@bastani/atomic 0.5.28-0 → 0.5.28-2

package/.claude/settings.json

@@ -10,7 +10,6 @@
     "defaultMode": "bypassPermissions"
   },
   "disabledMcpjsonServers": [
-    "github",
     "azure-devops"
   ],
   "enabledPlugins": {

package/.opencode/opencode.json

@@ -8,11 +8,16 @@
       "headers": {
         "Authorization": "Bearer ${env:GITHUB_PERSONAL_ACCESS_TOKEN}"
       },
-      "enabled": false
+      "enabled": true
     },
     "azure-devops": {
       "type": "local",
-      "command": ["bunx", "-y", "@azure-devops/mcp", "<your-org>"],
+      "command": [
+        "bunx",
+        "-y",
+        "@azure-devops/mcp",
+        "<your-org>"
+      ],
       "enabled": false
     }
   }

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

@@ -45,13 +45,24 @@ export declare function claudeHookDirs(): {
     queue: string;
     release: string;
     hil: string;
+    pid: string;
 };
 /** Options for {@link claudeStopHookCommand}. Primarily used by tests to shrink the wait budget. */
 export interface ClaudeStopHookOptions {
     /** Maximum time the hook waits for a queued follow-up prompt before letting Claude stop. */
     waitTimeoutMs?: number;
-    /** Polling interval for queue/release detection. */
+    /**
+     * Interval for the polling fallback that runs alongside the `fs.watch`
+     * watchers in case an inotify/FSEvent notification gets dropped. In the
+     * happy path, watcher events fire on create and the poll never matches.
+     */
     pollIntervalMs?: number;
+    /**
+     * Interval at which the hook checks whether the atomic workflow process
+     * that owns this session is still alive. Coarser than `pollIntervalMs`
+     * because atomic crashing is rare and `process.kill(pid, 0)` is a syscall.
+     */
+    livenessIntervalMs?: number;
 }
 /**
  * Handler for the hidden `_claude-stop-hook` subcommand.

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,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"}
+{"version":3,"file":"claude-stop-hook.d.ts","sourceRoot":"","sources":["../../../src/commands/cli/claude-stop-hook.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAQH,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;IAChC,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,GAAG,EAAE,MAAM,CAAC;IACZ,GAAG,EAAE,MAAM,CAAC;CACb,CAcA;AAED,oGAAoG;AACpG,MAAM,WAAW,qBAAqB;IACpC,4FAA4F;IAC5F,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB;;;;OAIG;IACH,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB;;;;OAIG;IACH,kBAAkB,CAAC,EAAE,MAAM,CAAC;CAC7B;AAsFD;;;;;;;;GAQG;AACH,wBAAsB,qBAAqB,CACzC,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,MAAM,CAAC,CAyMjB"}

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

@@ -288,6 +288,26 @@ export declare class HeadlessClaudeClientWrapper {
     start(): Promise<string>;
     stop(): Promise<void>;
 }
+/**
+ * Resolve the `claude` CLI binary for headless SDK queries.
+ *
+ * Pins the SDK to the same binary interactive stages already spawn via tmux
+ * (`AGENT_CONFIG.claude.cmd` on PATH), bypassing
+ * `@anthropic-ai/claude-agent-sdk`'s built-in resolver. That resolver probes
+ * optional native packages in a fixed order — on Linux it tries
+ * `linux-${arch}-musl` before `linux-${arch}` and returns whichever
+ * `require.resolve` finds first — so on a glibc host where both optional
+ * packages got installed (Bun installs every optionalDependency by default)
+ * it picks the musl binary, which can't exec because its dynamic linker
+ * (`/lib/ld-musl-*.so.1`) is absent. The SDK surfaces the resulting ENOENT
+ * as a misleading "Claude Code native binary not found" error.
+ *
+ * `chatCommand` and `workflowCommand` already fail fast when `claude` isn't
+ * on PATH (see `isCommandInstalled` in each), so in practice this lookup
+ * always succeeds. The throw here is a belt-and-suspenders guard that
+ * prefers a clear failure over silently falling back to the SDK's resolver.
+ */
+export declare function resolveHeadlessClaudeBin(): string;
 /**
  * Headless session wrapper for Claude stages. Uses the Agent SDK's `query()`
  * directly instead of tmux pane operations. Implements the same `query()`

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

@@ -1 +1 @@
-{"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;AAgCxC;;;;;;GAMG;AACH,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAWtE;AAqID,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AACH,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,MAAM,CAAC,CAexF;AAsID;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,eAAe,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAUnE;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,cAAc,CAClC,eAAe,EAAE,MAAM,EACvB,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,EACjC,MAAM,EAAE,WAAW,GAClB,OAAO,CAAC,IAAI,CAAC,CAyCf;AAMD;;;;;;GAMG;AACH,wBAAgB,SAAS,IAAI,MAAM,CAElC;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAE1D;AAED;;;;GAIG;AACH,wBAAgB,QAAQ,IAAI,MAAM,CAEjC;AAED,0EAA0E;AAC1E,wBAAgB,SAAS,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,IAAI,MAAM,CAEnC;AAED,4EAA4E;AAC5E,wBAAgB,WAAW,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAE3D;AAiED;;;;GAIG;AACH,wBAAsB,oBAAoB,CAAC,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAGjF;AAMD;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH;;GAEG;AACH,wBAAsB,WAAW,CAC/B,eAAe,EAAE,MAAM,EACvB,qBAAqB,EAAE,MAAM,GAC5B,OAAO,CAAC,cAAc,EAAE,CAAC,CAiG3B;AAMD,MAAM,WAAW,kBAAkB;IACjC,2CAA2C;IAC3C,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,MAAM,EAAE,MAAM,CAAC;IACf;;;;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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC,CA8FxF;AAMD;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,MAAM,EAAE,GAAG,SAAS,EAC9B,MAAM,EAAE,MAAM,EAAE,GACf,MAAM,EAAE,CAMV;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;;;;;;;OAOG;IACG,KAAK,IAAI,OAAO,CAAC,MAAM,CAAC;IAQ9B,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,KAAK,CAA2C;gBAG/D,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI;IAOpC;;;;;;;;OAQG;IACG,KAAK,CACT,MAAM,EAAE,MAAM,EACd,QAAQ,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,GAC7B,OAAO,CAAC,cAAc,EAAE,CAAC;IAQ5B,gEAAgE;IAC1D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAMD;;;GAGG;AACH,qBAAa,2BAA2B;IACtC;;;;;OAKG;IACG,KAAK,IAAI,OAAO,CAAC,MAAM,CAAC;IAGxB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAC5B;AAED;;;;;;;;;;GAUG;AACH,qBAAa,4BAA4B;IACvC,QAAQ,CAAC,MAAM,MAAM;IACrB;;;;;OAKG;IACH,OAAO,CAAC,cAAc,CAAc;IAEpC,IAAI,SAAS,IAAI,MAAM,CAEtB;IAEK,KAAK,CACT,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,cAAc,CAAC,EAC9C,OAAO,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,GAC5B,OAAO,CAAC,cAAc,EAAE,CAAC;IAqCtB,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAQD;;;;;GAKG;AACH,eAAO,MAAM,sBAAsB,+DAejC,CAAC"}
+{"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;AAgCxC;;;;;;GAMG;AACH,wBAAsB,kBAAkB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAiBtE;AAqID,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AACH,wBAAsB,mBAAmB,CAAC,OAAO,EAAE,oBAAoB,GAAG,OAAO,CAAC,MAAM,CAAC,CAqBxF;AAsID;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,eAAe,CAAC,QAAQ,EAAE,cAAc,EAAE,GAAG,OAAO,CAUnE;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,cAAc,CAClC,eAAe,EAAE,MAAM,EACvB,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,EACjC,MAAM,EAAE,WAAW,GAClB,OAAO,CAAC,IAAI,CAAC,CAyCf;AAMD;;;;;;GAMG;AACH,wBAAgB,SAAS,IAAI,MAAM,CAElC;AAED;;;;GAIG;AACH,wBAAgB,UAAU,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAE1D;AAED;;;;GAIG;AACH,wBAAgB,QAAQ,IAAI,MAAM,CAEjC;AAED,0EAA0E;AAC1E,wBAAgB,SAAS,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,IAAI,MAAM,CAEnC;AAED,4EAA4E;AAC5E,wBAAgB,WAAW,CAAC,eAAe,EAAE,MAAM,GAAG,MAAM,CAE3D;AAiED;;;;GAIG;AACH,wBAAsB,oBAAoB,CAAC,eAAe,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAGjF;AAsCD;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH;;GAEG;AACH,wBAAsB,WAAW,CAC/B,eAAe,EAAE,MAAM,EACvB,qBAAqB,EAAE,MAAM,GAC5B,OAAO,CAAC,cAAc,EAAE,CAAC,CAiG3B;AAMD,MAAM,WAAW,kBAAkB;IACjC,2CAA2C;IAC3C,MAAM,EAAE,MAAM,CAAC;IACf,yBAAyB;IACzB,MAAM,EAAE,MAAM,CAAC;IACf;;;;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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AACH,wBAAsB,WAAW,CAAC,OAAO,EAAE,kBAAkB,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC,CA8FxF;AAMD;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,MAAM,EAAE,GAAG,SAAS,EAC9B,MAAM,EAAE,MAAM,EAAE,GACf,MAAM,EAAE,CAMV;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;;;;;;;OAOG;IACG,KAAK,IAAI,OAAO,CAAC,MAAM,CAAC;IAQ9B,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,KAAK,CAA2C;gBAG/D,MAAM,EAAE,MAAM,EACd,SAAS,EAAE,MAAM,EACjB,KAAK,CAAC,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI;IAOpC;;;;;;;;OAQG;IACG,KAAK,CACT,MAAM,EAAE,MAAM,EACd,QAAQ,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,GAC7B,OAAO,CAAC,cAAc,EAAE,CAAC;IAQ5B,gEAAgE;IAC1D,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAMD;;;GAGG;AACH,qBAAa,2BAA2B;IACtC;;;;;OAKG;IACG,KAAK,IAAI,OAAO,CAAC,MAAM,CAAC;IAGxB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;CAC5B;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,wBAAwB,IAAI,MAAM,CAajD;AAED;;;;;;;;;;GAUG;AACH,qBAAa,4BAA4B;IACvC,QAAQ,CAAC,MAAM,MAAM;IACrB;;;;;OAKG;IACH,OAAO,CAAC,cAAc,CAAc;IAEpC,IAAI,SAAS,IAAI,MAAM,CAEtB;IAEK,KAAK,CACT,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,cAAc,CAAC,EAC9C,OAAO,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,GAC5B,OAAO,CAAC,cAAc,EAAE,CAAC;IAuCtB,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;CAClC;AAQD;;;;;GAKG;AACH,eAAO,MAAM,sBAAsB,+DAejC,CAAC"}

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

@@ -4,6 +4,23 @@
  * Checks that Copilot workflow source files use the runtime-managed
  * `s.client` and `s.session` instead of manual SDK client creation.
  */
+/**
+ * Env inherited by the Copilot CLI subprocess the SDK spawns.
+ *
+ * `NODE_NO_WARNINGS=1` silences the
+ * `ExperimentalWarning: SQLite is an experimental feature` banner that
+ * Node prints via the CLI's bundled `require("node:sqlite")`. The SDK
+ * pipes the subprocess's stderr through `process.stderr` with a
+ * `[CLI subprocess]` prefix, so without this override the warning
+ * leaks into every `atomic chat -a copilot` and `atomic workflow -a
+ * copilot` invocation.
+ *
+ * The SDK uses `options.env ?? process.env` as-is (no merge) when
+ * spawning, so we must fold the existing env in ourselves. Returns a
+ * fresh object per call so callers can layer additional env without
+ * mutating shared state.
+ */
+export declare function copilotSubprocessEnv(): Record<string, string | undefined>;
 /**
  * Validate a Copilot workflow source file for common mistakes.
  */

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

@@ -1 +1 @@
-{"version":3,"file":"copilot.d.ts","sourceRoot":"","sources":["../../../src/sdk/providers/copilot.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH;;GAEG;AACH,eAAO,MAAM,uBAAuB,+DAelC,CAAC"}
+{"version":3,"file":"copilot.d.ts","sourceRoot":"","sources":["../../../src/sdk/providers/copilot.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,oBAAoB,IAAI,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,CAEzE;AAED;;GAEG;AACH,eAAO,MAAM,uBAAuB,+DAelC,CAAC"}

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

@@ -1 +1 @@
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+{"version":3,"file":"executor.d.ts","sourceRoot":"","sources":["../../../src/sdk/runtime/executor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAMH,OAAO,KAAK,EACV,kBAAkB,EAMlB,SAAS,EAET,YAAY,EAMb,MAAM,aAAa,CAAC;AA0ErB,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAa5C,MAAM,WAAW,kBAAkB;IACjC,uCAAuC;IACvC,UAAU,EAAE,kBAAkB,CAAC;IAC/B,iBAAiB;IACjB,KAAK,EAAE,SAAS,CAAC;IACjB;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAChC,qEAAqE;IACrE,YAAY,EAAE,MAAM,CAAC;IACrB,qCAAqC;IACrC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB;;;;;OAKG;IACH,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAoDD;;;;;;;;;;;;;GAaG;AACH,wBAAgB,qBAAqB,IAAI,MAAM,GAAG,SAAS,CAgB1D;AAED;;;;;;GAMG;AACH,wBAAgB,4BAA4B,IAAI,OAAO,CAKtD;AAyBD;;;;;GAKG;AACH,wBAAgB,yBAAyB,IAAI,IAAI,CAMhD;AAuFD;;;;;;GAMG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAKzC;AAED;;;;;GAKG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAMzC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAC5B,GAAG,EAAE,MAAM,GAAG,SAAS,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAgBxB;AAMD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAAC,IAAI,CAAC,CAkFf;AAoDD,gGAAgG;AAChG,wBAAgB,UAAU,CAAC,KAAK,EAAE,OAAO,GAAG,KAAK,IAAI;IAAE,OAAO,EAAE,MAAM,CAAA;CAAE,CAOvE;AA2OD,wBAAgB,oBAAoB,CAAC,QAAQ,EAAE,YAAY,EAAE,GAAG,MAAM,CA0CrE;AAOD;;;;GAIG;AACH,MAAM,WAAW,yBAAyB;IACxC,EAAE,CAAC,SAAS,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC,KAAK,EAAE;QAAE,IAAI,CAAC,EAAE,OAAO,CAAA;KAAE,KAAK,IAAI,GAAG,MAAM,IAAI,CAAC;CACjF;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,eAAe,CAAC,CAAC,EAAE,CAAC,EAClC,OAAO,EAAE,yBAAyB,EAClC,UAAU,EAAE,CAAC,OAAO,EAAE,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,GACrC,CAAC,OAAO,EAAE,CAAC,KAAK,OAAO,CAAC,CAAC,CAAC,CAuB5B;AAED;;;;;;;;GAQG;AACH,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,CAAC;QAAC,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAA;KAAE,CAAC;CAC5D;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,wBAAsB,yBAAyB,CAC7C,MAAM,EAAE,aAAa,CAAC,gBAAgB,CAAC,EACvC,SAAS,EAAE,MAAM,EACjB,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,GAChC,OAAO,CAAC,IAAI,CAAC,CAef;AAED;;;;;GAKG;AACH,MAAM,WAAW,wBAAwB;IACvC,EAAE,CACA,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,CAAC,KAAK,EAAE;QAAE,IAAI,CAAC,EAAE,OAAO,CAAA;KAAE,KAAK,IAAI,GAC3C,MAAM,IAAI,CAAC;CACf;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,yBAAyB,CACvC,OAAO,EAAE,wBAAwB,EACjC,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,GAChC,MAAM,IAAI,CA0BZ;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,iCAAiC,CAC/C,OAAO,EAAE,wBAAwB,EACjC,KAAK,EAAE,CAAC,OAAO,EAAE,OAAO,KAAK,IAAI,GAChC,MAAM,IAAI,CAwBZ;AAsFD;;;GAGG;AACH,wBAAgB,kBAAkB,CAChC,QAAQ,EAAE,MAAM,EAAE,GAAG,SAAS,EAC9B,MAAM,EAAE,MAAM,EAAE,GACf,MAAM,EAAE,CAMV;AAslBD,wBAAsB,eAAe,IAAI,OAAO,CAAC,IAAI,CAAC,CAqMrD"}

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

@@ -21,6 +21,13 @@ export interface AgentConfig {
         source: string;
         destination: string;
         merge: boolean;
+        /**
+         * Top-level keys to strip from the source before copying or merging.
+         * Useful when a key is project-local by design (e.g. Claude's
+         * `disabledMcpjsonServers`) and must not leak into a global
+         * destination like `~/.claude/settings.json`.
+         */
+        excludeConfigKeys?: readonly string[];
     }>;
 }
 declare const AGENT_KEYS: readonly ["claude", "opencode", "copilot"];

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,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"}
+{"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;QACf;;;;;WAKG;QACH,iBAAiB,CAAC,EAAE,SAAS,MAAM,EAAE,CAAC;KACvC,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,CA8DtD,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": "0.5.28-0",
+  "version": "0.5.28-2",
   "description": "Configuration management CLI and SDK for coding agents",
   "type": "module",
   "license": "MIT",
@@ -75,11 +75,11 @@
     "typescript-language-server": "^5.1.3"
   },
   "dependencies": {
-    "@anthropic-ai/claude-agent-sdk": "^0.2.116",
+    "@anthropic-ai/claude-agent-sdk": "^0.2.117",
     "@clack/prompts": "^1.2.0",
     "@commander-js/extra-typings": "^14.0.0",
     "@github/copilot-sdk": "^0.2.2",
-    "@opencode-ai/sdk": "^1.14.19",
+    "@opencode-ai/sdk": "^1.14.20",
     "@opentui/core": "^0.1.102",
     "@opentui/react": "^0.1.102",
     "commander": "^14.0.3",

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

@@ -22,6 +22,7 @@ import { getCopilotScmDisableFlags } from "../../../services/config/scm-sync.ts"
 import { ensureProjectSetup } from "../init/index.ts";
 import { COLORS } from "../../../theme/colors.ts";
 import { isCommandInstalled } from "../../../services/system/detect.ts";
+import { checkAgentAuth, printAuthError } from "../../../services/system/auth.ts";
 import {
   ensureAtomicGlobalAgentConfigs,
 } from "../../../services/config/atomic-global-config.ts";
@@ -185,6 +186,16 @@ export async function chatCommand(options: ChatCommandOptions = {}): Promise<num
     return 1;
   }
 
+  // ── Preflight: authentication ──
+  // Copilot and Claude expose SDK-level login checks; run them now so
+  // users get a short actionable error instead of being dropped into a
+  // native CLI that immediately redirects them to /login.
+  const auth = await checkAgentAuth(agentType);
+  if (!auth.loggedIn) {
+    printAuthError(agentType, auth);
+    return 1;
+  }
+
   // ── Preflight: global config sync ──
   const projectRoot = process.cwd();
   const configRoot = getConfigRoot();

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

@@ -9,10 +9,11 @@
  * and clean up in `afterEach` so test runs never collide with each other
  * or with real marker/queue/release files.
  *
- * The hook's default wait for a queued follow-up prompt is 15 minutes.
- * Every test here passes a short `waitTimeoutMs` so the hook exits quickly
- * when no queue entry is present — we are testing the branching logic,
- * not the real-world wait budget.
+ * The hook's default wait for a queued follow-up prompt is effectively
+ * unbounded (~24 days) so the workflow can take as long as it needs between
+ * turns. Every test here passes a short `waitTimeoutMs` so the hook exits
+ * quickly when no queue entry is present — we are testing the branching
+ * logic, not the real-world wait budget.
  */
 
 import { describe, test, expect, afterEach, spyOn } from "bun:test";
@@ -20,7 +21,7 @@ import { access, rm, writeFile, mkdir } from "node:fs/promises";
 import { join } from "node:path";
 import { claudeStopHookCommand, claudeHookDirs } from "./claude-stop-hook.ts";
 
-const { marker: markerDir, queue: queueDir, release: releaseDir } = claudeHookDirs();
+const { marker: markerDir, queue: queueDir, release: releaseDir, pid: pidDir } = claudeHookDirs();
 
 const SHORT_TIMEOUT_MS = 300;
 
@@ -52,6 +53,7 @@ afterEach(async () => {
       rm(join(markerDir, id), { force: true }),
       rm(join(queueDir, id), { force: true }),
       rm(join(releaseDir, id), { force: true }),
+      rm(join(pidDir, id), { force: true }),
     ]);
   }
   sessionIdsToClean.length = 0;
@@ -268,4 +270,48 @@ describe("claudeStopHookCommand", () => {
     // No block decision emitted.
     expect(stdoutChunks.join("")).toBe("");
   });
+
+  // 9. Dead atomic PID → hook exits without waiting out the full timeout.
+  //
+  // Simulates the case where the atomic workflow was SIGKILL'd between
+  // turns: the pid file on disk points at a process that no longer exists,
+  // so the liveness check should fire and let the hook bail. We pick a
+  // deliberately-bogus PID (2^22 - 1) that is almost certainly unused.
+  test("dead atomic pid triggers liveness exit before the wait timeout", async () => {
+    const sessionId = crypto.randomUUID();
+    sessionIdsToClean.push(sessionId);
+
+    // Find a PID that doesn't currently exist. `process.kill(pid, 0)` throws
+    // ESRCH for free PIDs; we scan from a high number downward to dodge
+    // system-reserved low PIDs.
+    let deadPid = 4_194_303;
+    while (deadPid > 1) {
+      try {
+        process.kill(deadPid, 0);
+        deadPid -= 1;
+      } catch (e: unknown) {
+        if (e instanceof Error && "code" in e && (e as NodeJS.ErrnoException).code === "ESRCH") break;
+        deadPid -= 1;
+      }
+    }
+
+    await mkdir(pidDir, { recursive: true });
+    await writeFile(join(pidDir, sessionId), String(deadPid), "utf-8");
+
+    mockStdin(JSON.stringify({ session_id: sessionId }));
+
+    // Use a long wait timeout so the test only passes if the liveness check
+    // short-circuits the wait. livenessIntervalMs is short so the test runs fast.
+    const started = Date.now();
+    const code = await claudeStopHookCommand({
+      waitTimeoutMs: 30_000,
+      pollIntervalMs: 10_000,
+      livenessIntervalMs: 50,
+    });
+    const elapsed = Date.now() - started;
+
+    expect(code).toBe(0);
+    expect(elapsed).toBeLessThan(5_000);
+    expect(await fileExists(join(markerDir, sessionId))).toBe(true);
+  });
 });

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

@@ -29,6 +29,7 @@
  */
 
 import fs from "node:fs/promises";
+import { watch as watchDir } from "node:fs/promises";
 import { existsSync } from "node:fs";
 import path from "node:path";
 import os from "node:os";
@@ -60,13 +61,25 @@ function isClaudeStopHookPayload(value: unknown): value is ClaudeStopHookPayload
  *
  * Exported so tests and `src/sdk/providers/claude.ts` share one source of truth.
  */
-export function claudeHookDirs(): { marker: string; queue: string; release: string; hil: string } {
+export function claudeHookDirs(): {
+  marker: string;
+  queue: string;
+  release: string;
+  hil: string;
+  pid: string;
+} {
   const base = path.join(os.homedir(), ".atomic");
   return {
     marker: path.join(base, "claude-stop"),
     queue: path.join(base, "claude-queue"),
     release: path.join(base, "claude-release"),
     hil: path.join(base, "claude-hil"),
+    // Holds the PID of the atomic workflow process that owns each session.
+    // The Stop hook polls `process.kill(pid, 0)` against this value so that
+    // if atomic is SIGKILL'd (no chance to write a release marker), the hook
+    // can detect the orphaned session and self-exit instead of sitting in
+    // its wait loop for ~24 days.
+    pid: path.join(base, "claude-pid"),
   };
 }
 
@@ -74,12 +87,103 @@ export function claudeHookDirs(): { marker: string; queue: string; release: stri
 export interface ClaudeStopHookOptions {
   /** Maximum time the hook waits for a queued follow-up prompt before letting Claude stop. */
   waitTimeoutMs?: number;
-  /** Polling interval for queue/release detection. */
+  /**
+   * Interval for the polling fallback that runs alongside the `fs.watch`
+   * watchers in case an inotify/FSEvent notification gets dropped. In the
+   * happy path, watcher events fire on create and the poll never matches.
+   */
   pollIntervalMs?: number;
+  /**
+   * Interval at which the hook checks whether the atomic workflow process
+   * that owns this session is still alive. Coarser than `pollIntervalMs`
+   * because atomic crashing is rare and `process.kill(pid, 0)` is a syscall.
+   */
+  livenessIntervalMs?: number;
 }
 
-const DEFAULT_WAIT_TIMEOUT_MS = 15 * 60 * 1000;
+/**
+ * Effectively-unbounded default wait budget for the queue/release poll loop.
+ *
+ * The hook holds Claude Code in the Stop phase while the workflow runtime
+ * decides what to do next — either enqueueing a follow-up prompt (delivered
+ * back to Claude as `{decision:"block", reason:...}`) or writing a release
+ * marker on teardown. Any finite default here caps the time the workflow has
+ * between turns: when it expires, the hook exits 0, Claude stops, and the
+ * next `enqueuePrompt` writes to a file nobody's reading — the workflow
+ * hangs on `waitForIdle` for a turn that will never come.
+ *
+ * The Claude-side hook timeout (see `STOP_HOOK_TIMEOUT_SECONDS` in
+ * `src/sdk/providers/claude.ts`) is already set to ~24 days, so matching it
+ * here keeps the two bounds aligned — the hook either runs until the
+ * workflow releases it or until Claude Code itself gives up. Tests override
+ * `waitTimeoutMs` via options to keep runs fast.
+ *
+ * Expressed in ms: 2_147_483 s × 1000 = 2_147_483_000 ms, just under the
+ * max safe `setTimeout` value (2^31 - 1).
+ */
+const DEFAULT_WAIT_TIMEOUT_MS = 2_147_483_000;
 const DEFAULT_POLL_INTERVAL_MS = 100;
+const DEFAULT_LIVENESS_INTERVAL_MS = 5_000;
+
+/**
+ * Read the atomic PID that owns this session from `~/.atomic/claude-pid/<id>`,
+ * or return null if the file is missing / malformed. Missing is fine: older
+ * runtimes didn't write one, and we just skip the liveness check in that case.
+ */
+async function readAtomicPid(pidFilePath: string): Promise<number | null> {
+  let raw: string;
+  try {
+    raw = await fs.readFile(pidFilePath, "utf-8");
+  } catch {
+    return null;
+  }
+  const parsed = Number.parseInt(raw.trim(), 10);
+  return Number.isInteger(parsed) && parsed > 0 ? parsed : null;
+}
+
+/**
+ * Sleep that resolves early when `signal` is aborted. Used by the hook's
+ * wait loops so `ac.abort()` unblocks everything immediately instead of
+ * waiting for the next wake-up tick — otherwise a task that detects a hit
+ * (e.g. liveness check) can't meaningfully cancel its siblings.
+ */
+function abortableSleep(ms: number, signal: AbortSignal): Promise<void> {
+  return new Promise<void>((resolve) => {
+    if (signal.aborted) {
+      resolve();
+      return;
+    }
+    const timer = setTimeout(() => {
+      signal.removeEventListener("abort", onAbort);
+      resolve();
+    }, ms);
+    const onAbort = (): void => {
+      clearTimeout(timer);
+      resolve();
+    };
+    signal.addEventListener("abort", onAbort, { once: true });
+  });
+}
+
+/**
+ * True when a process with `pid` exists. Uses signal `0`, which performs the
+ * permission/existence check without delivering a signal. ESRCH means gone,
+ * EPERM means alive-but-not-ours (still alive for our purposes).
+ */
+function isProcessAlive(pid: number): boolean {
+  try {
+    process.kill(pid, 0);
+    return true;
+  } catch (e: unknown) {
+    if (e instanceof Error && "code" in e) {
+      const code = (e as NodeJS.ErrnoException).code;
+      if (code === "EPERM") return true;
+      if (code === "ESRCH") return false;
+    }
+    // Unknown error — assume alive to avoid false-positive teardown.
+    return true;
+  }
+}
 
 /**
  * Handler for the hidden `_claude-stop-hook` subcommand.
@@ -95,6 +199,8 @@ export async function claudeStopHookCommand(
 ): Promise<number> {
   const waitTimeoutMs = options.waitTimeoutMs ?? DEFAULT_WAIT_TIMEOUT_MS;
   const pollIntervalMs = options.pollIntervalMs ?? DEFAULT_POLL_INTERVAL_MS;
+  const livenessIntervalMs =
+    options.livenessIntervalMs ?? DEFAULT_LIVENESS_INTERVAL_MS;
 
   // 1. Read stdin
   const raw = await Bun.stdin.text();
@@ -135,6 +241,7 @@ export async function claudeStopHookCommand(
     fs.mkdir(dirs.marker, { recursive: true }),
     fs.mkdir(dirs.queue, { recursive: true }),
     fs.mkdir(dirs.release, { recursive: true }),
+    fs.mkdir(dirs.pid, { recursive: true }),
   ]);
 
   // 4. Write the marker file directly.
@@ -148,7 +255,7 @@ export async function claudeStopHookCommand(
   const markerPath = path.join(dirs.marker, payload.session_id);
   await Bun.write(markerPath, raw);
 
-  // 5. Block-poll for either a queued follow-up prompt or a release signal.
+  // 5. Wait for either a queued follow-up prompt or a release signal.
   //
   // The workflow's `waitForIdle` has already been unblocked by the marker
   // write above and is now returning control to the user's stage callback.
@@ -164,34 +271,130 @@ export async function claudeStopHookCommand(
   //      `~/.atomic/claude-release/<session_id>`. We exit 0 with no stdout
   //      payload and Claude stops as usual.
   //
-  //   c. Neither happens within `waitTimeoutMs`. We exit 0 on timeout as a
-  //      safety net — Claude stops rather than hanging its Stop hook forever.
+  //   c. Neither happens within `waitTimeoutMs`. We exit 0 so Claude Code
+  //      doesn't hang past its own per-hook timeout. The production default
+  //      for `waitTimeoutMs` is aligned with the Claude-side hook timeout
+  //      (~24 days), so this path is effectively unreachable in real runs —
+  //      it only fires in tests that pass a short override.
+  //
+  // Delivery uses `fs.watch` on the queue and release dirs for ~0-latency
+  // wake-up on create events, with a slower `existsSync` polling fallback
+  // in case a watcher notification gets dropped under fs load (same pattern
+  // as `watchHILMarker` in `src/sdk/providers/claude.ts`).
   const queuePath = path.join(dirs.queue, payload.session_id);
   const releasePath = path.join(dirs.release, payload.session_id);
 
-  const deadline = Date.now() + waitTimeoutMs;
-  while (Date.now() <= deadline) {
+  type Hit = { kind: "release" } | { kind: "queue"; prompt: string };
+
+  const check = async (): Promise<Hit | null> => {
     if (existsSync(releasePath)) {
       try { await fs.unlink(releasePath); } catch { /* ENOENT is fine */ }
-      return 0;
+      return { kind: "release" };
     }
     if (existsSync(queuePath)) {
       let prompt: string;
       try {
         prompt = await fs.readFile(queuePath, "utf-8");
       } catch {
-        return 0;
+        // Treat a failed read as a graceful release so the hook still exits.
+        return { kind: "release" };
       }
       try { await fs.unlink(queuePath); } catch { /* ENOENT is fine */ }
+      return { kind: "queue", prompt };
+    }
+    return null;
+  };
+
+  const emit = (hit: Hit): number => {
+    if (hit.kind === "queue") {
       process.stdout.write(JSON.stringify({
         decision: "block",
-        reason: prompt,
+        reason: hit.prompt,
       }));
-      return 0;
     }
-    await Bun.sleep(pollIntervalMs);
+    return 0;
+  };
+
+  // Initial synchronous check — the runtime may have enqueued/released before
+  // we attached watchers, and without this the hook could hang until the
+  // polling fallback fires.
+  const early = await check();
+  if (early) return emit(early);
+
+  const ac = new AbortController();
+  const overallTimer = setTimeout(() => ac.abort(), waitTimeoutMs);
+  let hit: Hit | null = null;
+
+  // Read the atomic workflow's PID (if the runtime wrote one for this
+  // session). Used by the liveness task below to detect an atomic crash.
+  const atomicPid = await readAtomicPid(
+    path.join(dirs.pid, payload.session_id),
+  );
+
+  // Watch a single directory for change events and resolve `hit` on the
+  // first one that matches. `event.filename` is unreliable across OSes
+  // (see the comment in `watchHILMarker`), so disk state is authoritative.
+  const runWatcher = async (dir: string): Promise<void> => {
+    try {
+      for await (const _event of watchDir(dir, { signal: ac.signal })) {
+        const result = await check();
+        if (result) {
+          hit = result;
+          ac.abort();
+          return;
+        }
+      }
+    } catch (e: unknown) {
+      if (!(e instanceof Error && e.name === "AbortError")) throw e;
+    }
+  };
+
+  // Polling fallback — catches the rare dropped inotify/FSEvent event.
+  // Only runs while the watchers are live; `ac.abort()` shuts it down.
+  const runPollFallback = async (): Promise<void> => {
+    while (!ac.signal.aborted) {
+      await abortableSleep(pollIntervalMs, ac.signal);
+      if (ac.signal.aborted) return;
+      const result = await check();
+      if (result) {
+        hit = result;
+        ac.abort();
+        return;
+      }
+    }
+  };
+
+  // Liveness check — if the atomic workflow process died without writing a
+  // release marker (e.g. SIGKILL), this task abandons the wait and lets
+  // Claude stop. No-op when there's no pid file (older sessions or non-
+  // runtime spawns) so the hook still functions standalone.
+  const runLivenessCheck = async (): Promise<void> => {
+    if (atomicPid === null) return;
+    while (!ac.signal.aborted) {
+      await abortableSleep(livenessIntervalMs, ac.signal);
+      if (ac.signal.aborted) return;
+      if (!isProcessAlive(atomicPid)) {
+        // hit stays null → the hook exits 0 without emitting a block decision.
+        ac.abort();
+        return;
+      }
+    }
+  };
+
+  try {
+    await Promise.all([
+      runWatcher(dirs.queue),
+      runWatcher(dirs.release),
+      runPollFallback(),
+      runLivenessCheck(),
+    ]);
+  } finally {
+    clearTimeout(overallTimer);
+    ac.abort();
   }
 
+  if (hit) return emit(hit);
+
   // Timeout — no queued prompt arrived. Let Claude stop normally.
   return 0;
 }

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

@@ -34,7 +34,12 @@ export async function applyManagedOnboardingFiles(
       managedFile.destination,
       projectRoot,
     );
-    await syncJsonFile(sourcePath, destinationPath, managedFile.merge);
+    await syncJsonFile(
+      sourcePath,
+      destinationPath,
+      managedFile.merge,
+      managedFile.excludeConfigKeys ?? [],
+    );
   }
 }