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

package/docs/workflows/operations.md

@@ -592,7 +592,9 @@ write committed.
 - Unsupported or inconsistent saved topology is refused rather than repaired by guessing. Preserve the run ID and diagnostic.
 - Running workflows cannot be resumed elsewhere. Explicit resume claims one owner before dispatch.
 
-**Privacy and retention.** DBOS persists workflow inputs, completed tool outputs, UI responses, stage outputs, and chat-session paths. Treat the configured database as sensitive. History does not automatically delete records by age or count; confirmed picker deletion removes inactive DBOS workflow state while preserving independent chat transcripts.
+**Privacy and retention.** DBOS persists workflow inputs, completed tool outputs, UI responses, stage outputs, message delivery receipts, and chat-session paths. Treat the configured database as sensitive. Atomic compacts superseded workflow metadata after saving a recoverable replacement. It keeps up to 50 recent settled messages across the root and all child runs in the root's metadata. Older delivery receipts remain separately so retrying a message ID does not deliver it again. Sticky messages remain available to future matching stages until the root finishes. Atomic archives receipts for completed, skipped, and failed stages before removing them from pending state, along with superseded session receipts. This compaction does not delete checkpoint history or independent chat transcripts. History does not automatically delete workflow records by age or count; confirmed picker deletion removes inactive DBOS workflow state while preserving independent chat transcripts.
+
+Sticky receipts suppress repeat delivery to the same recipient session, whether the message arrived as pre-start context or through live Intercom forwarding. This also holds after a failed stage retries or a cold resume. Repeated confirmations do not increase the delivery count. Delivery without an explicit recipient uses the stage's previous receipts; delivery to a new recipient session remains eligible.
 
 **Resume after editing a workflow.** Changes to definitions, validated inputs, or `ctx.*` call order can invalidate replay. Finish or delete retained runs before incompatible changes. On mismatch, restore the matching definition rather than changing names or arguments to bypass a checkpoint.
 
@@ -741,7 +743,7 @@ That history does not authorize any live release action.
 | **Internally cancelled workflow** | Marked `cancelled` in durable state and excluded from `/workflow resume` discovery. Start a new workflow run if you intentionally want to retry cancelled work. |
 | **Stage failure (recoverable)** | Workflow marked `failed` or `blocked` and remains resumable by default. `/workflow resume <id>` continues from the last completed checkpoint unless durable metadata explicitly sets `resumable: false`. |
 | **Stage failure (non-recoverable)** | Workflow marked `failed` or `blocked` with `resumable: false`, so it cannot resume execution. A failed root with saved checkpoint progress may still appear in read-only history for inspection; a blocked root does not. |
-| **Process crash** | Workflow remains `running` in durable state. Exact-id status/inspection reconstructs its retained checkpoint DAG as `crashed` once the owner heartbeat is stale and shows whether explicit resume is available. `/workflow resume <id>` is still required to claim the root and continue from the last completed checkpoint. |
+| **Process crash** | Workflow remains `running` in durable state. Exact-id status/inspection reconstructs its retained checkpoint DAG as `crashed` once the owner heartbeat is stale and shows whether resume is available. At startup, `resumeInFlight` controls recovery of eligible runs originally invoked in the current working directory. Use `/workflow resume <id>` for runs left untouched. |
 | **`ctx.tool` retry/default failure** | When `retriesAllowed: true`, the tool function is retried with exponential backoff. Cancellation is checked before each attempt, during retry backoff, and through the callback's own `signal`. Without `failureMode: "return"`, an exhausted callback error propagates and the workflow fails. |
 | **Recoverable `ctx.tool` failure** | With `failureMode: "return"`, exhausted callback failures are durably returned after retries. The tool node remains failed, downstream handoff is explicit, and replay returns the same outcome with `cached: true`. Cancellation and storage faults still throw. |
 | **`ctx.tool` node quit/pause** | `quit`/`pause` with a tool node id or name aborts that call's signal, marks the node `cancelled`, and leaves sibling stages and tools running. The action returns `status: "cancelled"` with the separately observed `workflowStatus`; it never reports the run as paused. No replayable `tool:` checkpoint and no `return_failure` outcome are written — return mode writes only inspection metadata — so resume re-runs exactly that call at the same ordinal and node id. |
@@ -852,7 +854,7 @@ Atomic loads workflow files with [jiti](https://github.com/unjs/jiti), so TypeSc
 
 Run `/workflow reload` after adding, editing, renaming, or deleting workflow modules or changing workflow config. Reload rescans project and user conventional directories, legacy `.pi` locations, configured file/directory paths, and package resources without restarting Atomic. The workflow tool's `reload` action uses the same in-process path.
 
-Reload is safe while workflows run: existing runs keep their starting definitions and controls, and new launches use the refreshed registry. A fatal refresh failure retains the previous registry. Top-level `/reload` also replaces extensions but preserves live runs in the same process. After a process exit, use explicit resume to replay checkpoints and retry only unfinished work.
+Reload is safe while workflows run: existing runs keep their starting definitions and controls, and new launches use the refreshed registry. A fatal refresh failure retains the previous registry. Top-level `/reload` also replaces extensions but preserves live runs in the same process. After a process exit, `resumeInFlight` controls startup recovery of eligible interrupted runs; use explicit resume for runs left untouched.
 
 `/new`, `/fork`, and `/resume` are different: they leave the current session, so they quit running workflows. When any are running, Atomic asks first ("Quit N running workflows and start a new session?"). Confirming quits each run immediately at its last checkpoint; declining, or a confirmation prompt that fails, cancels the command and the runs keep going. Without an interactive UI (RPC, or an extension that switches sessions), the switch proceeds and the runs are quit the same way. Resume a quit run later with `/workflow resume`.
 
@@ -937,7 +939,7 @@ Example config:
   "budget": { "maxDurationMs": 0, "maxTokens": 0, "maxCost": 0, "warnAtPercent": 80 },
   "persistRuns": true,
   "statusFile": false,
-  "resumeInFlight": "ask",
+  "resumeInFlight": "never",
   "workflowNotifications": {
     "enabled": true,
     "notifyOn": ["started", "completed", "failed", "blocked", "budget_warning", "awaiting_input", "paused", "quit", "resumed"]
@@ -957,11 +959,17 @@ Runtime config defaults:
 | `budget` | `{ maxDurationMs: 0, maxTokens: 0, maxCost: 0, warnAtPercent: 80 }` | Default per-run budget declaration; `0` disables a dimension; warnings default to `80` percent |
 | `persistRuns` | `true` | Persist run metadata for status/resume/history |
 | `statusFile` | `false` | Write a derived status file; defaults under `.atomic/workflows/status.json` when enabled |
-| `resumeInFlight` | `"ask"` | Behavior when discovering resumable in-flight work |
+| `resumeInFlight` | `"never"` | At process startup, `"never"` leaves interrupted durable workflows for manual `/workflow resume`, `"ask"` requests confirmation, and `"auto"` resumes them |
 | `workflowNotifications.enabled` | `true` | Emit workflow lifecycle notices into the active main chat |
 | `workflowNotifications.notifyOn` | `["started", "completed", "failed", "blocked", "budget_warning", "awaiting_input", "paused", "quit", "resumed"]` | Lifecycle states to track; terminal `completed`/`failed`/`blocked` outcomes, active recoverable blocks, duration budget warnings, and attributed user `started`/`quit`/`resumed` actions on a top-level run create main-chat notices. `pause` does not attribute an actor; `awaiting_input` is tracked for dedupe/restore without waking the main agent. |
 | `worktree.symlinkDirectories` | `["node_modules"]` | Main-root directories symlinked into each runner-managed temporary worktree during post-creation setup |
 
+Startup recovery uses the durable catalog, not session transcripts. Only interrupted, checkpointed workflows still marked `running` without pending human prompts and originally invoked in the current working directory are eligible. Runs from other projects sharing the database, or older runs without a recorded invocation directory, remain untouched and available through `/workflow resume`. Fresh-heartbeat live owners, paused or quit runs, failed or blocked runs, and runs awaiting input are not restarted automatically. `"ask"` leaves runs untouched when no confirmation UI is available or you decline. `/workflow resume` remains available in every mode. Session switches and `/reload` do not trigger startup recovery. Workflow resources must be enabled and available at startup. If project trust or missing resources prevent recovery, enable them and use `/workflow resume`. If recovery fails, Atomic reports a warning; use `/workflow resume` to retry.
+
+Recovered agent-owned workflows belong to the recovering session, so its agent can inspect and control them. Adoption requires the same working directory and confirmation that the previous owner has stopped. Atomic will not take ownership from a live or unverified owner or override another session's recovery.
+
+After accepting startup recovery, inspect the original run ID with `/workflow status <full-run-uuid>` to confirm its next stages progress. If an older version failed with `This extension ctx is stale`, upgrade, restart Atomic, and resume the same run ID rather than launch a duplicate workflow.
+
 Invalid JSON or invalid shapes produce `CONFIG_INVALID` diagnostics. Missing config files are ignored.
 
 ## Settings

package/npm-shrinkwrap.json

@@ -1,16 +1,16 @@
 {
 	"name": "@bastani/atomic",
-	"version": "0.9.28-alpha.1",
+	"version": "0.9.28-alpha.3",
 	"lockfileVersion": 3,
 	"requires": true,
 	"packages": {
 		"": {
 			"name": "@bastani/atomic",
-			"version": "0.9.28-alpha.1",
+			"version": "0.9.28-alpha.3",
 			"license": "MIT",
 			"dependencies": {
-				"@bastani/atomic-natives": "0.9.28-alpha.1",
-				"@bastani/pi-ai": "0.9.28-alpha.1",
+				"@bastani/atomic-natives": "0.9.28-alpha.3",
+				"@bastani/pi-ai": "0.9.28-alpha.3",
 				"@dbos-inc/dbos-sdk": "4.25.14",
 				"@earendil-works/pi-agent-core": "1.0.4",
 				"@earendil-works/pi-client": "1.0.4",
@@ -432,18 +432,18 @@
 			}
 		},
 		"node_modules/@bastani/atomic-natives": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives/-/atomic-natives-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives/-/atomic-natives-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"optionalDependencies": {
-				"@bastani/atomic-natives-darwin-arm64": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-darwin-x64": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-linux-arm64-gnu": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-linux-arm64-musl": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-linux-x64-gnu": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-linux-x64-musl": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-win32-arm64-msvc": "0.9.28-alpha.1",
-				"@bastani/atomic-natives-win32-x64-msvc": "0.9.28-alpha.1"
+				"@bastani/atomic-natives-darwin-arm64": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-darwin-x64": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-linux-arm64-gnu": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-linux-arm64-musl": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-linux-x64-gnu": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-linux-x64-musl": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-win32-arm64-msvc": "0.9.28-alpha.3",
+				"@bastani/atomic-natives-win32-x64-msvc": "0.9.28-alpha.3"
 			},
 			"engines": {
 				"bun": ">=1.4.2",
@@ -451,8 +451,8 @@
 			}
 		},
 		"node_modules/@bastani/atomic-natives-darwin-arm64": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-arm64/-/atomic-natives-darwin-arm64-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-arm64/-/atomic-natives-darwin-arm64-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"darwin"
@@ -463,8 +463,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-darwin-x64": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-x64/-/atomic-natives-darwin-x64-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-darwin-x64/-/atomic-natives-darwin-x64-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"darwin"
@@ -475,8 +475,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-arm64-gnu": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-gnu/-/atomic-natives-linux-arm64-gnu-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-gnu/-/atomic-natives-linux-arm64-gnu-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -490,8 +490,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-arm64-musl": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-musl/-/atomic-natives-linux-arm64-musl-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-arm64-musl/-/atomic-natives-linux-arm64-musl-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -505,8 +505,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-x64-gnu": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-gnu/-/atomic-natives-linux-x64-gnu-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-gnu/-/atomic-natives-linux-x64-gnu-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -520,8 +520,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-linux-x64-musl": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-musl/-/atomic-natives-linux-x64-musl-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-linux-x64-musl/-/atomic-natives-linux-x64-musl-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"linux"
@@ -535,8 +535,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-win32-arm64-msvc": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-arm64-msvc/-/atomic-natives-win32-arm64-msvc-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-arm64-msvc/-/atomic-natives-win32-arm64-msvc-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"win32"
@@ -547,8 +547,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/atomic-natives-win32-x64-msvc": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-x64-msvc/-/atomic-natives-win32-x64-msvc-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/atomic-natives-win32-x64-msvc/-/atomic-natives-win32-x64-msvc-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"os": [
 				"win32"
@@ -559,8 +559,8 @@
 			"optional": true
 		},
 		"node_modules/@bastani/pi-ai": {
-			"version": "0.9.28-alpha.1",
-			"resolved": "https://registry.npmjs.org/@bastani/pi-ai/-/pi-ai-0.9.28-alpha.1.tgz",
+			"version": "0.9.28-alpha.3",
+			"resolved": "https://registry.npmjs.org/@bastani/pi-ai/-/pi-ai-0.9.28-alpha.3.tgz",
 			"license": "MIT",
 			"dependencies": {
 				"@anthropic-ai/sdk": "0.129.0",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.9.28-alpha.1",
+  "version": "0.9.28-alpha.3",
   "description": "Atomic coding agent CLI with read, bash, edit, write tools and session management",
   "type": "module",
   "atomicConfig": {
@@ -80,8 +80,8 @@
     "prepublishOnly": "bun run clean && bun run build && bun run shrinkwrap"
   },
   "dependencies": {
-    "@bastani/atomic-natives": "0.9.28-alpha.1",
-    "@bastani/pi-ai": "0.9.28-alpha.1",
+    "@bastani/atomic-natives": "0.9.28-alpha.3",
+    "@bastani/pi-ai": "0.9.28-alpha.3",
     "@dbos-inc/dbos-sdk": "4.25.14",
     "@earendil-works/pi-agent-core": "1.0.4",
     "@earendil-works/pi-client": "1.0.4",