9 @@ function isMonitoringConnectionFailure(error) {
     return ["ECONNREFUSED", "ECONNRESET", "EPIPE", "ETIMEDOUT", "57P01", "57P02", "57P03"].includes(String(error.code));
   return error.message === "timeout expired" || error.message === "Connection terminated due to connection timeout";
 }
+function isQueryReadTimeout(error) {
+  return error instanceof Error && error.message === "Query read timeout";
+}
 
 class PostgresHealth {
   operations;
@@ -6340,11 +6343,20 @@ class PostgresHealth {
     try {
       if (this.stopped)
         throw new DbosDependencyError;
-      await this.operations.validate?.(client);
+      try {
+        await this.operations.validate?.(client);
+      } catch (error) {
+        if (!isQueryReadTimeout(error) || this.stopped)
+          throw error;
+        await this.operations.validate?.(client);
+      }
     } catch (error) {
       this.failure = error instanceof Error ? error : new Error(String(error));
-      this.invalidate();
-      throw error;
+      if (!isQueryReadTimeout(error)) {
+        this.invalidate();
+        throw error;
+      }
+      throw new DbosDependencyError("Managed PostgreSQL did not answer a connection identity check in time.");
     }
   }
   check() {
@@ -6378,7 +6390,7 @@ class PostgresHealth {
     try {
       identity = await this.operations.probe();
     } catch (error) {
-      if (!isMonitoringConnectionFailure(error) || this.stopped)
+      if (!(isMonitoringConnectionFailure(error) || isQueryReadTimeout(error)) || this.stopped)
         throw error;
       try {
         identity = await this.operations.probe();
@@ -6408,6 +6420,10 @@ class PostgresHealth {
       if (ready !== undefined)
         return ready;
     } catch (error) {
+      if (isQueryReadTimeout(error)) {
+        this.failure = new DbosDependencyError("Managed PostgreSQL did not answer a health check in time.");
+        throw this.failure;
+      }
       this.failure = error instanceof Error ? error : new Error(String(error));
       if (!(error instanceof Error && ("code" in error) && error.code === "53300"))
         this.invalidate();
@@ -6670,6 +6686,7 @@ var POSTGRES_IDENTITY_SQL = `SELECT current_setting('data_directory') AS data_di
 	split_part(pg_read_file('postmaster.pid'), E'\\n', 3) AS started,
 	system_identifier::text, current_setting('server_version') AS server_version FROM pg_control_system()`;
 var POSTGRES_TIMEZONE_SQL = "SELECT set_config('timezone_abbreviations', 'Default', true)";
+var POSTGRES_HEALTH_QUERY_TIMEOUT_MS = 3000;
 async function probePostgresTimezoneData(port) {
   const client = new Client({
     host: "127.0.0.1",
@@ -6679,8 +6696,8 @@ async function probePostgresTimezoneData(port) {
     database: "postgres",
     ssl: false,
     connectionTimeoutMillis: 1000,
-    query_timeout: 1000,
-    statement_timeout: 1000
+    query_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS,
+    statement_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS
   });
   client.on("error", () => {});
   try {
@@ -6699,8 +6716,8 @@ async function probePostgresIdentity(port) {
     database: "postgres",
     ssl: false,
     connectionTimeoutMillis: 1000,
-    query_timeout: 1000,
-    statement_timeout: 1000
+    query_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS,
+    statement_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS
   });
   client.on("error", () => {});
   try {
@@ -6708,6 +6725,8 @@ async function probePostgresIdentity(port) {
     const result = await client.query(POSTGRES_IDENTITY_SQL);
     return result.rows[0];
   } catch (error) {
+    if (isQueryReadTimeout(error))
+      throw error;
     const code = error instanceof Error && "code" in error ? error.code : undefined;
     if (code === "ECONNREFUSED" || code === "ECONNRESET" || code === "EPIPE" || code === "57P01" || code === "57P02" || code === "57P03" || error instanceof Error && /timeout|timed out|connection terminated/i.test(error.message))
       return;
@@ -6875,6 +6894,15 @@ async function ensureCluster(options = {}) {
       }
       let verified;
       const existingServerProbe = () => options.probeIdentity ?? probePostgresIdentity;
+      const startupServerProbe = async (probePort) => {
+        try {
+          return await existingServerProbe()(probePort);
+        } catch (error) {
+          if (isQueryReadTimeout(error))
+            return;
+          throw error;
+        }
+      };
       let prepared = options.prepared ? options.binaries : undefined;
       let selectedIdentity = options.runtimeIdentity;
       let reservedLiveGeneration;
@@ -6995,7 +7023,7 @@ async function ensureCluster(options = {}) {
         }
       } else if (existing) {
         await waitForClusterReadiness(logFile, undefined, async () => {
-          verified = await verifyPostgresIdentity(metadata, port, existing.pid, existingServerProbe());
+          verified = await verifyPostgresIdentity(metadata, port, existing.pid, startupServerProbe);
           return verified !== undefined || managedPostmaster(metadata) === undefined;
         }, READY_ATTEMPTS, delay, port, dataDir);
       }
@@ -7027,7 +7055,7 @@ async function ensureCluster(options = {}) {
             startedCluster = { lease };
             activeCluster = startedCluster;
             await waitForClusterReadiness(logFile, startedCluster, async () => {
-              verified = await verifyPostgresIdentity(metadata, port, lease.pid, options.probeIdentity);
+              verified = await verifyPostgresIdentity(metadata, port, lease.pid, startupServerProbe);
               return verified !== undefined;
             }, READY_ATTEMPTS, delay, port, dataDir);
             break;
@@ -7096,14 +7124,14 @@ async function ensureCluster(options = {}) {
           probe: () => inspect(),
           validate: async (client) => {
             const identity = await inspect(async () => {
-              const query = { text: POSTGRES_IDENTITY_SQL, query_timeout: 1000 };
+              const query = { text: POSTGRES_IDENTITY_SQL, query_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS };
               const result = await client.query(query);
               return result.rows[0];
             });
             if (!identity)
               throw new DbosDependencyError;
             if (options.probeIdentity === undefined) {
-              const query = { text: POSTGRES_TIMEZONE_SQL, query_timeout: 1000 };
+              const query = { text: POSTGRES_TIMEZONE_SQL, query_timeout: POSTGRES_HEALTH_QUERY_TIMEOUT_MS };
               await client.query(query);
             }
           },

package/dist/builtin/workflows/builtin/{chunk-cpw5gtzg.js → chunk-rqmasd3d.js}

@@ -39,7 +39,7 @@ import {
   reviewerFailureText,
   summarizeReviewConvergence,
   reverify_consolidated_batch
-} from "./chunk-e1254zvd.js";
+} from "./chunk-kfsnh3w7.js";
 import {
   fold_usage
 } from "./chunk-tgt0s5e5.js";

package/dist/builtin/workflows/builtin/{chunk-qy6g0baf.js → chunk-wz783pvd.js}

@@ -38,7 +38,7 @@ import {
   reviewerFailureText,
   summarizeReviewConvergence,
   reverify_consolidated_batch
-} from "./chunk-e1254zvd.js";
+} from "./chunk-kfsnh3w7.js";
 import {
   VERIFICATION_SCALE
 } from "./chunk-n1910xc4.js";

package/dist/builtin/workflows/builtin/goal.js

@@ -1,7 +1,7 @@
 import {
   goal_default
-} from "./chunk-qy6g0baf.js";
-import"./chunk-e1254zvd.js";
+} from "./chunk-wz783pvd.js";
+import"./chunk-kfsnh3w7.js";
 import"./chunk-2377r57g.js";
 import"./chunk-z0d03ktm.js";
 import"./chunk-n1910xc4.js";

package/dist/builtin/workflows/builtin/index.js

@@ -14,11 +14,11 @@ import {
 import {
   generate_and_filter_default
 } from "./chunk-kb7s3gx2.js";
-import"./chunk-e1254zvd.js";
+import"./chunk-kfsnh3w7.js";
 import"./chunk-z0d03ktm.js";
 import {
   goal_default
-} from "./chunk-qy6g0baf.js";
+} from "./chunk-wz783pvd.js";
 import {
   open_claude_design_default
 } from "./chunk-nkj4qhj6.js";
@@ -27,7 +27,7 @@ import {
 } from "./chunk-94f8zfz1.js";
 import {
   ralph_default
-} from "./chunk-cpw5gtzg.js";
+} from "./chunk-rqmasd3d.js";
 import {
   tournament_default
 } from "./chunk-wf876n16.js";

package/dist/builtin/workflows/builtin/ralph.js

@@ -1,7 +1,7 @@
 import {
   ralph_default
-} from "./chunk-cpw5gtzg.js";
-import"./chunk-e1254zvd.js";
+} from "./chunk-rqmasd3d.js";
+import"./chunk-kfsnh3w7.js";
 import"./chunk-2377r57g.js";
 import"./chunk-z0d03ktm.js";
 import"./chunk-n1910xc4.js";

package/dist/builtin/workflows/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/workflows",
-  "version": "0.9.25-alpha.2",
+  "version": "0.9.25-alpha.4",
   "private": true,
   "description": "Atomic extension for multi-stage workflow authoring and execution.",
   "contributors": [
@@ -85,7 +85,7 @@
   },
   "peerDependencies": {
     "@bastani/atomic": "*",
-    "@earendil-works/pi-tui": "^0.99.1",
+    "@earendil-works/pi-tui": "^0.99.2",
     "typebox": "*"
   },
   "peerDependenciesMeta": {