@bastani/atomic 0.5.16 → 0.5.17-0

package/.agents/skills/workflow-creator/references/agent-sessions.md

@@ -99,7 +99,9 @@ Claude maintains conversation context across calls within the same pane. Call `s
 
 ### Advanced: Claude Agent SDK `query()` API
 
-For programmatic control beyond tmux automation, the Claude Agent SDK provides `query()`:
+For programmatic control beyond tmux automation, the Claude Agent SDK provides `query()`. **Do not call it from inside a non-headless `ctx.stage()`** — that spawns a TUI in a tmux pane that goes unused while the SDK runs in-process (see `failure-modes.md` §F17). Either set `headless: true` on the stage and pass SDK options through `s.session.query(prompt, options)` (the headless wrapper forwards them to `query()`), or use the interactive TUI route below with `chatFlags: ["--agent", "<name>", ...]` plus `s.session.query(prompt)`.
+
+The example below is reference for the SDK option surface — in real workflow code, prefer `s.session.query()` so the runtime, not your callback, decides which transport to use:
 
 ```ts
 import { query } from "@anthropic-ai/claude-agent-sdk";

package/.agents/skills/workflow-creator/references/failure-modes.md

@@ -46,6 +46,7 @@ Silent failures are catalogued first below. Loud failures are grouped at the end
 | [F14](#f14-forgetting-to-await-ctxstage) | Forgetting to `await` `ctx.stage()` | all | silent |
 | [F15](#f15-using-a-pending-sessionhandle-before-completion) | Using a pending `SessionHandle` before completion | all | silent |
 | [F16](#f16-headless-stage-errors-are-invisible-in-the-graph) | Headless stage errors are invisible in the graph | all | silent |
+| [F17](#f17-claude-importing-sdk-query-inside-a-non-headless-stage) | Claude: importing the SDK `query()` inside a non-headless stage (anti-pattern) | Claude | silent |
 
 ---
 
@@ -713,6 +714,144 @@ full error for each failed headless stage.
 
 ---
 
+## F17. Claude: importing the SDK `query()` inside a non-headless stage
+
+**Symptom.** A reviewer / extractor / structured-output stage shows up in
+the workflow graph as a tmux pane, but the pane sits idle on the Claude
+welcome screen for the entire stage duration. The stage still produces a
+result — but the visible session never moved. CPU and token cost double:
+two Claude processes ran, one in the pane (idle) and one in-process (the
+SDK call that actually did the work).
+
+**Root cause.** The stage was registered without `headless: true`, so the
+runtime spawned an interactive Claude TUI in a tmux pane and bound
+`s.session` to it. The callback ignored that and called
+`query()` from `@anthropic-ai/claude-agent-sdk` directly:
+
+```ts
+import { query } from "@anthropic-ai/claude-agent-sdk";
+// ...
+ctx.stage({ name: "review" }, {}, {}, async (s) => {
+  for await (const msg of query({ prompt, options: { outputFormat: ... } })) { /* ... */ }
+});
+```
+
+That import bypasses `s.session` entirely. The runtime cannot route the
+SDK call through the TUI it just started, so:
+
+1. The visible pane never receives a prompt — the user sees a blank Claude
+   session in the graph.
+2. A second Claude process spins up in the orchestrator process to service
+   the SDK call. Both processes count against rate limits and token spend.
+3. Idle detection on the pane never fires because no prompt was ever sent;
+   the runtime relies on session-state events that won't arrive, and stage
+   completion happens only because the callback returned (not because the
+   pane finished work).
+
+The runtime exposes exactly two routes for an SDK feature:
+
+| You want to use… | Stage shape | Code in callback |
+|---|---|---|
+| `outputFormat`, custom `agents`, `maxBudgetUsd`, etc. **without** a visible pane | `{ headless: true }` | `s.session.query(prompt, sdkOptions)` — wraps `HeadlessClaudeSessionWrapper.query()` which forwards `options` to the SDK |
+| The visible TUI with a sub-agent | omit `headless` and pass `chatFlags: ["--agent", "<name>", ...]` | `s.session.query(prompt)` — sends through tmux send-keys |
+
+The one option that does **not** exist is "visible pane + in-process SDK call".
+That combination is always wrong — pick one route or the other.
+
+**Affected SDKs.** Claude only. Copilot and OpenCode don't expose a
+parallel "import the bare SDK" foot-gun in this codebase.
+
+### ❌ Wrong — visible pane + bypassed-SDK call
+
+```ts
+import { query as claudeSdkQuery } from "@anthropic-ai/claude-agent-sdk";
+
+await ctx.stage({ name: "review" }, {}, {}, async (s) => {
+  // Visible TUI was started, but we're ignoring it.
+  for await (const msg of claudeSdkQuery({
+    prompt: reviewPrompt,
+    options: {
+      outputFormat: { type: "json_schema", schema: REVIEW_SCHEMA },
+    },
+  })) {
+    if (msg.type === "result") { /* ... */ }
+  }
+  s.save(s.sessionId);
+});
+```
+
+### ✅ Right (a) — visible TUI with sub-agent + chatFlags
+
+When you want the user to watch the review happen, run the sub-agent in
+the pane via `--agent` and parse JSON out of the assistant text. The
+prompt should enumerate the schema fields so the model emits matching
+JSON; a tolerant parser (last-fenced-block + last-balanced-object
+fallback, F8) handles any prose the model adds:
+
+```ts
+await ctx.stage(
+  { name: "review" },
+  { chatFlags: ["--agent", "reviewer", "--allow-dangerously-skip-permissions", "--dangerously-skip-permissions"] },
+  {},
+  async (s) => {
+    const messages = await s.session.query(reviewPrompt);
+    s.save(s.sessionId);
+    return parseReviewResult(extractAssistantText(messages, 0));
+  },
+);
+```
+
+This is the pattern used by `src/sdk/workflows/builtin/ralph/claude/index.ts`
+for its planner, orchestrator, reviewer, and debugger stages.
+
+### ✅ Right (b) — headless stage with SDK options via `s.session.query()`
+
+When you don't need the pane (e.g. background data gathering), set
+`headless: true` and pass SDK options as the second argument to
+`s.session.query()`. The runtime uses `HeadlessClaudeSessionWrapper`,
+which calls the SDK's `query()` in-process and exposes the full options
+surface (`agent`, `outputFormat`, `permissionMode`, `maxBudgetUsd`, etc.):
+
+```ts
+await ctx.stage(
+  { name: "review", headless: true },
+  {}, {},
+  async (s) => {
+    const messages = await s.session.query(reviewPrompt, {
+      agent: "reviewer",
+      permissionMode: "bypassPermissions",
+      allowDangerouslySkipPermissions: true,
+    });
+    s.save(s.sessionId);
+    return extractAssistantText(messages, 0);
+  },
+);
+```
+
+> **Note on `--json-schema`.** The CLI's `--json-schema` flag requires
+> `-p` (print mode) and therefore can't be passed via `chatFlags` to the
+> interactive TUI. If you need SDK-validated structured output, use route
+> (b) — set `headless: true` and pass `outputFormat: { type: "json_schema", schema }`
+> in the `s.session.query()` options. Pair (a)'s visible TUI with a
+> tolerant JSON parser instead. (Note: `s.session.query()`'s headless
+> wrapper currently returns `SessionMessage[]` and discards the SDK
+> result event's `structured_output` field — for now, parse JSON out of
+> the assistant text either way.)
+
+**Detection.**
+1. Grep your workflow for `from "@anthropic-ai/claude-agent-sdk"` —
+   `query`, `tool`, `createSdkMcpServer` and similar imports inside a
+   `.run()` callback are the smell. Workflow code should import from
+   `@bastani/atomic/workflows` and access the SDK exclusively through
+   `s.client` and `s.session`.
+2. Watch the workflow run. If a visible pane shows the Claude welcome
+   screen for the entire duration of a stage and never receives a prompt,
+   you have F17.
+3. Cost monitoring. F17 roughly doubles the Claude process count — if
+   stage spend looks 2× a single run, audit imports.
+
+---
+
 ## Design checklist
 
 Before shipping a multi-session workflow, walk the list:
@@ -729,3 +868,4 @@ Before shipping a multi-session workflow, walk the list:
 - [ ] `SessionHandle` values are only used after the promise resolves (F15)
 - [ ] If provider-level resume/fork is used at all, it stays within the same agent role (F12)
 - [ ] Headless stage callbacks include descriptive error context so failures can be diagnosed without a graph node (F16)
+- [ ] Claude stages never import `query` (or other entry points) from `@anthropic-ai/claude-agent-sdk` directly — go through `s.session.query()` so the runtime routes to the TUI (interactive) or the SDK (headless) consistently (F17)

package/.claude/settings.json

@@ -5,6 +5,7 @@
     "CLAUDE_CODE_NO_FLICKER": "1"
   },
   "includeCoAuthoredBy": false,
+  "skipDangerousModePermissionPrompt": true,
   "permissions": {
     "defaultMode": "bypassPermissions"
   },

package/dist/sdk/components/header.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"header.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/header.tsx"],"names":[],"mappings":"AAAA,sCAAsC;AAetC,wBAAgB,MAAM,8BA2CrB"}

package/dist/sdk/components/layout.d.ts.map

@@ -1 +1 @@
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package/dist/sdk/components/node-card.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"node-card.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/node-card.tsx"],"names":[],"mappings":"AAAA,sCAAsC;AAEtC,OAAO,KAAK,MAAM,OAAO,CAAC;AAI1B,OAAO,EAAU,KAAK,UAAU,EAAE,MAAM,aAAa,CAAC;AAEtD,eAAO,MAAM,QAAQ,uEAKlB;IACD,IAAI,EAAE,UAAU,CAAC;IACjB,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,CAAC;CAClB,qBAkEC,CAAC"}

package/dist/sdk/components/orchestrator-panel-store.d.ts

@@ -27,6 +27,8 @@ export declare class PanelStore {
     startSession(name: string): void;
     completeSession(name: string): void;
     failSession(name: string, error: string): void;
+    awaitingInput(name: string): void;
+    resumeSession(name: string): void;
     addSession(session: SessionData): void;
     setCompletion(workflowName: string, transcriptsPath: string): void;
     setFatalError(message: string): void;

package/dist/sdk/components/orchestrator-panel-store.d.ts.map

@@ -1 +1 @@
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package/dist/sdk/components/orchestrator-panel-types.d.ts

@@ -1,4 +1,4 @@
-export type SessionStatus = "pending" | "running" | "complete" | "error";
+export type SessionStatus = "pending" | "running" | "complete" | "error" | "awaiting_input";
 export type ViewMode = "graph" | "attached";
 export interface PanelSession {
     name: string;

package/dist/sdk/components/orchestrator-panel-types.d.ts.map

@@ -1 +1 @@
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package/dist/sdk/components/orchestrator-panel.d.ts

@@ -30,6 +30,8 @@ export declare class OrchestratorPanel {
     sessionSuccess(name: string): void;
     /** Mark a session as failed in the graph UI and display the error message. */
     sessionError(name: string, message: string): void;
+    sessionAwaitingInput(name: string): void;
+    sessionResumed(name: string): void;
     /** Dynamically add a new session node to the graph UI. */
     addSession(name: string, parents: string[]): void;
     /** Increment the background task counter (shown in the statusline footer). */

package/dist/sdk/components/orchestrator-panel.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator-panel.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/orchestrator-panel.tsx"],"names":[],"mappings":"AAAA,sCAAsC;AACtC;;;GAGG;AAEH,OAAO,EAAqB,KAAK,WAAW,EAAE,MAAM,eAAe,CAAC;AAOpE,OAAO,KAAK,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,+BAA+B,CAAC;AAIhF,qBAAa,iBAAiB;IAC5B,OAAO,CAAC,KAAK,CAAa;IAC1B,OAAO,CAAC,QAAQ,CAAc;IAC9B,OAAO,CAAC,SAAS,CAAS;IAE1B,OAAO;IAsCP;;;;;OAKG;WACU,MAAM,CAAC,OAAO,EAAE,YAAY,GAAG,OAAO,CAAC,iBAAiB,CAAC;IAQtE,0EAA0E;IAC1E,MAAM,CAAC,kBAAkB,CACvB,QAAQ,EAAE,WAAW,EACrB,OAAO,EAAE,YAAY,GACpB,iBAAiB;IAOpB;;;OAGG;IACH,gBAAgB,CACd,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,QAAQ,EAAE,YAAY,EAAE,EACxB,MAAM,EAAE,MAAM,GACb,IAAI;IAIP,iDAAiD;IACjD,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAIhC,gEAAgE;IAChE,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAIlC,8EAA8E;IAC9E,YAAY,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,GAAG,IAAI;IAIjD,oBAAoB,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAIxC,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI;IAIlC,0DAA0D;IAC1D,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI;IAUjD,8EAA8E;IAC9E,qBAAqB,IAAI,IAAI;IAI7B,8EAA8E;IAC9E,sBAAsB,IAAI,IAAI;IAI9B,0EAA0E;IAC1E,cAAc,CAAC,YAAY,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,GAAG,IAAI;IAInE,+CAA+C;IAC/C,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,IAAI;IAIrC;;;OAGG;IACH,WAAW,IAAI,OAAO,CAAC,IAAI,CAAC;IAO5B;;;OAGG;IACH,YAAY,IAAI,OAAO,CAAC,IAAI,CAAC;IAM7B,yEAAyE;IACzE,OAAO,IAAI,IAAI;CAOhB"}

package/dist/sdk/components/status-helpers.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"status-helpers.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/status-helpers.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAEnD,wBAAgB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,GAAG,MAAM,CASrE;AAED,wBAAgB,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAKlD;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAEjD;AAID,wBAAgB,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAG9C"}
+{"version":3,"file":"status-helpers.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/status-helpers.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAEnD,wBAAgB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,GAAG,MAAM,CAUrE;AAED,wBAAgB,WAAW,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAKlD;AAED,wBAAgB,UAAU,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,CAEjD;AAID,wBAAgB,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAG9C"}

package/dist/sdk/providers/claude.d.ts

@@ -55,6 +55,31 @@ export interface ClaudeSessionOptions {
  * ```
  */
 export declare function createClaudeSession(options: ClaudeSessionOptions): Promise<void>;
+/**
+ * Returns true if the most recent assistant message contains an
+ * `AskUserQuestion` tool_use block that has not yet been resolved
+ * by a corresponding `tool_result` in a subsequent user message.
+ *
+ * Pure function — no side effects, safe to call from a watch loop.
+ *
+ * Exported as `_hasUnresolvedHILTool` for unit testing.
+ */
+export declare function _hasUnresolvedHILTool(messages: SessionMessage[]): boolean;
+/**
+ * Core HIL watcher loop — pure logic, dependency-injected for testability.
+ *
+ * Iterates an async iterable of "file change" events (each event triggers a
+ * transcript read via `readMessages`). Calls `onHIL(true)` when
+ * `_hasUnresolvedHILTool` first returns true, `onHIL(false)` when it returns
+ * false after having been true. The `wasHIL` guard prevents redundant
+ * callbacks on repeated events with the same HIL state.  Read errors from
+ * `readMessages` are swallowed so a single corrupt JSONL write doesn't kill
+ * the watcher.
+ *
+ * Exported as `_runHILWatcher` for unit testing (event source and message
+ * reader are injected rather than hard-coded to `fs.watch` / `getSessionMessages`).
+ */
+export declare function _runHILWatcher(events: AsyncIterable<unknown>, readMessages: () => Promise<SessionMessage[]>, onHIL: (waiting: boolean) => void): Promise<void>;
 export interface ClaudeQueryOptions {
     /** tmux pane ID where Claude is running */
     paneId: string;
@@ -68,6 +93,12 @@ export interface ClaudeQueryOptions {
     maxSubmitRounds?: number;
     /** Timeout in ms waiting for pane to be ready before sending (default: 30s) */
     readyTimeoutMs?: number;
+    /**
+     * Called when the agent's human-in-the-loop state changes.
+     * `waiting=true`  → AskUserQuestion is pending (agent blocked on user input).
+     * `waiting=false` → AskUserQuestion was resolved (agent resumed processing).
+     */
+    onHIL?: (waiting: boolean) => void;
 }
 /**
  * Extract text content from assistant messages in a transcript slice.
@@ -145,7 +176,8 @@ export declare class ClaudeSessionWrapper {
     readonly paneId: string;
     readonly sessionId: string;
     private readonly defaults;
-    constructor(paneId: string, sessionId: string, defaults?: ClaudeQueryDefaults);
+    private readonly onHIL;
+    constructor(paneId: string, sessionId: string, defaults?: ClaudeQueryDefaults, onHIL?: (waiting: boolean) => void);
     /** Send a prompt to Claude and wait for the response. */
     query(prompt: string, opts?: Partial<ClaudeQueryDefaults & SDKOptions>): Promise<SessionMessage[]>;
     /** Noop — for API symmetry with CopilotSession.disconnect(). */

package/dist/sdk/providers/claude.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"claude.d.ts","sourceRoot":"","sources":["../../../src/sdk/providers/claude.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAIL,KAAK,cAAc,EACnB,KAAK,cAAc,EACnB,KAAK,OAAO,IAAI,UAAU,EAC3B,MAAM,gCAAgC,CAAC;AA8BxC;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAEvD;AAYD,MAAM,WAAW,oBAAoB;IACnC,kDAAkD;IAClD,MAAM,EAAE,MAAM,CAAC;IACf,sIAAsI;IACtI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,sEAAsE;IACtE,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CAyCtF;AAkGD;;;;;;;;GAQG;AACH,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAgCzE;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAsB,cAAc,CAClC,MAAM,EAAE,aAAa,CAAC,OAAO,CAAC,EAC9B,YAAY,EAAE,MAAM,OAAO,CAAC,cAAc,EAAE,CAAC,EAC7C,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,GAChC,OAAO,CAAC,IAAI,CAAC,CAef;AA+HD,MAAM,WAAW,kBAAkB;IACjC,2CAA2C;IAC3C,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,MAAM,EAAE,MAAM,CAAC;IACf,6CAA6C;IAC7C,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,qEAAqE;IACrE,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,4DAA4D;IAC5D,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,+EAA+E;IAC/E,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;;;;OAIG;IACH,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,CAAC;CACpC;AAED;;;;;;;;;GASG;AACH,wBAAgB,oBAAoB,CAClC,IAAI,EAAE,aAAa,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,OAAO,CAAA;CAAE,CAAC,EACvD,UAAU,EAAE,MAAM,GACjB,MAAM,CAoBR;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC,CAwHxF;AAMD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC,6CAA6C;IAC7C,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,0DAA0D;IAC1D,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,4DAA4D;IAC5D,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,+EAA+E;IAC/E,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAoD;gBAGvE,MAAM,EAAE,MAAM,EACd,IAAI,GAAE;QAAE,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;QAAC,cAAc,CAAC,EAAE,MAAM,CAAA;KAAO;IAM9D,gFAAgF;IAC1E,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAQ5B,yEAAyE;IACnE,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAC5B;AAED;;;GAGG;AACH,qBAAa,oBAAoB;IAC/B,QAAQ,CAAC,MAAM,EAAE,MAAM,CAAC;IACxB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAsB;IAC/C,OAAO,CAAC,QAAQ,CAAC,KAAK,CAA2C;gBAG/D,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,QAAQ,GAAE,mBAAwB,EAClC,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI;IAQpC,yDAAyD;IACnD,KAAK,CACT,MAAM,EAAE,MAAM,EACd,IAAI,CAAC,EAAE,OAAO,CAAC,mBAAmB,GAAG,UAAU,CAAC,GAC/C,OAAO,CAAC,cAAc,EAAE,CAAC;IAU5B,gEAAgE;IAC1D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAMD;;;GAGG;AACH,qBAAa,2BAA2B;IAChC,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IACtB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAC5B;AAED;;;;;;;;;;GAUG;AACH,qBAAa,4BAA4B;IACvC,QAAQ,CAAC,MAAM,MAAM;IACrB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;gBAEf,SAAS,EAAE,MAAM;IAIvB,KAAK,CACT,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,cAAc,CAAC,EAC9C,OAAO,CAAC,EAAE,OAAO,CAAC,mBAAmB,GAAG,UAAU,CAAC,GAClD,OAAO,CAAC,cAAc,EAAE,CAAC;IAuBtB,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAQD;;;;;GAKG;AACH,eAAO,MAAM,sBAAsB,+DAejC,CAAC"}

package/dist/sdk/runtime/executor.d.ts

@@ -68,5 +68,93 @@ export declare function hasContent(value: unknown): value is {
     content: string;
 };
 export declare function renderMessagesToText(messages: SavedMessage[]): string;
+/**
+ * Minimal Copilot session surface required by `wrapCopilotSend()`.
+ * Uses a generic `on` signature to remain compatible with both the real
+ * CopilotSession and lightweight test mocks.
+ */
+export interface CopilotSendSessionSurface {
+    on(eventType: string, handler: (event: {
+        data?: unknown;
+    }) => void): () => void;
+}
+/**
+ * Wraps a Copilot session's `send()` to block until `session.idle` fires.
+ *
+ * Copilot's `send()` is fire-and-forget — it returns immediately after
+ * queuing the message.  This wrapper blocks the returned promise until the
+ * session emits `session.idle` (turn complete) or `session.error`.
+ *
+ * HIL detection for Copilot is handled separately by
+ * `watchCopilotSessionForHIL()`, which subscribes to the session's
+ * `tool.execution_start` / `tool.execution_complete` events for the
+ * `ask_user` built-in tool.  Those events fire regardless of whether
+ * an `onUserInputRequest` handler is registered, so we can detect HIL
+ * via native SDK events while the CLI continues to handle user input
+ * locally in the tmux pane.
+ *
+ * Exported for unit testing.
+ */
+export declare function wrapCopilotSend<O, R>(session: CopilotSendSessionSurface, nativeSend: (options: O) => Promise<R>): (options: O) => Promise<R>;
+/**
+ * Minimal shape of an event as produced by the OpenCode v2 SDK event stream.
+ * Using a structural interface rather than the SDK's generated union type keeps
+ * this helper independently unit-testable with plain objects.
+ *
+ * `sessionID` is optional because many OpenCode event types (e.g.
+ * `file.edited`, `session.compacted`) carry properties without that field.
+ * The `watchOpencodeStreamForHIL` implementation guards with a runtime check.
+ */
+export interface OpenCodeHILEvent {
+    type: string;
+    properties: {
+        sessionID?: string;
+        [key: string]: unknown;
+    };
+}
+/**
+ * Consume an OpenCode SSE event stream and call `onHIL` whenever the session
+ * with `sessionId` enters or exits a human-in-the-loop (HIL) state:
+ *
+ *   - `question.asked`    → `onHIL(true)`   (agent awaiting user input)
+ *   - `question.replied`  → `onHIL(false)`  (user answered, agent resumes)
+ *   - `question.rejected` → `onHIL(false)`  (user dismissed, agent resumes)
+ *
+ * Events for other sessions are silently ignored.  The function returns when
+ * the stream is exhausted (i.e. the server closes the connection).
+ *
+ * Exported for unit testing.
+ */
+export declare function watchOpencodeStreamForHIL(stream: AsyncIterable<OpenCodeHILEvent>, sessionId: string, onHIL: (waiting: boolean) => void): Promise<void>;
+/**
+ * Minimal Copilot session surface required by `watchCopilotSessionForHIL()`.
+ * A structural `on()` signature keeps this helper independently unit-testable
+ * with plain objects and compatible with both the real CopilotSession and
+ * test mocks.
+ */
+export interface CopilotHILSessionSurface {
+    on(eventType: string, handler: (event: {
+        data?: unknown;
+    }) => void): () => void;
+}
+/**
+ * Subscribe to a Copilot session's tool-execution events to track HIL state
+ * for the `ask_user` built-in tool:
+ *
+ *   - `tool.execution_start`    with `toolName === "ask_user"` → `onHIL(true)`
+ *   - `tool.execution_complete` with matching `toolCallId`     → `onHIL(false)`
+ *
+ * These events fire regardless of whether an `onUserInputRequest` handler is
+ * registered, so we can detect HIL without providing one — letting the CLI
+ * keep its native tmux-pane dialog.
+ *
+ * Overlapping `ask_user` invocations are tracked by `toolCallId` so
+ * `onHIL(false)` only fires after the last active request resolves.
+ *
+ * Returns an unsubscribe function that removes both listeners.
+ *
+ * Exported for unit testing.
+ */
+export declare function watchCopilotSessionForHIL(session: CopilotHILSessionSurface, onHIL: (waiting: boolean) => void): () => void;
 export declare function runOrchestrator(): Promise<void>;
 //# sourceMappingURL=executor.d.ts.map

package/dist/sdk/runtime/executor.d.ts.map

@@ -1 +1 @@
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package/dist/sdk/workflows/builtin/deep-research-codebase/claude/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6DG;;AA4BH,wBA2Oa"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6DG;;AA4BH,wBA4Na"}

package/dist/sdk/workflows/builtin/ralph/claude/index.d.ts

@@ -7,9 +7,13 @@
  *   - {@link MAX_LOOPS} iterations have completed, OR
  *   - Two parallel reviewer passes both return zero findings.
  *
- * The reviewer stages use the Claude Agent SDK's structured output
- * (`outputFormat`) to guarantee the review result matches the
- * {@link ReviewResultSchema} — no manual JSON parsing required.
+ * The reviewer stages run the `reviewer` sub-agent in a visible TUI via the
+ * `--agent reviewer` chatFlag, then parse the JSON review out of the
+ * assistant text with {@link parseReviewResult}. The prompt enumerates the
+ * {@link ReviewResultSchema} fields so the model emits matching JSON. We
+ * deliberately avoid invoking the Claude Agent SDK's `query()` from inside a
+ * non-headless stage — that would spawn a TUI pane that goes unused while
+ * the SDK runs in-process (see workflow-creator skill, failure-modes F17).
  *
  * Run: atomic workflow -n ralph -a claude "<your spec>"
  */

package/dist/sdk/workflows/builtin/ralph/claude/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/ralph/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;;AAkEH,wBAiLa"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/ralph/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;;AAmCH,wBAkMa"}

package/dist/services/config/definitions.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"definitions.d.ts","sourceRoot":"","sources":["../../../src/services/config/definitions.ts"],"names":[],"mappings":"AAAA;;GAEG;AAKH,MAAM,WAAW,WAAW;IAC1B,iCAAiC;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,mCAAmC;IACnC,GAAG,EAAE,MAAM,CAAC;IACZ,kEAAkE;IAClE,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,qFAAqF;IACrF,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,0CAA0C;IAC1C,MAAM,EAAE,MAAM,CAAC;IACf,wCAAwC;IACxC,WAAW,EAAE,MAAM,CAAC;IACpB,yDAAyD;IACzD,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,qEAAqE;IACrE,gBAAgB,EAAE,KAAK,CAAC;QACtB,MAAM,EAAE,MAAM,CAAC;QACf,WAAW,EAAE,MAAM,CAAC;QACpB,KAAK,EAAE,OAAO,CAAC;KAChB,CAAC,CAAC;CACJ;AAED,QAAA,MAAM,UAAU,4CAA6C,CAAC;AAC9D,MAAM,MAAM,QAAQ,GAAG,CAAC,OAAO,UAAU,CAAC,CAAC,MAAM,CAAC,CAAC;AAEnD,eAAO,MAAM,YAAY,EAAE,MAAM,CAAC,QAAQ,EAAE,WAAW,CAiEtD,CAAC;AAEF;;;;;;;GAOG;AACH,MAAM,WAAW,iBAAiB;IAChC,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAClC;AAED,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,QAAQ,CAEzD;AAED,wBAAgB,cAAc,CAAC,GAAG,EAAE,QAAQ,GAAG,WAAW,CAEzD;AAED,wBAAgB,YAAY,IAAI,QAAQ,EAAE,CAEzC;AAED;;GAEG;AAEH,6BAA6B;AAC7B,QAAA,MAAM,QAAQ,gCAAiC,CAAC;AAEhD,oEAAoE;AACpE,MAAM,MAAM,iBAAiB,GAAG,CAAC,OAAO,QAAQ,CAAC,CAAC,MAAM,CAAC,CAAC;AAE1D,MAAM,WAAW,SAAS;IACxB,+BAA+B;IAC/B,WAAW,EAAE,MAAM,CAAC;IACpB,mCAAmC;IACnC,OAAO,EAAE,MAAM,CAAC;IAChB,+CAA+C;IAC/C,YAAY,EAAE,MAAM,CAAC;IACrB,8EAA8E;IAC9E,SAAS,EAAE,MAAM,CAAC;CACnB;AAED,eAAO,MAAM,UAAU,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,CAa3D,CAAC;AAEF;;;;;;;;GAQG;AACH,eAAO,MAAM,kBAAkB,EAAE,MAAM,CAAC,iBAAiB,EAAE,SAAS,MAAM,EAAE,CAIzE,CAAC;AAEJ,4EAA4E;AAC5E,eAAO,MAAM,cAAc,EAAE,SAAS,MAAM,EAG3C,CAAC;AAEF;;GAEG;AACH,wBAAgB,UAAU,IAAI,iBAAiB,EAAE,CAEhD;AAED;;GAEG;AACH,wBAAgB,UAAU,CAAC,GAAG,EAAE,MAAM,GAAG,GAAG,IAAI,iBAAiB,CAEhE;AAED;;;;;GAKG;AACH,wBAAsB,aAAa,CACjC,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC,CAWnC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.5.16",
+  "version": "0.5.17-0",
   "description": "Configuration management CLI and SDK for coding agents",
   "type": "module",
   "license": "MIT",
@@ -68,17 +68,17 @@
   "devDependencies": {
     "@types/bun": "^1.3.12",
     "@types/react": "^19.2.14",
-    "lefthook": "^2.1.5",
+    "lefthook": "^2.1.6",
     "oxlint": "^1.60.0",
     "typescript": "^6.0.2",
     "typescript-language-server": "^5.1.3"
   },
   "dependencies": {
-    "@anthropic-ai/claude-agent-sdk": "^0.2.108",
+    "@anthropic-ai/claude-agent-sdk": "^0.2.111",
     "@clack/prompts": "^1.2.0",
     "@commander-js/extra-typings": "^14.0.0",
     "@github/copilot-sdk": "^0.2.2",
-    "@opencode-ai/sdk": "^1.4.3",
+    "@opencode-ai/sdk": "^1.4.6",
     "@opentui/core": "^0.1.99",
     "@opentui/react": "^0.1.99",
     "commander": "^14.0.3",
@@ -87,6 +87,6 @@
     "zod": "^4.3.6"
   },
   "peerDependencies": {
-    "react": ">=19.0.0"
+    "react": "^19.2.5"
   }
 }

package/src/commands/cli/init/onboarding.ts

@@ -1,8 +1,22 @@
 import { join } from "node:path";
+import { homedir } from "node:os";
 import { AGENT_CONFIG, type AgentKey } from "../../../services/config/index.ts";
 import { pathExists } from "../../../services/system/copy.ts";
 import { syncJsonFile } from "../../../lib/merge.ts";
 
+/**
+ * Resolve an onboarding destination path. A leading `~/` is expanded to
+ * the user's home directory so providers can target global config roots
+ * (e.g. `~/.claude/settings.json`); anything else resolves against the
+ * project root.
+ */
+function resolveDestination(destination: string, projectRoot: string): string {
+  if (destination === "~" || destination.startsWith("~/")) {
+    return join(homedir(), destination.slice(1));
+  }
+  return join(projectRoot, destination);
+}
+
 export async function applyManagedOnboardingFiles(
   agentKey: AgentKey,
   projectRoot: string,
@@ -16,7 +30,10 @@ export async function applyManagedOnboardingFiles(
       continue;
     }
 
-    const destinationPath = join(projectRoot, managedFile.destination);
+    const destinationPath = resolveDestination(
+      managedFile.destination,
+      projectRoot,
+    );
     await syncJsonFile(sourcePath, destinationPath, managedFile.merge);
   }
 }
@@ -32,7 +49,7 @@ export async function hasProjectOnboardingFiles(
 
   const checks = await Promise.all(
     onboardingFiles.map((managedFile) =>
-      pathExists(join(projectRoot, managedFile.destination))
+      pathExists(resolveDestination(managedFile.destination, projectRoot))
     ),
   );
   return checks.every(Boolean);

package/src/sdk/components/header.tsx

@@ -19,7 +19,7 @@ export function Header() {
   const storeVersion = useStoreVersion(store);
 
   const counts = useMemo(() => {
-    const c: Record<SessionStatus, number> = { complete: 0, running: 0, pending: 0, error: 0 };
+    const c: Record<SessionStatus, number> = { complete: 0, running: 0, pending: 0, error: 0, awaiting_input: 0 };
     for (const s of store.sessions) c[s.status]++;
     return c;
   }, [storeVersion]);
@@ -50,6 +50,7 @@ export function Header() {
       <box flexGrow={1} justifyContent="flex-end" flexDirection="row" gap={2}>
         <CountBadge color={theme.success} icon={"\u2713"} count={counts.complete} />
         <CountBadge color={theme.warning} icon={"\u25CF"} count={counts.running} />
+        <CountBadge color={theme.info} icon={"?"} count={counts.awaiting_input} />
         <CountBadge color={theme.textDim} icon={"\u25CB"} count={counts.pending} />
         <CountBadge color={theme.error} icon={"\u2717"} count={counts.error} />
       </box>

package/src/sdk/components/layout.ts

@@ -152,7 +152,8 @@ export function computeLayout(sessions: SessionData[]): LayoutResult {
 
   const rowH: Record<number, number> = {};
   for (const n of Object.values(map)) {
-    rowH[n.depth] = Math.max(rowH[n.depth] ?? 0, NODE_H);
+    const nodeHeight = n.status === "awaiting_input" ? 6 : NODE_H;
+    rowH[n.depth] = Math.max(rowH[n.depth] ?? 0, nodeHeight);
   }
 
   function yAt(d: number): number {

package/src/sdk/components/node-card.tsx

@@ -21,6 +21,7 @@ export const NodeCard = React.memo(function NodeCard({
   const sc = statusColor(node.status, theme);
   const isPending = node.status === "pending";
   const isRunning = node.status === "running";
+  const isAwaitingInput = node.status === "awaiting_input";
 
   // Border: running nodes smoothly pulse, others show status color
   let borderCol: string;
@@ -29,6 +30,11 @@ export const NodeCard = React.memo(function NodeCard({
     borderCol = focused
       ? lerpColor(theme.warning, "#ffffff", 0.2)
       : lerpColor(theme.border, theme.warning, t);
+  } else if (isAwaitingInput) {
+    const t = (Math.sin((pulsePhase / 32) * Math.PI * 2 - Math.PI / 2) + 1) / 2;
+    borderCol = focused
+      ? lerpColor(theme.info, "#ffffff", 0.2)
+      : lerpColor(theme.border, theme.info, t);
   } else if (isPending) {
     borderCol = focused ? sc : theme.borderActive;
   } else {
@@ -64,6 +70,16 @@ export const NodeCard = React.memo(function NodeCard({
       <box alignItems="center">
         <text fg={durCol}>{duration}</text>
       </box>
+      {isAwaitingInput && (
+        <>
+          <box alignItems="center">
+            <text fg={theme.info}>waiting for response</text>
+          </box>
+          <box alignItems="center">
+            <text fg={theme.textDim}>↵ enter to respond</text>
+          </box>
+        </>
+      )}
     </box>
   );
 });