@bastani/atomic 0.5.19 → 0.5.20

package/.claude/settings.json

@@ -21,5 +21,17 @@
     "kotlin-lsp@claude-plugins-official": true,
     "swift-lsp@claude-plugins-official": true,
     "lua-lsp@claude-plugins-official": true
+  },
+  "hooks": {
+    "Stop": [
+      {
+        "hooks": [
+          {
+            "type": "command",
+            "command": "atomic _claude-stop-hook"
+          }
+        ]
+      }
+    ]
   }
 }

package/.mcp.json

@@ -3,7 +3,9 @@
     "github": {
       "type": "http",
       "url": "https://api.githubcopilot.com/mcp",
-      "headers": { "Authorization": "Bearer ${GITHUB_PERSONAL_ACCESS_TOKEN}" }
+      "headers": {
+        "Authorization": "Bearer ${GITHUB_PERSONAL_ACCESS_TOKEN}"
+      }
     }
   }
 }

package/dist/sdk/components/workflow-picker-panel.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"workflow-picker-panel.d.ts","sourceRoot":"","sources":["../../../src/sdk/components/workflow-picker-panel.tsx"],"names":[],"mappings":"AAAA,sCAAsC;AACtC;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AAEH,OAAO,EAEL,KAAK,WAAW,EAIjB,MAAM,eAAe,CAAC;AAQvB,OAAO,EAAgB,KAAK,aAAa,EAAE,MAAM,qBAAqB,CAAC;AACvE,OAAO,KAAK,EAAE,SAAS,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAC5D,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,yBAAyB,CAAC;AASpE,MAAM,WAAW,WAAW;IAC1B,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,EAAE,MAAM,CAAC;IACxB,iBAAiB,EAAE,MAAM,CAAC;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,aAAa,EAAE,MAAM,EAAE,OAAO,GAAG,WAAW,CAuBlF;AAeD,KAAK,MAAM,GAAG,OAAO,GAAG,QAAQ,GAAG,SAAS,CAAC;AAG7C,qEAAqE;AACrE,MAAM,WAAW,oBAAoB;IACnC,kDAAkD;IAClD,QAAQ,EAAE,oBAAoB,CAAC;IAC/B,mFAAmF;IACnF,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAChC;AA6BD;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAsBvE;AAID,UAAU,SAAS;IACjB,QAAQ,EAAE,oBAAoB,CAAC;IAC/B,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,KAAK,OAAO,GACR;IAAE,IAAI,EAAE,SAAS,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,GACnC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,SAAS,CAAA;CAAE,CAAC;AAExC;;;GAGG;AACH,wBAAgB,iBAAiB,CAC/B,SAAS,EAAE,oBAAoB,EAAE,GAChC,oBAAoB,EAAE,CASxB;AAED,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,oBAAoB,EAAE,GAChC,SAAS,EAAE,CAkCb;AAED,wBAAgB,SAAS,CAAC,OAAO,EAAE,SAAS,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,EAAE,CAexE;AAID,wBAAgB,YAAY,CAAC,KAAK,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAIzE;AAyiCD,UAAU,cAAc;IACtB,KAAK,EAAE,WAAW,CAAC;IACnB,KAAK,EAAE,SAAS,CAAC;IACjB,SAAS,EAAE,oBAAoB,EAAE,CAAC;IAClC,QAAQ,EAAE,CAAC,MAAM,EAAE,oBAAoB,KAAK,IAAI,CAAC;IACjD,QAAQ,EAAE,MAAM,IAAI,CAAC;CACtB;AAED,wBAAgB,cAAc,CAAC,EAC7B,KAAK,EACL,KAAK,EACL,SAAS,EACT,QAAQ,EACR,QAAQ,GACT,EAAE,cAAc,6BA0IhB;AAID,MAAM,WAAW,0BAA0B;IACzC,KAAK,EAAE,SAAS,CAAC;IACjB,yEAAyE;IACzE,SAAS,EAAE,oBAAoB,EAAE,CAAC;CACnC;AAED;;;;GAIG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAc;IAC9B,OAAO,CAAC,IAAI,CAAO;IACnB,OAAO,CAAC,SAAS,CAAS;IAC1B,OAAO,CAAC,gBAAgB,CACjB;IACP,OAAO,CAAC,gBAAgB,CAAuC;IAE/D,OAAO;IAyCP;;;;OAIG;WACU,MAAM,CACjB,OAAO,EAAE,0BAA0B,GAClC,OAAO,CAAC,mBAAmB,CAAC;IAgB/B,0EAA0E;IAC1E,MAAM,CAAC,kBAAkB,CACvB,QAAQ,EAAE,WAAW,EACrB,OAAO,EAAE,0BAA0B,GAClC,mBAAmB;IAItB;;;;OAIG;IACH,gBAAgB,IAAI,OAAO,CAAC,oBAAoB,GAAG,IAAI,CAAC;IAIxD,8CAA8C;IAC9C,OAAO,IAAI,IAAI;IAef,OAAO,CAAC,YAAY;IAOpB,OAAO,CAAC,YAAY;CAMrB"}

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

@@ -90,6 +90,55 @@ export declare function _hasUnresolvedHILTool(messages: SessionMessage[]): boole
  * 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 of the directory where the claude-stop-hook writes marker files.
+ * Each Claude turn creates `~/.atomic/claude-stop/<session_id>` atomically
+ * via rename, which triggers the `fs.watch` event in `waitForIdle`.
+ *
+ * @internal Exported for unit tests.
+ */
+export declare function markerDir(): string;
+/**
+ * Return the marker file path for a given Claude session ID.
+ *
+ * @internal Exported for unit tests.
+ */
+export declare function markerPath(claudeSessionId: string): string;
+/**
+ * Wait for the Claude session to become idle using `fs.watch` on the
+ * `~/.atomic/claude-stop/` marker directory.
+ *
+ * When Claude finishes a turn, the `atomic _claude-stop-hook` Stop hook writes
+ * `~/.atomic/claude-stop/<session_id>` atomically (tmp file + rename).  The
+ * rename triggers an OS-native `fs.watch` event on the parent directory —
+ * far more reliable than polling tmux pane glyphs, which vary between Claude
+ * Code versions.
+ *
+ * Algorithm:
+ * 1. Watch the marker directory for events whose `filename` matches
+ *    `claudeSessionId`.
+ * 2. On a matching event, read the session transcript via
+ *    `getSessionMessages` and test `_hasUnresolvedHILTool`.
+ *    - If unresolved HIL: call `onHIL(true)`, unlink the marker (so the next
+ *      turn's hook can fire again), and continue watching.
+ *    - If no unresolved HIL after a prior HIL: call `onHIL(false)`.
+ *    - If truly idle: slice messages from `transcriptBeforeCount` and return.
+ * 3. Clean up the `fs.watch` watcher on any exit path via AbortController.
+ *
+ * The function signature is intentionally identical to the previous polling
+ * implementation so all callers remain unchanged.
+ *
+ * @param paneId           - tmux pane (kept in signature for caller compat; not used here)
+ * @param claudeSessionId  - Claude's session UUID (used to identify marker file)
+ * @param transcriptBeforeCount - number of messages in transcript before this turn
+ * @param beforeContent    - (unused) pane content before send; kept for compat
+ * @param pollIntervalMs   - (unused) kept for compat; watch is event-driven
+ * @param onHIL            - optional callback for HIL state changes
+ */
+/**
+ * @internal Exported for unit tests.
+ */
+export declare function waitForIdle(_paneId: string, claudeSessionId: string | undefined, transcriptBeforeCount: number, _beforeContent: string, _pollIntervalMs: number, onHIL?: (waiting: boolean) => void): Promise<SessionMessage[]>;
 export interface ClaudeQueryOptions {
     /** tmux pane ID where Claude is running */
     paneId: string;

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,EAGL,KAAK,cAAc,EACnB,KAAK,cAAc,EACnB,KAAK,OAAO,IAAI,UAAU,EAC3B,MAAM,gCAAgC,CAAC;AAgDxC;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI,CAEvD;AAYD,MAAM,WAAW,oBAAoB;IACnC,kDAAkD;IAClD,MAAM,EAAE,MAAM,CAAC;IACf;;;OAGG;IACH,UAAU,EAAE,MAAM,CAAC;IACnB,sIAAsI;IACtI,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;IACrB,sEAAsE;IACtE,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AACH,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,IAAI,CAAC,CAetF;AAsHD;;;;;;;;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;AAMD;;;;;;GAMG;AACH,wBAAgB,SAAS,IAAI,MAAM,CAElC;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAE1D;AAyBD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8BG;AACH;;GAEG;AACH,wBAAsB,WAAW,CAC/B,OAAO,EAAE,MAAM,EACf,eAAe,EAAE,MAAM,GAAG,SAAS,EACnC,qBAAqB,EAAE,MAAM,EAC7B,cAAc,EAAE,MAAM,EACtB,eAAe,EAAE,MAAM,EACvB,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,GACjC,OAAO,CAAC,cAAc,EAAE,CAAC,CAuE3B;AAMD,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,CAiIxF;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;IACzE,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;gBAGlC,MAAM,EAAE,MAAM,EACd,IAAI,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,EAAE,CAAC;QAAC,cAAc,CAAC,EAAE,MAAM,CAAA;KAAE,YAAK,EAC5D,UAAU,EAAE,MAAM;IAOpB,gFAAgF;IAC1E,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAS5B,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/services/config/definitions.d.ts

@@ -16,7 +16,7 @@ export interface AgentConfig {
     install_url: string;
     /** Paths to exclude when copying (relative to folder) */
     exclude: string[];
-    /** Project files managed by `atomic init` for provider onboarding */
+    /** Project files applied during `atomic chat` preflight for provider onboarding */
     onboarding_files: Array<{
         source: string;
         destination: string;

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

@@ -1 +1 @@
-{"version":3,"file":"definitions.d.ts","sourceRoot":"","sources":["../../../src/services/config/definitions.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,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,CA2DtD,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"}
+{"version":3,"file":"definitions.d.ts","sourceRoot":"","sources":["../../../src/services/config/definitions.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,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,mFAAmF;IACnF,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,CA2DtD,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"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/atomic",
-  "version": "0.5.19",
+  "version": "0.5.20",
   "description": "Configuration management CLI and SDK for coding agents",
   "type": "module",
   "license": "MIT",

package/src/cli.ts

@@ -283,6 +283,16 @@ Examples:
             process.exit(exitCode);
         });
 
+    // ── Internal: Claude Stop hook handler ────────────────────────────────
+    program
+        .command("_claude-stop-hook", { hidden: true })
+        .description("Internal: Claude Code Stop hook handler — writes a marker file for idle detection")
+        .action(async () => {
+            const { claudeStopHookCommand } = await import("./commands/cli/claude-stop-hook.ts");
+            const exitCode = await claudeStopHookCommand();
+            process.exit(exitCode);
+        });
+
     // ── Completions command ────────────────────────────────────────────────
     program
         .command("completions")
@@ -333,7 +343,8 @@ async function main(): Promise<void> {
             argv.includes("--help") ||
             argv.includes("-h") ||
             argv[0] === "completions" ||
-            argv[0] === "_footer";
+            argv[0] === "_footer" ||
+            argv[0] === "_claude-stop-hook";
 
         if (!isInfoCommand) {
             const { autoSyncIfStale } = await import("./services/system/auto-sync.ts");

package/src/commands/cli/chat/index.ts

@@ -190,7 +190,15 @@ export async function chatCommand(options: ChatCommandOptions = {}): Promise<num
   const args = await buildAgentArgs(agentType, passthroughArgs, projectRoot);
   const cmd = [config.cmd, ...args];
   const overrides = await getProviderOverrides(agentType, projectRoot);
-  const envVars = { ...config.env_vars, ...overrides.envVars };
+  // ATOMIC_AGENT must be baked into the launcher env so the agent CLI
+  // (and anything it spawns) can read it. `setSessionEnv` below only
+  // affects processes spawned *after* the initial command, so it cannot
+  // populate the env of the agent CLI that `new-session` kicks off.
+  const envVars = {
+    ...config.env_vars,
+    ...overrides.envVars,
+    ATOMIC_AGENT: agentType,
+  };
 
   // ── No TTY: tmux attach requires a real terminal ──
   if (!process.stdin.isTTY) {

package/src/commands/cli/claude-stop-hook.test.ts

@@ -0,0 +1,140 @@
+/**
+ * Tests for claudeStopHookCommand.
+ *
+ * Strategy: monkey-patch `Bun.stdin.text` to return preset strings so we can
+ * call the function directly without spawning subprocesses.  This is
+ * consistent with how other CLI-command tests in this directory work.
+ *
+ * Filesystem isolation: we use `crypto.randomUUID()` for unique session IDs
+ * and clean up in `afterEach` so test runs never collide with each other
+ * or with real marker files.
+ */
+
+import { describe, test, expect, afterEach, mock, spyOn } from "bun:test";
+import { access, rm } from "node:fs/promises";
+import { join } from "node:path";
+import { homedir } from "node:os";
+import { claudeStopHookCommand } from "./claude-stop-hook.ts";
+
+// Paths we'll need in every test.
+const markerDir = join(homedir(), ".atomic", "claude-stop");
+
+/** Returns true when a file exists at `filePath`. */
+async function fileExists(filePath: string): Promise<boolean> {
+  try {
+    await access(filePath);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
+/** Patch `Bun.stdin.text` for the duration of one test. */
+function mockStdin(text: string): void {
+  // Bun.stdin is a readonly property on the global `Bun` object.
+  // We reach it through the prototype chain the same way other tests
+  // in this repo patch globals (e.g. process.stdout.write).
+  (Bun.stdin as { text: () => Promise<string> }).text = () =>
+    Promise.resolve(text);
+}
+
+// ---------------------------------------------------------------------------
+// Cleanup
+// ---------------------------------------------------------------------------
+
+const sessionIdsToClean: string[] = [];
+
+afterEach(async () => {
+  // Remove any marker files created during the test.
+  for (const id of sessionIdsToClean) {
+    await rm(join(markerDir, id), { force: true });
+    await rm(join(markerDir, `${id}.tmp`), { force: true });
+  }
+  sessionIdsToClean.length = 0;
+});
+
+// ---------------------------------------------------------------------------
+// Tests
+// ---------------------------------------------------------------------------
+
+describe("claudeStopHookCommand", () => {
+  // 1. Valid payload → writes marker file
+  test("valid payload writes marker file and returns 0", async () => {
+    const sessionId = crypto.randomUUID();
+    sessionIdsToClean.push(sessionId);
+
+    mockStdin(JSON.stringify({ session_id: sessionId }));
+
+    const code = await claudeStopHookCommand();
+
+    expect(code).toBe(0);
+    expect(await fileExists(join(markerDir, sessionId))).toBe(true);
+    expect(await fileExists(join(markerDir, `${sessionId}.tmp`))).toBe(false);
+  });
+
+  // 2. stop_hook_active: true → no-op
+  test("stop_hook_active:true is a no-op and returns 0", async () => {
+    const sessionId = crypto.randomUUID();
+    sessionIdsToClean.push(sessionId);
+
+    mockStdin(
+      JSON.stringify({ session_id: sessionId, stop_hook_active: true }),
+    );
+
+    const code = await claudeStopHookCommand();
+
+    expect(code).toBe(0);
+    expect(await fileExists(join(markerDir, sessionId))).toBe(false);
+    expect(await fileExists(join(markerDir, `${sessionId}.tmp`))).toBe(false);
+  });
+
+  // 3. Malformed JSON → returns 0, logs to console.error
+  test("malformed JSON returns 0 and logs an error", async () => {
+    mockStdin("not json {{{");
+
+    // Spy on console.error so the error doesn't bleed into test output.
+    const errorSpy = spyOn(console, "error").mockImplementation(() => {});
+
+    const code = await claudeStopHookCommand();
+
+    expect(code).toBe(0);
+    expect(errorSpy).toHaveBeenCalled();
+
+    errorSpy.mockRestore();
+  });
+
+  // 4. Missing session_id → returns 0, logs to console.error
+  test("missing session_id returns 0 and logs an error", async () => {
+    mockStdin(JSON.stringify({}));
+
+    const errorSpy = spyOn(console, "error").mockImplementation(() => {});
+
+    const code = await claudeStopHookCommand();
+
+    expect(code).toBe(0);
+    expect(errorSpy).toHaveBeenCalled();
+
+    errorSpy.mockRestore();
+  });
+
+  // 5. Extra payload fields are tolerated
+  test("valid payload with optional fields writes marker and returns 0", async () => {
+    const sessionId = crypto.randomUUID();
+    sessionIdsToClean.push(sessionId);
+
+    mockStdin(
+      JSON.stringify({
+        session_id: sessionId,
+        transcript_path: "/tmp/transcript.json",
+        cwd: "/home/user/project",
+        stop_hook_active: false,
+      }),
+    );
+
+    const code = await claudeStopHookCommand();
+
+    expect(code).toBe(0);
+    expect(await fileExists(join(markerDir, sessionId))).toBe(true);
+    expect(await fileExists(join(markerDir, `${sessionId}.tmp`))).toBe(false);
+  });
+});

package/src/commands/cli/claude-stop-hook.ts

@@ -0,0 +1,90 @@
+/**
+ * Claude Stop Hook command — internal handler for Claude Code's Stop hook.
+ *
+ * Claude invokes `atomic _claude-stop-hook` at the end of every turn,
+ * piping a JSON payload via stdin. This handler writes a marker file that
+ * another part of the system watches via `fs.watch`, replacing tmux-pane-
+ * scraping idle detection with a clean event-driven approach.
+ *
+ * Usage (configured in Claude's Stop hook):
+ *   atomic _claude-stop-hook
+ *
+ * Payload (JSON via stdin):
+ *   {
+ *     "session_id": "abc123",
+ *     "transcript_path": "/path/to/transcript",
+ *     "cwd": "/path/to/cwd",
+ *     "stop_hook_active": false
+ *   }
+ */
+
+import fs from "node:fs/promises";
+import path from "node:path";
+import os from "node:os";
+
+/** Shape of the JSON payload Claude pipes to the Stop hook via stdin. */
+export interface ClaudeStopHookPayload {
+  session_id: string;
+  transcript_path?: string;
+  cwd?: string;
+  stop_hook_active?: boolean;
+}
+
+/**
+ * Type guard to verify that a parsed value conforms to ClaudeStopHookPayload.
+ */
+function isClaudeStopHookPayload(value: unknown): value is ClaudeStopHookPayload {
+  if (typeof value !== "object" || value === null) return false;
+  const obj = value as Record<string, unknown>;
+  if (typeof obj["session_id"] !== "string") return false;
+  if (obj["transcript_path"] !== undefined && typeof obj["transcript_path"] !== "string") return false;
+  if (obj["cwd"] !== undefined && typeof obj["cwd"] !== "string") return false;
+  if (obj["stop_hook_active"] !== undefined && typeof obj["stop_hook_active"] !== "boolean") return false;
+  return true;
+}
+
+/**
+ * Handler for the hidden `_claude-stop-hook` subcommand.
+ *
+ * Returns an exit code (0 on success or benign failure).  The caller
+ * in src/cli.ts does `process.exit(exitCode)`, so we just return the code.
+ *
+ * We always return 0 — a non-zero exit would surface as a hook error in
+ * Claude's transcript, which is not what we want.
+ */
+export async function claudeStopHookCommand(): Promise<number> {
+  // 1. Read stdin
+  const raw = await Bun.stdin.text();
+
+  // 2. Parse JSON
+  let payload: ClaudeStopHookPayload;
+  try {
+    const parsed: unknown = JSON.parse(raw);
+    if (!isClaudeStopHookPayload(parsed)) {
+      console.error("[claude-stop-hook] Invalid payload: missing or malformed 'session_id'");
+      return 0;
+    }
+    payload = parsed;
+  } catch {
+    console.error("[claude-stop-hook] Failed to parse stdin as JSON");
+    return 0;
+  }
+
+  // 3. Guard against infinite Stop-hook loops
+  if (payload.stop_hook_active === true) {
+    return 0;
+  }
+
+  // 4. Write the marker file atomically
+  const markerDir = path.join(os.homedir(), ".atomic", "claude-stop");
+  await fs.mkdir(markerDir, { recursive: true });
+
+  const tmpPath = path.join(markerDir, `${payload.session_id}.tmp`);
+  const finalPath = path.join(markerDir, payload.session_id);
+
+  // Write contents — the watcher only cares that the file appears.
+  await Bun.write(tmpPath, raw);
+  await fs.rename(tmpPath, finalPath);
+
+  return 0;
+}

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

@@ -1,5 +1,5 @@
 /**
- * Automatic project setup — replaces the interactive `atomic init` command.
+ * Automatic project setup.
  *
  * Applies onboarding files (MCP configs, settings). Called transparently
  * during `atomic chat` preflight so users never need to think about

package/src/sdk/components/workflow-picker-panel.tsx

@@ -572,6 +572,21 @@ function TextAreaContent({
   const onInputRef = useLatest(onInput);
   const lastTextRef = useRef(value);
 
+  // Read plainText on the next microtask so the textarea has applied the
+  // keystroke/paste before we observe its content, then fire onInput if
+  // it changed.
+  const flushPending = useCallback(() => {
+    queueMicrotask(() => {
+      const inst = instanceRef.current;
+      if (!inst) return;
+      const current = inst.plainText;
+      if (current !== lastTextRef.current) {
+        lastTextRef.current = current;
+        onInputRef.current(current);
+      }
+    });
+  }, []);
+
   const refCallback = useCallback((instance: TextareaRenderable | null) => {
     instanceRef.current = instance;
   }, []);
@@ -585,23 +600,14 @@ function TextAreaContent({
     }
   }, [value]);
 
-  // Detect text changes after each keypress. The native Zig edit buffer's
-  // "content-changed" event is unreliable for propagating to the JS
-  // _contentChangeListener in certain installed environments. Instead,
-  // we hook into useKeyboard (which fires before the textarea processes
-  // the key) and defer the read with queueMicrotask so the textarea has
+  // flushPending fires on each keystroke via useKeyboard; onPaste handles
+  // bracketed pastes (which don't fire keydown). The native Zig edit
+  // buffer's "content-changed" event is unreliable for propagating to the
+  // JS _contentChangeListener in certain installed environments, so we
+  // hook into useKeyboard (which fires before the textarea processes the
+  // key) and defer the read with queueMicrotask so the textarea has
   // processed the keystroke by the time we read plainText.
-  useKeyboard(useCallback(() => {
-    queueMicrotask(() => {
-      const inst = instanceRef.current;
-      if (!inst) return;
-      const current = inst.plainText;
-      if (current !== lastTextRef.current) {
-        lastTextRef.current = current;
-        onInputRef.current(current);
-      }
-    });
-  }, []));
+  useKeyboard(flushPending);
 
   return (
     <textarea
@@ -616,6 +622,7 @@ function TextAreaContent({
       placeholderColor={theme.textDim}
       wrapMode="word"
       flexGrow={1}
+      onPaste={flushPending}
     />
   );
 }

package/src/sdk/providers/claude.ts

@@ -37,10 +37,11 @@ import {
   waitForPaneReady,
   attemptSubmitRounds,
 } from "../runtime/tmux.ts";
-import { watch } from "node:fs/promises";
+import { watch, unlink, mkdir } from "node:fs/promises";
 import { existsSync, writeFileSync } from "node:fs";
 import { join } from "node:path";
 import { randomUUID } from "node:crypto";
+import os from "node:os";
 
 // ---------------------------------------------------------------------------
 // Session tracking — ensures createClaudeSession is called before claudeQuery
@@ -346,95 +347,161 @@ export async function _runHILWatcher(
 // Helpers
 // ---------------------------------------------------------------------------
 
+/**
+ * Path of the directory where the claude-stop-hook writes marker files.
+ * Each Claude turn creates `~/.atomic/claude-stop/<session_id>` atomically
+ * via rename, which triggers the `fs.watch` event in `waitForIdle`.
+ *
+ * @internal Exported for unit tests.
+ */
+export function markerDir(): string {
+  return join(os.homedir(), ".atomic", "claude-stop");
+}
+
+/**
+ * Return the marker file path for a given Claude session ID.
+ *
+ * @internal Exported for unit tests.
+ */
+export function markerPath(claudeSessionId: string): string {
+  return join(markerDir(), claudeSessionId);
+}
+
+/**
+ * Ensure the marker directory exists and remove any stale marker left from a
+ * previous turn of this session. Call this BEFORE submitting the prompt so
+ * the subsequent `waitForIdle` watch loop doesn't fire on a stale file.
+ *
+ * Ignores ENOENT on `unlink` — the file simply doesn't exist yet.
+ */
+async function clearStaleMarker(claudeSessionId: string): Promise<void> {
+  await mkdir(markerDir(), { recursive: true });
+  try {
+    await unlink(markerPath(claudeSessionId));
+  } catch (e: unknown) {
+    // ENOENT is expected — ignore it; rethrow anything else
+    if (!(e instanceof Error && "code" in e && (e as NodeJS.ErrnoException).code === "ENOENT")) {
+      throw e;
+    }
+  }
+}
+
 // ---------------------------------------------------------------------------
-// Idle detection via pane capture
+// Idle detection via marker file watch
 // ---------------------------------------------------------------------------
 
 /**
- * Wait for the Claude session to become idle by polling the tmux pane.
+ * Wait for the Claude session to become idle using `fs.watch` on the
+ * `~/.atomic/claude-stop/` marker directory.
+ *
+ * When Claude finishes a turn, the `atomic _claude-stop-hook` Stop hook writes
+ * `~/.atomic/claude-stop/<session_id>` atomically (tmp file + rename).  The
+ * rename triggers an OS-native `fs.watch` event on the parent directory —
+ * far more reliable than polling tmux pane glyphs, which vary between Claude
+ * Code versions.
  *
- * Interactive Claude Code sessions don't write idle or result events to the
- * JSONL session file (those only flow through the SDK streaming output for
- * headless consumers). The pane prompt indicator is the only reliable idle
- * signal for interactive sessions.
+ * Algorithm:
+ * 1. Watch the marker directory for events whose `filename` matches
+ *    `claudeSessionId`.
+ * 2. On a matching event, read the session transcript via
+ *    `getSessionMessages` and test `_hasUnresolvedHILTool`.
+ *    - If unresolved HIL: call `onHIL(true)`, unlink the marker (so the next
+ *      turn's hook can fire again), and continue watching.
+ *    - If no unresolved HIL after a prior HIL: call `onHIL(false)`.
+ *    - If truly idle: slice messages from `transcriptBeforeCount` and return.
+ * 3. Clean up the `fs.watch` watcher on any exit path via AbortController.
  *
- * Once idle is detected, assistant output is extracted from the session
- * transcript via `getSessionMessages()` rather than scraping the pane —
- * the transcript has structured content blocks, not terminal escape codes.
+ * The function signature is intentionally identical to the previous polling
+ * implementation so all callers remain unchanged.
  *
- * No timeout is imposed. The loop runs until the pane shows the idle prompt.
+ * @param paneId           - tmux pane (kept in signature for caller compat; not used here)
+ * @param claudeSessionId  - Claude's session UUID (used to identify marker file)
+ * @param transcriptBeforeCount - number of messages in transcript before this turn
+ * @param beforeContent    - (unused) pane content before send; kept for compat
+ * @param pollIntervalMs   - (unused) kept for compat; watch is event-driven
+ * @param onHIL            - optional callback for HIL state changes
  */
-async function waitForIdle(
-  paneId: string,
+/**
+ * @internal Exported for unit tests.
+ */
+export async function waitForIdle(
+  _paneId: string,
   claudeSessionId: string | undefined,
   transcriptBeforeCount: number,
-  beforeContent: string,
-  pollIntervalMs: number,
+  _beforeContent: string,
+  _pollIntervalMs: number,
   onHIL?: (waiting: boolean) => void,
 ): Promise<SessionMessage[]> {
-  // Give Claude time to start processing before first poll
-  await Bun.sleep(3_000);
+  // Without a session ID we cannot watch the marker directory — return empty.
+  if (!claudeSessionId) {
+    return [];
+  }
 
-  let hilActive = false;
+  const dir = markerDir();
+  const sessionId = claudeSessionId;
+  const ac = new AbortController();
 
-  while (true) {
-    const currentContent = normalizeTmuxLines(capturePaneScrollback(paneId));
-
-    // Must have new content compared to before we sent
-    if (currentContent !== beforeContent) {
-      const visible = capturePaneVisible(paneId);
-      if (paneLooksReady(visible) && !paneHasActiveTask(visible)) {
-        // Pane looks idle — but it might be waiting for user input (HIL).
-        // Check the transcript for an unresolved AskUserQuestion before
-        // treating this as a true completion.
-        if (claudeSessionId) {
-          try {
-            const msgs = await getSessionMessages(claudeSessionId, {
-              dir: process.cwd(),
-              includeSystemMessages: true,
-            });
-
-            if (_hasUnresolvedHILTool(msgs)) {
-              // Agent is blocked on user input — signal HIL and keep waiting
-              if (!hilActive && onHIL) {
-                onHIL(true);
-                hilActive = true;
-              }
-              await Bun.sleep(pollIntervalMs);
-              continue;
-            }
+  let hilActive = false;
 
-            // HIL was active but is now resolved — signal resumption
-            if (hilActive && onHIL) {
-              onHIL(false);
-              hilActive = false;
-              // Agent may still be processing after HIL resolution — keep
-              // polling instead of returning immediately
-              await Bun.sleep(pollIntervalMs);
-              continue;
-            }
+  try {
+    for await (const event of watch(dir, { signal: ac.signal })) {
+      // Filter: only care about events for our session's marker file
+      if (event.filename !== sessionId) continue;
+
+      // Marker appeared — read transcript
+      let msgs: SessionMessage[];
+      try {
+        msgs = await getSessionMessages(sessionId, {
+          dir: process.cwd(),
+          includeSystemMessages: true,
+        });
+      } catch {
+        // Transcript read failed — wait for the next marker event
+        continue;
+      }
 
-            // Truly idle — return transcript messages from this turn
-            if (msgs.length > transcriptBeforeCount) {
-              return msgs.slice(transcriptBeforeCount);
-            }
-          } catch {
-            // Transcript read failed — return empty
-          }
+      if (_hasUnresolvedHILTool(msgs)) {
+        // Agent is blocked on user input (HIL).
+        if (!hilActive) {
+          onHIL?.(true);
+          hilActive = true;
         }
-        return [];
-      } else if (hilActive) {
-        // Pane is active again (user responded, agent resumed processing).
-        // Clear HIL state.
-        if (onHIL) {
-          onHIL(false);
-          hilActive = false;
+        // Remove the marker so the Stop hook can write a new one after the
+        // user responds and Claude finishes its next turn.
+        try {
+          await unlink(markerPath(sessionId));
+        } catch {
+          // ENOENT is fine — ignore
         }
+        // Continue watching for the next marker event
+        continue;
       }
-    }
 
-    await Bun.sleep(pollIntervalMs);
+      // No unresolved HIL — if we were in HIL state, signal resolution.
+      if (hilActive) {
+        onHIL?.(false);
+        hilActive = false;
+      }
+
+      // Truly idle — return transcript messages produced during this turn.
+      const result = msgs.length > transcriptBeforeCount
+        ? msgs.slice(transcriptBeforeCount)
+        : [];
+
+      ac.abort();
+      return result;
+    }
+  } catch (e: unknown) {
+    // AbortError is expected when we call ac.abort() to stop watching.
+    if (e instanceof Error && e.name === "AbortError") {
+      // Normal exit — return value was already set and returned above.
+      // If we somehow reach here without returning, fall through to [].
+    } else {
+      throw e;
+    }
   }
+
+  return [];
 }
 
 // ---------------------------------------------------------------------------
@@ -542,6 +609,11 @@ export async function claudeQuery(options: ClaudeQueryOptions): Promise<SessionM
   const dir = process.cwd();
   const claudeSessionId = paneState.claudeSessionId;
 
+  // ── Clear any stale marker left from a previous turn before submitting. ──
+  // This ensures `waitForIdle`'s watch loop doesn't fire on the marker written
+  // by the Stop hook at the end of the LAST turn instead of the current one.
+  await clearStaleMarker(claudeSessionId);
+
   // ── First query: spawn `claude --session-id <UUID> 'Read the prompt in <path>'`.
   // The prompt is delivered via Claude's Read tool on its first turn — no
   // paste-buffer, no submit retries. Subsequent queries fall through to the

package/src/services/config/atomic-global-config.ts

@@ -330,8 +330,8 @@ export async function hasAtomicGlobalAgentConfigs(
 }
 
 /**
- * Verify-and-repair entrypoint for user-facing commands (`atomic init`,
- * `atomic chat`). If every bundled agent file is present at its
+ * Verify-and-repair entrypoint for user-facing commands (`atomic chat`).
+ * If every bundled agent file is present at its
  * destination, returns immediately without touching disk. Otherwise
  * runs a merge re-sync, which fills the missing files from the local
  * config data dir while leaving user-added files alone.

package/src/services/config/definitions.ts

@@ -17,7 +17,7 @@ export interface AgentConfig {
   install_url: string;
   /** Paths to exclude when copying (relative to folder) */
   exclude: string[];
-  /** Project files managed by `atomic init` for provider onboarding */
+  /** Project files applied during `atomic chat` preflight for provider onboarding */
   onboarding_files: Array<{
     source: string;
     destination: string;