@bastani/atomic 0.5.22 → 0.5.23-0

package/.agents/skills/workflow-creator/SKILL.md

@@ -232,7 +232,7 @@ defineWorkflow({
 | Behaviour | Unset (default) | Set to a version newer than the installed CLI |
 |---|---|---|
 | Loader | Always loads | Refuses to load, returns `IncompatibleSDKError` |
-| `atomic workflow -l` | Normal row | `⚠ needs v<X> (installed v<Y>)` — dim name, visible |
+| `atomic workflow list` | Normal row | `⚠ needs v<X> (installed v<Y>)` — dim name, visible |
 | Picker | Normal row | `⚠ update required` glyph + preview explains the gap; Enter is disabled |
 | `atomic workflow -n <name>` | Runs | Errors with an upgrade hint, non-zero exit |
 
@@ -314,7 +314,7 @@ Use `.for<"agent">()` on the builder to narrow all context types and get correct
 | Agent | Builder Chain | Primary Session API |
 |-------|---------------|---------------------|
 | Claude | `defineWorkflow({...}).for<"claude">()` | `s.session.query(prompt)` — sends prompt to the Claude TUI pane |
-| Copilot | `defineWorkflow({...}).for<"copilot">()` | `s.session.send({ prompt })` — fire-and-forget; use `sendAndWait({ prompt }, timeoutMs)` only when the user explicitly requests timeout-based waiting |
+| Copilot | `defineWorkflow({...}).for<"copilot">()` | `s.session.send({ prompt })` — the runtime wraps `send` to block until `session.idle` with no timeout (see `failure-modes.md` §F10); do not use `sendAndWait` in Atomic workflows |
 | OpenCode | `defineWorkflow({...}).for<"opencode">()` | `s.client.session.prompt({ sessionID: s.session.id, parts: [...] })` |
 
 The runtime manages client/session lifecycle automatically. For native SDK types and advanced APIs, import directly from the provider packages (`@github/copilot-sdk`, `@anthropic-ai/claude-agent-sdk`, `@opencode-ai/sdk/v2`).

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

@@ -6,7 +6,7 @@ Each `ctx.stage()` call inside a workflow's `.run()` callback creates an isolate
 
 ## Claude Agent SDK
 
-Claude runs as a full interactive TUI in a tmux pane. The runtime auto-starts the Claude CLI (via `s.client`) and creates a session wrapper (`s.session`) before the callback runs. Pass CLI flags via `clientOpts` (2nd arg) and query defaults via `sessionOpts` (3rd arg).
+Claude runs as a full interactive TUI in a tmux pane. The runtime auto-starts the Claude CLI (via `s.client`) and creates a session wrapper (`s.session`) before the callback runs. Pass CLI flags via `clientOpts` (2nd arg). Claude has **no per-session options** — the 3rd arg must be `{}`.
 
 ### Session lifecycle
 
@@ -18,7 +18,7 @@ import { defineWorkflow } from "@bastani/atomic/workflows";
   await ctx.stage(
     { name: "implement", description: "Implement the feature" },
     {}, // clientOpts: chatFlags and readyTimeoutMs go here
-    {}, // sessionOpts: query defaults (pollIntervalMs, readyTimeoutMs, etc.) go here
+    {}, // sessionOpts: must be {} for Claude — no per-session options exist
     async (s) => {
       // s.client — Claude CLI wrapper (already started by runtime)
       // s.session — session wrapper (ready to accept queries via s.session.query())
@@ -43,11 +43,9 @@ Client options (2nd arg to `ctx.stage()`):
 - `chatFlags` — CLI flags (default: `["--allow-dangerously-skip-permissions", "--dangerously-skip-permissions"]`)
 - `readyTimeoutMs` — timeout waiting for TUI readiness (default: 30s)
 
-Session options (3rd arg to `ctx.stage()`), applied as defaults to every `s.session.query()` call:
-- `pollIntervalMs` — polling interval (default: 2000ms)
-- `submitPresses` — C-m presses per submit round (default: 1)
-- `maxSubmitRounds` — max submit rounds (default: 6)
-- `readyTimeoutMs` — timeout waiting for pane readiness before sending (default: 30s)
+Session options (3rd arg to `ctx.stage()`): **none**. The Claude session wrapper takes no configuration — interactive delivery is driven entirely by the CLI's Stop hook, and idle detection watches the Stop-hook marker automatically. Pass `{}`.
+
+For **headless Claude** (`headless: true` in `stageOpts`), `s.session.query(prompt, options)` forwards its second argument as `Partial<SDKOptions>` to the Agent SDK — that's where you pass `agent`, `permissionMode`, `allowDangerouslySkipPermissions`, etc. (see the headless example further down).
 
 No manual timeout is needed — idle detection watches for the pane prompt to return, and the session transcript is used to extract the response text.
 
@@ -292,30 +290,27 @@ export default defineWorkflow({
 
 ### `send` vs `sendAndWait`: choosing the right method
 
-**Default to `send`** for all Copilot workflow stages. `send` dispatches the
-prompt and returns the `messageId` immediately — no timeout to guess, no
-constants to tune, no risk of aborting a long-running agent mid-work.
+**Always use `send`** for Copilot workflow stages. Inside a stage callback the
+Atomic runtime wraps `s.session.send()` so the returned promise only resolves
+when the session emits `session.idle` — the same semantics as Claude's
+`query()` and OpenCode's `session.prompt()`. The wrapper has **no timeout**,
+so long-running planners and reviewers are safe. This is different from the
+raw Copilot SDK, where `send` is fire-and-forget; the wrapper is installed
+per-stage by the runtime (`wrapCopilotSend` in `src/sdk/runtime/executor.ts`).
 
 ```ts
-// Default pattern — clean, no timeout guessing
+// Default pattern — blocks until the agent is idle, no timeout
 await s.session.send({ prompt });
+const messages = await s.session.getMessages(); // safe to read now
 ```
 
-**Use `sendAndWait` only when the user explicitly requests timeout-based
-waiting.** `sendAndWait` blocks until the session emits `session.idle` or the
-timeout fires. If you must use it, ask the user for a reasonable timeout. If
-they aren't sure, default to **5 minutes** (300 000 ms).
-
-```ts
-// Only when the user explicitly wants timeout-gated waiting
-const SEND_TIMEOUT_MS = 5 * 60 * 1000; // 5 minutes default; ask the user
-await s.session.sendAndWait({ prompt }, SEND_TIMEOUT_MS);
-```
-
-**Why not `sendAndWait` by default?** The 60-second default timeout is almost
-never correct for real agent work — planners, reviewers, and orchestrators
-routinely exceed it. Guessing large timeouts (30-60 min) adds messy constants
-and still risks aborting work prematurely. `send` avoids the problem entirely.
+**Do not use `sendAndWait` in Atomic workflows.** It keeps the SDK's native
+60-second default timeout, which is almost never enough for real agent work —
+planners, reviewers, and orchestrators routinely exceed it, and the throw
+propagates out of `run()` and halts the whole workflow (see
+`failure-modes.md` §F10). `send` already blocks until idle with no timeout,
+so `sendAndWait` buys you nothing but a failure mode. If you think you need
+it, you almost certainly want `send`.
 
 ### Critical pitfall: session lifecycle controls what context is available
 

package/.agents/skills/workflow-creator/references/discovery-and-verification.md

@@ -164,7 +164,7 @@ discovery but marked **incompatible** — it never silently vanishes:
 |---|---|
 | `WorkflowLoader.loadWorkflow()` | Returns `{ ok: false, stage: "load", error: IncompatibleSDKError }` carrying `requiredVersion` + `currentVersion` |
 | `loadWorkflowsMetadata()` | Yields an entry with `status: { kind: "incompatible", requiredVersion, currentVersion, message }` |
-| `atomic workflow -l` | Row is dimmed, with an inline `⚠ needs v<X> (installed v<Y>)` badge after the name |
+| `atomic workflow list` | Row is dimmed, with an inline `⚠ needs v<X> (installed v<Y>)` badge after the name |
 | `atomic workflow -a <agent>` picker | Row shows a `⚠` gutter glyph; preview pane explains the version gap and remediation; Enter does not advance to the prompt phase; bottom hint dims `↵ select` to `↵ unavailable` |
 | `atomic workflow -n <name> -a <agent>` | Exits non-zero, prints the `IncompatibleSDKError` message (`requires Atomic SDK v<X>, but v<Y> is installed. Update Atomic, or re-save the workflow against the current SDK.`) |
 

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

@@ -485,20 +485,27 @@ log the length. A 0-length or JSON-that-isn't-prose signature = F9.
 subsequent `ctx.stage()` call never executes — the throw propagates out of
 `run()` and halts the workflow.
 
-**Fix.** Use `send` instead of `sendAndWait` — it has no timeout and avoids
-the problem entirely. Only use `sendAndWait` when the user explicitly
-requests timeout-based waiting, and always pass an explicit timeout (default
-to 5 minutes if the user is unsure).
+**Root cause.** The raw Copilot SDK's `sendAndWait(options, timeout?)`
+defaults to a 60-second timeout that throws on expiry. Real agent work
+(planners, reviewers, orchestrators) routinely exceeds this.
+
+**Fix.** Use `send` instead. Inside an Atomic stage the runtime wraps
+`s.session.send()` so it blocks until `session.idle` with **no timeout** —
+the same blocking semantics as Claude's `query()` and OpenCode's
+`session.prompt()`. The wrapper lives in `wrapCopilotSend`
+(`src/sdk/runtime/executor.ts`) and is installed per-stage.
 
 ```ts
-// Default pattern — no timeout, no risk
+// Correct: send() in an Atomic stage blocks until idle, no timeout.
 await s.session.send({ prompt });
-
-// Only when the user explicitly wants timeout-gated waiting
-const SEND_TIMEOUT_MS = 5 * 60 * 1000; // ask the user for a value
-await s.session.sendAndWait({ prompt }, SEND_TIMEOUT_MS);
+const messages = await s.session.getMessages(); // safe to read
 ```
 
+**Do not reach for `sendAndWait` with a larger explicit timeout.** `send`
+already waits for idle; `sendAndWait` just adds a throw-on-timeout failure
+mode on top. If you catch yourself writing `sendAndWait(..., 5 * 60 * 1000)`
+to "be safe", you want `send`.
+
 ---
 
 ## F11. ~~Manual Claude session initialization~~ (resolved by runtime)

package/.agents/skills/workflow-creator/references/getting-started.md

@@ -234,7 +234,6 @@ The `@bastani/atomic/workflows` package exports the workflow authoring primitive
 - `ProviderClient<A>` — the `s.client` type, resolved by agent type
 - `ProviderSession<A>` — the `s.session` type, resolved by agent type
 - `ClaudeSessionWrapper` — Atomic wrapper for Claude sessions (exposes `s.session.query()`, which returns `SessionMessage[]`)
-- `ClaudeQueryDefaults` — per-stage query defaults (timeouts, poll interval) for Claude sessions
 - `SessionRef` — `string | SessionHandle<unknown>` for transcript/message lookups
 - `WorkflowContext` — top-level context passed to `.run()` callback
 - `WorkflowOptions` — `{ name, description? }` workflow metadata

package/.agents/skills/workflow-creator/references/session-config.md

@@ -19,16 +19,12 @@ await ctx.stage({ name: "..." }, {
 
 ### Session options (`sessionOpts` — 3rd arg to `ctx.stage()`)
 
-These are `ClaudeQueryDefaults` and set defaults for every `s.session.query()`
-call inside the callback. The available fields are: `pollIntervalMs`,
-`submitPresses`, `maxSubmitRounds`, `readyTimeoutMs`. Note that `timeoutMs` no
-longer exists — idle detection is automatic (pane capture for interactive
-stages, SDK streaming for headless stages).
+Claude has **no per-session options** — the type is `Record<string, never>` and the 3rd arg must be `{}`. Interactive delivery is driven entirely by the CLI's Stop hook; idle detection is automatic (pane capture for interactive stages, SDK streaming for headless stages).
+
+If you want to configure agent/permission/tools behavior for a **headless** Claude stage, pass those fields as the second argument to `s.session.query(prompt, options)` — they flow through as `Partial<SDKOptions>` to the Agent SDK (see the headless example below).
 
 ```ts
-await ctx.stage({ name: "..." }, {}, {
-  pollIntervalMs: 1_000,         // Poll interval for output
-}, async (s) => {
+await ctx.stage({ name: "..." }, {}, {}, async (s) => {
   await s.session.query((ctx.inputs.prompt ?? ""));
   s.save(s.sessionId);
 });
@@ -103,7 +99,7 @@ const result = query({
 the pane ID from `s.paneId` automatically. Call it inside the stage callback:
 
 ```ts
-import { extractAssistantText } from "@anthropic-ai/claude-agent-sdk";
+import { extractAssistantText } from "@bastani/atomic/workflows";
 
 await ctx.stage({ name: "..." }, {}, {}, async (s) => {
   const result = await s.session.query("Your prompt");
@@ -113,9 +109,6 @@ await ctx.stage({ name: "..." }, {}, {}, async (s) => {
 });
 ```
 
-The query defaults (poll interval, submit presses, etc.) can be configured via
-`sessionOpts` as shown above.
-
 For **headless stages**, SDK options (such as `permissionMode`, `agent`,
 `allowDangerouslySkipPermissions`) can be passed directly as the second
 argument to `s.session.query()`:

package/.agents/skills/workflow-creator/references/workflow-inputs.md

@@ -214,7 +214,7 @@ redefining the canonical version of a workflow in a way that confuses
 teammates or breaks automation.
 
 You'll still see shadowed local/global workflows in
-`atomic workflow -l` output so the collision is visible, but running
+`atomic workflow list` output so the collision is visible, but running
 `atomic workflow -n ralph -a claude` will always land on the builtin.
 
 The practical implication: **don't name a new workflow `ralph` or
@@ -225,7 +225,7 @@ this.
 
 ```bash
 # List everything, grouped by source
-atomic workflow -l
+atomic workflow list
 
 # Launch the picker for a pinned agent
 atomic workflow -a claude

package/.claude/agents/reviewer.md

@@ -80,7 +80,7 @@ OUTPUT FORMAT:
       "confidence_score": <float 0.0-1.0>,
       "priority": <int 0-3, optional>,
       "code_location": {
-        "absolute_file_path": "<file path>",
+        "file_path": "<repo-relative path>",
         "line_range": {"start": <int>, "end": <int>}
       }
     }
@@ -92,7 +92,7 @@ OUTPUT FORMAT:
 ```
 
 - **Do not** wrap the JSON in markdown fences or extra prose.
-- The code_location field is required and must include absolute_file_path and line_range.
+- The code_location field is required and must include file_path (repo-relative) and line_range.
 - Line ranges must be as short as possible for interpreting the issue (avoid ranges over 5–10 lines; pick the most suitable subrange).
 - The code_location should overlap with the diff.
 - Do not generate a PR fix.

package/.github/agents/reviewer.md

@@ -77,7 +77,7 @@ OUTPUT FORMAT:
       "confidence_score": <float 0.0-1.0>,
       "priority": <int 0-3, optional>,
       "code_location": {
-        "absolute_file_path": "<file path>",
+        "file_path": "<repo-relative path>",
         "line_range": {"start": <int>, "end": <int>}
       }
     }
@@ -89,7 +89,7 @@ OUTPUT FORMAT:
 ```
 
 - **Do not** wrap the JSON in markdown fences or extra prose.
-- The code_location field is required and must include absolute_file_path and line_range.
+- The code_location field is required and must include file_path (repo-relative) and line_range.
 - Line ranges must be as short as possible for interpreting the issue (avoid ranges over 5–10 lines; pick the most suitable subrange).
 - The code_location should overlap with the diff.
 - Do not generate a PR fix.

package/.opencode/agents/reviewer.md

@@ -85,7 +85,7 @@ OUTPUT FORMAT:
       "confidence_score": <float 0.0-1.0>,
       "priority": <int 0-3, optional>,
       "code_location": {
-        "absolute_file_path": "<file path>",
+        "file_path": "<repo-relative path>",
         "line_range": {"start": <int>, "end": <int>}
       }
     }
@@ -97,7 +97,7 @@ OUTPUT FORMAT:
 ```
 
 - **Do not** wrap the JSON in markdown fences or extra prose.
-- The code_location field is required and must include absolute_file_path and line_range.
+- The code_location field is required and must include file_path (repo-relative) and line_range.
 - Line ranges must be as short as possible for interpreting the issue (avoid ranges over 5–10 lines; pick the most suitable subrange).
 - The code_location should overlap with the diff.
 - Do not generate a PR fix.

package/dist/commands/cli/claude-stop-hook.d.ts

@@ -44,6 +44,7 @@ export declare function claudeHookDirs(): {
     marker: string;
     queue: string;
     release: string;
+    hil: string;
 };
 /** Options for {@link claudeStopHookCommand}. Primarily used by tests to shrink the wait budget. */
 export interface ClaudeStopHookOptions {

package/dist/commands/cli/claude-stop-hook.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"claude-stop-hook.d.ts","sourceRoot":"","sources":["../../../src/commands/cli/claude-stop-hook.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAOH,yEAAyE;AACzE,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAeD;;;;;GAKG;AACH,wBAAgB,cAAc,IAAI;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAOnF;AAED,oGAAoG;AACpG,MAAM,WAAW,qBAAqB;IACpC,4FAA4F;IAC5F,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,oDAAoD;IACpD,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAKD;;;;;;;;GAQG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,MAAM,CAAC,CAsGjB"}
+{"version":3,"file":"claude-stop-hook.d.ts","sourceRoot":"","sources":["../../../src/commands/cli/claude-stop-hook.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAOH,yEAAyE;AACzE,MAAM,WAAW,qBAAqB;IACpC,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAeD;;;;;GAKG;AACH,wBAAgB,cAAc,IAAI;IAAE,MAAM,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,CAQhG;AAED,oGAAoG;AACpG,MAAM,WAAW,qBAAqB;IACpC,4FAA4F;IAC5F,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,oDAAoD;IACpD,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAKD;;;;;;;;GAQG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,MAAM,CAAC,CAsGjB"}

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

@@ -63,16 +63,6 @@ export interface ClaudeSessionOptions {
  * ```
  */
 export declare function createClaudeSession(options: ClaudeSessionOptions): Promise<string>;
-/**
- * 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;
 /**
  * Returns true when the most recent assistant message in the transcript
  * ended with `stop_reason: "tool_use"` — i.e. the agent stopped the current
@@ -93,47 +83,19 @@ export declare function _hasUnresolvedHILTool(messages: SessionMessage[]): boole
  */
 export declare function _isMidAgentLoop(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>;
-/**
- * Path helpers for the transcript JSONL written by Claude Code.
- * @internal Exported for tests.
- */
-export declare function transcriptDir(): string;
-/** @internal Exported for tests. */
-export declare function transcriptPath(claudeSessionId: string): string;
-/**
- * Watch this session's transcript JSONL and call `onHIL` on every HIL-state
- * transition — independently of the Stop hook.
- *
- * Why not piggyback on the Stop hook? `AskUserQuestion` is a deferred tool
- * (`shouldDefer: true`, see Claude Code's
- * `src/tools/AskUserQuestionTool/AskUserQuestionTool.tsx`). While the question
- * is pending, Claude's agent loop blocks on the tool with
- * `needsFollowUp === true`, so `handleStopHooks` never runs
- * (`src/query.ts`: `if (!needsFollowUp)`). A watcher tied to the Stop-hook
- * marker would sleep through the entire HIL window and only wake up after
- * the user has already answered.
+ * Watch `~/.atomic/claude-hil/` for this session's marker file and fire
+ * `onHIL(true|false)` on create/unlink. Returns when `signal` is aborted.
  *
- * Watches the parent session directory rather than the file itself so the
- * attach is safe before Claude has created the JSONL on first query. Events
- * are filtered by `<sessionId>.jsonl`. Returns when `signal` is aborted.
+ * The marker is written by the `_claude-ask-hook enter` subcommand from
+ * Claude Code's `PreToolUse` hook (matched on `AskUserQuestion`) and removed
+ * by `_claude-ask-hook exit` from `PostToolUse` / `PostToolUseFailure`. That
+ * makes the signal deterministic and independent of Claude Code's batched
+ * JSONL flush timing, which used to hide the HIL window entirely when
+ * tool_use and tool_result landed in the same file write.
  *
  * @internal Exported for tests.
  */
-export declare function watchTranscriptForHIL(claudeSessionId: string, onHIL: (waiting: boolean) => void, signal: AbortSignal): Promise<void>;
+export declare function watchHILMarker(claudeSessionId: string, onHIL: (waiting: boolean) => void, signal: AbortSignal): Promise<void>;
 /**
  * Path of the directory where the claude-stop-hook writes marker files.
  * Each Claude turn creates `~/.atomic/claude-stop/<session_id>` which

package/dist/sdk/providers/claude.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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyDG;;AAsCH,wBA6Ta"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/claude/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyDG;;AAsCH,wBAwTa"}

package/dist/sdk/workflows/builtin/deep-research-codebase/copilot/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/copilot/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;;AA6CH,wBAiSa"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/copilot/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;;AA6CH,wBA4Ra"}

package/dist/sdk/workflows/builtin/deep-research-codebase/helpers/prompts.d.ts

@@ -51,7 +51,6 @@ export declare function buildScoutPrompt(opts: {
 export declare function buildLocatorPrompt(opts: {
     question: string;
     partition: PartitionUnit[];
-    root: string;
     scoutOverview: string;
     index: number;
     total: number;
@@ -60,7 +59,6 @@ export declare function buildLocatorPrompt(opts: {
 export declare function buildPatternFinderPrompt(opts: {
     question: string;
     partition: PartitionUnit[];
-    root: string;
     scoutOverview: string;
     index: number;
     total: number;
@@ -70,7 +68,6 @@ export declare function buildAnalyzerPrompt(opts: {
     question: string;
     partition: PartitionUnit[];
     locatorOutput: string;
-    root: string;
     scoutOverview: string;
     index: number;
     total: number;
@@ -80,20 +77,17 @@ export declare function buildOnlineResearcherPrompt(opts: {
     question: string;
     partition: PartitionUnit[];
     locatorOutput: string;
-    root: string;
     index: number;
     total: number;
 }): string;
 /** codebase-research-locator — find prior research docs about the topic. */
 export declare function buildHistoryLocatorPrompt(opts: {
     question: string;
-    root: string;
 }): string;
 /** codebase-research-analyzer — synthesize insights from located research docs. */
 export declare function buildHistoryAnalyzerPrompt(opts: {
     question: string;
     locatorOutput: string;
-    root: string;
 }): string;
 export declare function buildAggregatorPrompt(opts: {
     question: string;

package/dist/sdk/workflows/builtin/deep-research-codebase/helpers/prompts.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/opencode/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;;AAsCH,wBAoVa"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/deep-research-codebase/opencode/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;;AAsCH,wBA8Ua"}

package/dist/sdk/workflows/builtin/ralph/helpers/prompts.d.ts

@@ -19,7 +19,7 @@ export declare const ReviewFindingSchema: z.ZodObject<{
     confidence_score: z.ZodOptional<z.ZodNumber>;
     priority: z.ZodOptional<z.ZodNumber>;
     code_location: z.ZodOptional<z.ZodObject<{
-        absolute_file_path: z.ZodString;
+        file_path: z.ZodString;
         line_range: z.ZodObject<{
             start: z.ZodNumber;
             end: z.ZodNumber;
@@ -34,7 +34,7 @@ export declare const ReviewResultSchema: z.ZodObject<{
         confidence_score: z.ZodOptional<z.ZodNumber>;
         priority: z.ZodOptional<z.ZodNumber>;
         code_location: z.ZodOptional<z.ZodObject<{
-            absolute_file_path: z.ZodString;
+            file_path: z.ZodString;
             line_range: z.ZodObject<{
                 start: z.ZodNumber;
                 end: z.ZodNumber;
@@ -53,7 +53,7 @@ export declare const REVIEW_RESULT_JSON_SCHEMA: z.core.ZodStandardJSONSchemaPayl
         confidence_score: z.ZodOptional<z.ZodNumber>;
         priority: z.ZodOptional<z.ZodNumber>;
         code_location: z.ZodOptional<z.ZodObject<{
-            absolute_file_path: z.ZodString;
+            file_path: z.ZodString;
             line_range: z.ZodObject<{
                 start: z.ZodNumber;
                 end: z.ZodNumber;
@@ -143,7 +143,7 @@ export interface ReviewFinding {
     confidence_score?: number;
     priority?: number;
     code_location?: {
-        absolute_file_path: string;
+        file_path: string;
         line_range: {
             start: number;
             end: number;

package/dist/sdk/workflows/builtin/ralph/helpers/prompts.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"prompts.d.ts","sourceRoot":"","sources":["../../../../../../src/sdk/workflows/builtin/ralph/helpers/prompts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAMxB,8CAA8C;AAC9C,eAAO,MAAM,mBAAmB;;;;;;;;;;;;iBAsC9B,CAAC;AAEH,wDAAwD;AACxD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;iBAgB7B,CAAC;AAEH,kFAAkF;AAClF,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;kBAAqC,CAAC;AAE5E,mEAAmE;AACnE,MAAM,WAAW,sBAAsB;IACrC,oFAAoF;IACpF,UAAU,EAAE,YAAY,GAAG,IAAI,CAAC;IAChC,8DAA8D;IAC9D,GAAG,EAAE,MAAM,CAAC;CACb;AAED;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAChC,CAAC,EAAE,sBAAsB,EACzB,CAAC,EAAE,sBAAsB,GACxB,sBAAsB,CA4CxB;AAMD,MAAM,WAAW,cAAc;IAC7B,0EAA0E;IAC1E,SAAS,EAAE,MAAM,CAAC;IAClB,wEAAwE;IACxE,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;;;;;;;GAQG;AACH,wBAAgB,kBAAkB,CAChC,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,cAAiC,GACzC,MAAM,CA2GR;AAKD,MAAM,WAAW,mBAAmB;IAClC;;;;;;OAMG;IACH,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED;;;;;;;;;GASG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,MAAM,EACZ,OAAO,GAAE,mBAAwB,GAChC,MAAM,CAwIR;AAMD,0EAA0E;AAC1E,MAAM,WAAW,qBAAqB;IACpC,iDAAiD;IACjD,OAAO,EAAE,MAAM,CAAC;IAChB,kDAAkD;IAClD,QAAQ,EAAE,MAAM,CAAC;IACjB,wDAAwD;IACxD,aAAa,EAAE,MAAM,CAAC;CACvB;AAED;;;;;;;;GAQG;AACH,wBAAgB,0BAA0B,IAAI,qBAAqB,CAwGlE;AAMD,oDAAoD;AACpD,MAAM,WAAW,aAAa;IAC5B,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,aAAa,CAAC,EAAE;QACd,SAAS,EAAE,MAAM,CAAC;QAClB,UAAU,EAAE;YAAE,KAAK,EAAE,MAAM,CAAC;YAAC,GAAG,EAAE,MAAM,CAAA;SAAE,CAAC;KAC5C,CAAC;CACH;AAED,mCAAmC;AACnC,MAAM,WAAW,YAAY;IAC3B,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,wBAAwB,CAAC,EAAE,MAAM,CAAC;CACnC;AAED,MAAM,WAAW,aAAa;IAC5B;;;;;OAKG;IACH,SAAS,EAAE;QACT,UAAU,EAAE,MAAM,CAAC;QACnB,QAAQ,EAAE,MAAM,CAAC;QACjB,WAAW,EAAE,MAAM,CAAC;QACpB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;IACF,2DAA2D;IAC3D,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB;;;;OAIG;IACH,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB;;;;;OAKG;IACH,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;;;GAIG;AACH,wBAAgB,iBAAiB,CAC/B,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,aAAa,GACrB,MAAM,CAgMR;AAMD,MAAM,WAAW,eAAe;IAC9B,8DAA8D;IAC9D,SAAS,EAAE,MAAM,CAAC;IAClB;;;OAGG;IACH,SAAS,EAAE;QACT,UAAU,EAAE,MAAM,CAAC;QACnB,QAAQ,EAAE,MAAM,CAAC;QACjB,WAAW,EAAE,MAAM,CAAC;QACpB,UAAU,EAAE,MAAM,CAAC;QACnB,MAAM,EAAE,MAAM,EAAE,CAAC;KAClB,CAAC;CACH;AAED;;;;;GAKG;AACH,wBAAgB,yBAAyB,CACvC,MAAM,EAAE,YAAY,GAAG,IAAI,EAC3B,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,eAAe,GACvB,MAAM,CAoHR;AAMD;;;;;;;;GAQG;AACH,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,MAAM,GAAG,YAAY,GAAG,IAAI,CAgDtE;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE;IACvC,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,mBAAmB,EAAE,MAAM,CAAC;IAC5B,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,wBAAwB,CAAC,EAAE,MAAM,CAAC;CACnC,GAAG,YAAY,CAUf;AAED;;;;;;;GAOG;AACH,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,CAS5D"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.5.22",
+  "version": "0.5.23-0",
   "description": "Configuration management CLI and SDK for coding agents",
   "type": "module",
   "license": "MIT",

package/src/cli.ts

@@ -347,6 +347,21 @@ Examples:
             process.exit(exitCode);
         });
 
+    // ── Internal: Claude AskUserQuestion hook handler ─────────────────────
+    program
+        .command("_claude-ask-hook", { hidden: true })
+        .description("Internal: Claude Code AskUserQuestion hook handler — writes/removes HIL marker")
+        .argument("<mode>", "enter (PreToolUse) or exit (PostToolUse / PostToolUseFailure)")
+        .action(async (mode: string) => {
+            if (mode !== "enter" && mode !== "exit") {
+                console.error(`[claude-ask-hook] Invalid mode: ${mode}`);
+                process.exit(0);
+            }
+            const { claudeAskHookCommand } = await import("./commands/cli/claude-ask-hook.ts");
+            const exitCode = await claudeAskHookCommand(mode);
+            process.exit(exitCode);
+        });
+
     // ── Completions command ────────────────────────────────────────────────
     program
         .command("completions")
@@ -398,7 +413,8 @@ async function main(): Promise<void> {
             argv.includes("-h") ||
             argv[0] === "completions" ||
             argv[0] === "_footer" ||
-            argv[0] === "_claude-stop-hook";
+            argv[0] === "_claude-stop-hook" ||
+            argv[0] === "_claude-ask-hook";
 
         if (!isInfoCommand) {
             const { autoSyncIfStale } = await import("./services/system/auto-sync.ts");