@bastani/atomic 0.9.28-alpha.1 → 0.9.28-alpha.3

package/CHANGELOG.md

@@ -2,6 +2,66 @@
 
 ## [Unreleased]
 
+## [0.9.28-alpha.3] - 2026-10-07
+
+### Added
+
+- Added OpenAI's GPT-6 Luna classifier through the Decisions API with `OPENAI_API_KEY`, and image input for codemode's `models.classify()` context. See [Classifier models](docs/models.md#use-classifier-models).
+- Added native classification for llama.cpp decision models through `/v1/systemone`. Decision-only models stay out of the chat selector, while chat models keep the next-token classifier fallback. Cached native classifiers remain available after restart.
+- Added exact-name `+name` and `-name` modifiers to CLI `--tools` and SDK `tools`, for example `atomic --tools +codemode,-write`. They change the resolved defaults instead of replacing them and persist across `/reload`.
+
+### Changed
+
+- Changed `atomic mcp login --timeout` to limit the whole sign-in, including requests to the authorization server, instead of only the wait for the browser.
+
+### Fixed
+
+- Fixed a false `Timeout waiting for response to resume_queued_messages` error when you send a message while a paused queue is still waiting for the agent's current turn to finish, and the follow-up `Agent is already processing` error caused by the stale paused state. The resume now waits for the turn instead of giving up after 30 seconds ([#3493](https://github.com/bastani-inc/atomic/issues/3493)).
+- Fixed extension `session_shutdown` handlers being cut off when you quit the interactive CLI. The engine now gets up to 5 seconds to finish extension shutdown, instead of about 750 ms, before it is force-stopped.
+- Fixed slow extension loading and `/reload` on Windows. Imports such as `./helper.js` that point at TypeScript sources no longer make the loader try hundreds of missing files before finding `helper.ts`.
+- Fixed `/mcp` waiting for startup connections before opening. The manager now updates live and stays usable while enabling, disabling, or reconnecting servers.
+- Fixed images being dropped as unresizable under `node --watch` when Node sends its own messages on the image resize worker channel.
+- Fixed codemode's tool description omitting `await` for `searchTools()`, `describeTool()`, and `describeNamespace()`, which could make scripts return unresolved promises instead of tool information.
+- Fixed slash commands and shell-command drafts typed during interactive startup running before Enter, including when launching with `--model` or `--provider`. Enter-terminated input stays ordered and unfinished text remains in the editor.
+- Fixed a stuck MCP server startup blocking re-enabling the server or shutting down after it was disabled.
+- Fixed clipboard paste doing nothing in Termux, and failed copies there omitting the Termux:API install hint.
+- Fixed `!` and RPC `bash` output keeping fragments of color codes, such as a stray `m`, when a code was split across output chunks.
+- Fixed MCP OAuth sign-ins that could not be cancelled while waiting on the authorization server and kept running after the session ended. The sign-in screen now cancels with Esc at every step, session shutdown aborts a running sign-in, and each request to the authorization server times out after 15 seconds.
+- Fixed shutdown waiting up to 15 seconds to refresh an MCP OAuth token that was about to expire, only to close the server's session.
+
+## [0.9.28-alpha.2] - 2026-10-07
+
+### Added
+
+- Added `compactionModel` and a **Compaction model** selector in `/settings` to choose a compactor independently of the chat model ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Added verbatim classifier compaction with registered models such as `typesafe/jev-latest`, retaining protected context and recent messages ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Added Morph verbatim compaction with `morph/morph-compactor`, authenticated through `/login morph` or `MORPH_API_KEY` ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Added `session.workflows.observe(observer)`, so SDK hosts can follow the workflow runs the agent launches without writing an extension. The observer receives a snapshot first, then changes in order. Root activity now includes an optional `graph` that lists each stage and `ctx.tool` node with its status, parents, and pending prompt, plus any run-level prompts ([#3476](https://github.com/bastani-inc/atomic/issues/3476)).
+- Added `RunOpts.onStageSessionEvent` so workflow `run()` callers receive each stage session's events, such as message updates and tool executions, tagged with the run and stage ids. Events continue across fallback-model sessions and include nested workflow stages ([#3474](https://github.com/bastani-inc/atomic/issues/3474)).
+- Added `createTranscript()`, which turns session events into the assistant's output as ordered, JSON-serializable text, thinking, and tool call parts, with each tool call joined to its result ([#3475](https://github.com/bastani-inc/atomic/issues/3475)).
+- Added `createAgentSessionAdapter(baseOptions?)` to `@bastani/atomic/workflows`, which builds the default workflow stage-session adapter with `createAgentSession` options shared by every stage ([#3472](https://github.com/bastani-inc/atomic/issues/3472)).
+- Added `ctx.isPresentationOnly` so extension lifecycle hooks can leave execution to the isolated interactive engine while retaining host-side UI ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Exported `publishExtensionContextEffect(ctx, effect, phase?)` with a synchronous commit phase for generation identity handoff, and `registerExtensionContextRetirementEffect(ctx, dispose)` for observer cleanup before authority revocation ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+
+### Changed
+
+- Compaction planners now receive structured per-message lines instead of a numbered transcript ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Compaction cards show the backend and model used, including `summary (pi fallback)` for policy-refusal summaries ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+
+### Fixed
+
+- Policy refusals from any chat compaction model, including `auto`, explicit chat-model IDs, and borrowed fallback entries, now try pi's summary compaction on the same model before continuing through fallback models. Summary requests retry recoverable errors; policy refusals are never retried. Classifier and Morph failures advance directly to fallback models ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Morph compaction failures now include the HTTP status and a bounded, credential-redacted response excerpt in error diagnostics ([#3470](https://github.com/bastani-inc/atomic/issues/3470)).
+- Fixed Herdr publishing duplicate pane activity when startup workflow recovery refreshes an unchanged activity snapshot ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed Herdr skipping a return to an earlier pane activity after an intervening report timed out or failed ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed project `.atomic/settings.json`, extensions, skills, and other trust-gated resources being ignored without notice in untrusted projects. Interactive sessions now show a warning that points to `/trust`, matching upstream pi.
+- Fixed `@bastani/atomic/workflows` type declarations disagreeing with the runtime: `StageSnapshot` now declares `parentIds`, `executionOrder`, `model`, `startedAt`, `endedAt`, and `durationMs`; `Store` now declares `snapshot()`, `graphSnapshot()`, and `subscribe()`; and an `AgentSessionAdapter.create` can return `createAgentSession(...)` directly without a type cast ([#3473](https://github.com/bastani-inc/atomic/issues/3473)).
+- Fixed `run()` from `@bastani/atomic/workflows` failing at the first `ctx.task` or `ctx.stage` with "prompt adapter not configured" when `opts.adapters` was omitted. Stages now default to in-process `createAgentSession` sessions with in-memory session managers ([#3472](https://github.com/bastani-inc/atomic/issues/3472)).
+- Fixed startup extension confirmations, including workflow recovery prompts, losing keyboard focus during terminal initialization ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed queued protected workflow notices producing `SessionClosed` replies during reload. Successful reload now preserves those notices for the replacement extensions without releasing an explicitly paused queue ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed idle workflow status and control commands not displaying their output in isolated interactive sessions, including after `/reload` ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed extension reload skipping remaining commit effects and predecessor shutdown when a commit effect and an SDK error observer both throw. Reload now retains both failures while keeping the replacement extensions active ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+
 ## [0.9.28-alpha.1] - 2026-10-05
 
 ### Added

package/dist/builtin/intercom/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/intercom",
-  "version": "0.9.28-alpha.1",
+  "version": "0.9.28-alpha.3",
   "private": true,
   "description": "Atomic extension providing a private coordination channel between parent and child agent sessions. Fork of: https://github.com/nicobailon/pi-intercom",
   "contributors": [

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

@@ -6,6 +6,8 @@ Relative TypeScript imports use .js extensions for Atomic's compiled package.
 Atomic patches OAuth discovery to refresh changed authorization-server metadata.
 OAuth client metadata documents and exact callback path checks are ported from
 1499466d8581035a4dec6c869725b8712aea4bbe. Atomic does not use Pi's hosted client identity.
+OAuth request cancellation and session close without a token refresh are ported from
+f10993bc7f28145df1375f3ff39c7f5c4cfc05f0.
 Upstream's license is reproduced below. The additional MCP TypeScript SDK
 notice is retained in LICENSES/modelcontextprotocol-typescript-sdk.txt.
 

package/dist/builtin/mcp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/mcp",
-  "version": "0.9.28-alpha.1",
+  "version": "0.9.28-alpha.3",
   "private": true,
   "description": "Atomic's pi-compatible MCP integration for server connections, OAuth, tools, resources, and terminal management.",
   "contributors": [

package/dist/builtin/subagents/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/subagents",
-  "version": "0.9.28-alpha.1",
+  "version": "0.9.28-alpha.3",
   "private": true,
   "description": "Atomic extension for delegating tasks to subagents with parallel execution. Fork of: https://github.com/nicobailon/pi-subagents",
   "contributors": [

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

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/web-access",
-  "version": "0.9.28-alpha.1",
+  "version": "0.9.28-alpha.3",
   "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": [

package/dist/builtin/workflows/CHANGELOG.md

@@ -6,6 +6,40 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ## [Unreleased]
 
+## [0.9.28-alpha.3] - 2026-10-07
+
+### Changed
+
+- Changed the `resumeInFlight` default from `"ask"` to `"never"`. Atomic no longer prompts at startup to resume interrupted durable workflows; resume them with `/workflow resume`, or set `resumeInFlight` to `"ask"` or `"auto"` in the workflow config to restore startup recovery.
+
+### Fixed
+
+- Fixed Atomic hanging at startup, never accepting input, when the current directory had interrupted durable workflows and `resumeInFlight` was `ask`. Startup no longer waits for workflow recovery; the "Resume interrupted workflows?" prompt now appears after the session is ready.
+- Fixed startup recovery and SDK crash recovery skipping interrupted workflows when the project directory was reached through a symlink, such as `/tmp` or `/var` on macOS.
+
+## [0.9.28-alpha.2] - 2026-10-07
+
+### Added
+
+- Added `createAgentSessionAdapter(baseOptions?)`, which builds the default workflow stage-session adapter with `createAgentSession` options shared by every stage ([#3472](https://github.com/bastani-inc/atomic/issues/3472)).
+
+### Fixed
+
+- Fixed long workflow runs retaining a full metadata snapshot for every checkpoint and message update. Atomic now compacts superseded snapshots, removes their duplicate input payloads, and bounds settled delivery state across root and child runs, including failed-stage sticky receipts, while preserving resume and message deduplication ([#3467](https://github.com/bastani-inc/atomic/issues/3467)).
+- Fixed archived sticky message receipts being ignored when a failed stage retries delivery without an explicit recipient or through live Intercom transport. Retry forwarding and confirmation deduplication survive cold resume, while a new recipient session can still receive the message ([#3467](https://github.com/bastani-inc/atomic/issues/3467)).
+- Fixed sticky messages delivered as pre-start context being forwarded again to the same live session, including after receipt archival and cold resume. Concurrent confirmations remain deduplicated when a stage finishes before they are saved, while a new recipient session can still receive the message ([#3467](https://github.com/bastani-inc/atomic/issues/3467)).
+- Fixed interrupted sticky receipt saves losing delivery counts after retry or cold resume and incorrectly reporting delivered messages as undeliverable ([#3467](https://github.com/bastani-inc/atomic/issues/3467)).
+- Fixed Goal infrastructure failures incorrectly ending the goal as `needs_human`. The ledger now stays `active`, and direct resume in the same session retries the interrupted stage and completes its turn without quitting Atomic. Malformed reviewer output, including exhausted schema corrections, still requires human attention. Older synthetic failure verdicts with identifiable database/checkpoint diagnostics are also recoverable; ambiguous old failures remain unchanged ([#3466](https://github.com/bastani-inc/atomic/issues/3466)).
+- Fixed Goal treating exhausted reviewer corrections for invalid `structured_output` inputs, including whitespace-only instructions and empty named state, as resumable infrastructure failures instead of `needs_human` ([#3466](https://github.com/bastani-inc/atomic/issues/3466)).
+- Fixed Goal reviewer corrections hiding an earlier provider failure when a later `structured_output` call has invalid inputs. If no correction succeeds, the goal remains resumable instead of becoming `needs_human` ([#3466](https://github.com/bastani-inc/atomic/issues/3466)).
+- Fixed `run()` failing at the first `ctx.task` or `ctx.stage` with "prompt adapter not configured" when `opts.adapters` was omitted. Stages now default to in-process `createAgentSession` sessions with in-memory session managers ([#3472](https://github.com/bastani-inc/atomic/issues/3472)).
+- Fixed `resumeInFlight` having no effect at startup. `auto` now resumes eligible interrupted durable workflows, `ask` requests confirmation when a UI is available, and `never` leaves them for `/workflow resume`. Paused, quit, blocked, failed, awaiting-input, and live-owned runs are not automatically restarted ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed startup recovery of agent-owned workflows retaining the previous session's ownership. Safely recovered runs now allow the current session's agent to inspect and control them ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed recovered workflows disconnecting Intercom with pending-stage authorization errors when workflow extension modules load more than once ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed recovered agent stages failing with a stale extension context after accepted startup recovery. Committed host generations hand off synchronously and retired Store observers detach before authority revocation, independently of shutdown handler order ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed startup recovery offering or restarting another project's workflows when projects share a database. Automatic recovery now requires the original invocation directory to match the current working directory; cross-project recovery remains available through `/workflow resume` ([#3468](https://github.com/bastani-inc/atomic/issues/3468)).
+- Fixed durable-workflow shutdown returning before ownership and protected SQL connections terminated, including pending SQL acquisitions, so immediate recovery no longer races a stale executor lock ([#3489](https://github.com/bastani-inc/atomic/issues/3489)).
+
 ## [0.9.28-alpha.1] - 2026-10-05
 
 ### Fixed