@stigmer/runner 3.1.12 → 3.1.14

package/dist/.build-fingerprint

@@ -1 +1 @@
-{"hash":"75f2b51188de780a","builtAt":"2026-07-13T15:51:35.558Z","fileCount":247}
+{"hash":"ed793424cdc6f1dd","builtAt":"2026-07-14T06:46:16.601Z","fileCount":249}

package/dist/activities/execute-deep-agent/cas-capture-backend.d.ts

@@ -1,6 +1,5 @@
 /**
- * A capture-mode `FilesystemBackend` that observes gitignored file mutations for
- * CAS review (design docs 08/11/12; the `.gitignored` half of apply-then-review).
+ * CAS-capturing deepagents backends for the native harness.
  *
  * WHY A BACKEND WRAPPER, NOT THE APPROVAL GATE
  * --------------------------------------------
@@ -12,31 +11,52 @@
  * escape review under auto-approve-all. Observing at the backend keeps CAS
  * capture gate-independent, so it is symmetric with the git-tracked path.
  *
- * THIS CLASS IS A THIN ADAPTER
- * ----------------------------
- * All capture state and logic live in the shared {@link CasCaptureObserver} (one
- * per turn). The parent graph and every sub-agent graph are each handed a backend
- * pointing at the SAME observer, so their gitignored writes compose into one CAS
- * change set with race-free first-touch-wins (see the observer's docs). This
- * backend only forwards the mutation point to the observer before delegating to
- * the base `FilesystemBackend`.
+ * SHELL VS PLAN MODE
+ * ------------------
+ * Outside plan mode the harness uses {@link CasCaptureShellBackend} (deepagents
+ * LocalShellBackend + CAS observation) so the `execute` tool is available and
+ * approval-gated. Plan mode keeps {@link CasCaptureFilesystemBackend} because
+ * deepagents rejects filesystem `permissions` combined with an execution-capable
+ * backend — plan mode is read-only by construction, so no shell tool there.
  *
  * deepagents mutates only via `write` (create/overwrite) and `edit` (modify);
  * there is no backend delete/rename, so this observes CREATE and MODIFY. A
  * gitignored delete can only arrive via shell, which stays on the approval gate.
  *
  * @since File-Change HITL Redesign (Phase 3 — CAS deep-agent wiring); sub-agent
- * gitignored capture parity (Session 26, DD-19)
+ * gitignored capture parity (Session 26, DD-19); shell restore (issue #248)
  */
-import { FilesystemBackend } from "deepagents";
+import { FilesystemBackend, LocalShellBackend } from "deepagents";
+import type { LocalShellBackendOptions } from "deepagents";
 import type { CasCaptureObserver } from "./cas-capture-observer.js";
 export type { CasBeforeMap } from "./cas-capture-observer.js";
 type FilesystemBackendOptions = NonNullable<ConstructorParameters<typeof FilesystemBackend>[0]>;
+type CasCaptureDeps = {
+    readonly observer: CasCaptureObserver;
+};
 export declare class CasCaptureFilesystemBackend extends FilesystemBackend {
     private readonly observer;
-    constructor(options: FilesystemBackendOptions, deps: {
-        readonly observer: CasCaptureObserver;
-    });
+    constructor(options: FilesystemBackendOptions, deps: CasCaptureDeps);
     write(filePath: string, content: string): Promise<import("deepagents").WriteResult>;
     edit(filePath: string, oldString: string, newString: string, replaceAll?: boolean): Promise<import("deepagents").EditResult>;
 }
+export declare class CasCaptureShellBackend extends LocalShellBackend {
+    private readonly observer;
+    constructor(options: LocalShellBackendOptions, deps: CasCaptureDeps);
+    write(filePath: string, content: string): Promise<import("deepagents").WriteResult>;
+    edit(filePath: string, oldString: string, newString: string, replaceAll?: boolean): Promise<import("deepagents").EditResult>;
+}
+export type CasCaptureBackend = CasCaptureFilesystemBackend | CasCaptureShellBackend;
+export interface CreateCasCaptureBackendOptions {
+    readonly rootDir: string;
+    readonly observer: CasCaptureObserver;
+    /** When set, builds a shell-capable backend with this env for `execute`. */
+    readonly shellEnv?: Record<string, string>;
+}
+/**
+ * Construct the CAS-observing backend for a deepagents agent graph.
+ *
+ * Shell-capable when `shellEnv` is provided; otherwise filesystem-only (plan mode).
+ * Shell backends honor LocalShellBackend's documented initialize contract.
+ */
+export declare function createCasCaptureBackend(options: CreateCasCaptureBackendOptions): Promise<CasCaptureBackend>;

package/dist/activities/execute-deep-agent/cas-capture-backend.js

@@ -1,6 +1,5 @@
 /**
- * A capture-mode `FilesystemBackend` that observes gitignored file mutations for
- * CAS review (design docs 08/11/12; the `.gitignored` half of apply-then-review).
+ * CAS-capturing deepagents backends for the native harness.
  *
  * WHY A BACKEND WRAPPER, NOT THE APPROVAL GATE
  * --------------------------------------------
@@ -12,23 +11,22 @@
  * escape review under auto-approve-all. Observing at the backend keeps CAS
  * capture gate-independent, so it is symmetric with the git-tracked path.
  *
- * THIS CLASS IS A THIN ADAPTER
- * ----------------------------
- * All capture state and logic live in the shared {@link CasCaptureObserver} (one
- * per turn). The parent graph and every sub-agent graph are each handed a backend
- * pointing at the SAME observer, so their gitignored writes compose into one CAS
- * change set with race-free first-touch-wins (see the observer's docs). This
- * backend only forwards the mutation point to the observer before delegating to
- * the base `FilesystemBackend`.
+ * SHELL VS PLAN MODE
+ * ------------------
+ * Outside plan mode the harness uses {@link CasCaptureShellBackend} (deepagents
+ * LocalShellBackend + CAS observation) so the `execute` tool is available and
+ * approval-gated. Plan mode keeps {@link CasCaptureFilesystemBackend} because
+ * deepagents rejects filesystem `permissions` combined with an execution-capable
+ * backend — plan mode is read-only by construction, so no shell tool there.
  *
  * deepagents mutates only via `write` (create/overwrite) and `edit` (modify);
  * there is no backend delete/rename, so this observes CREATE and MODIFY. A
  * gitignored delete can only arrive via shell, which stays on the approval gate.
  *
  * @since File-Change HITL Redesign (Phase 3 — CAS deep-agent wiring); sub-agent
- * gitignored capture parity (Session 26, DD-19)
+ * gitignored capture parity (Session 26, DD-19); shell restore (issue #248)
  */
-import { FilesystemBackend } from "deepagents";
+import { FilesystemBackend, LocalShellBackend } from "deepagents";
 export class CasCaptureFilesystemBackend extends FilesystemBackend {
     observer;
     constructor(options, deps) {
@@ -44,4 +42,34 @@ export class CasCaptureFilesystemBackend extends FilesystemBackend {
         return super.edit(filePath, oldString, newString, replaceAll);
     }
 }
+export class CasCaptureShellBackend extends LocalShellBackend {
+    observer;
+    constructor(options, deps) {
+        super(options);
+        this.observer = deps.observer;
+    }
+    async write(filePath, content) {
+        await this.observer.recordBefore(filePath);
+        return super.write(filePath, content);
+    }
+    async edit(filePath, oldString, newString, replaceAll) {
+        await this.observer.recordBefore(filePath);
+        return super.edit(filePath, oldString, newString, replaceAll);
+    }
+}
+/**
+ * Construct the CAS-observing backend for a deepagents agent graph.
+ *
+ * Shell-capable when `shellEnv` is provided; otherwise filesystem-only (plan mode).
+ * Shell backends honor LocalShellBackend's documented initialize contract.
+ */
+export async function createCasCaptureBackend(options) {
+    const { rootDir, observer, shellEnv } = options;
+    if (shellEnv !== undefined) {
+        const backend = new CasCaptureShellBackend({ rootDir, env: shellEnv }, { observer });
+        await backend.initialize();
+        return backend;
+    }
+    return new CasCaptureFilesystemBackend({ rootDir }, { observer });
+}
 //# sourceMappingURL=cas-capture-backend.js.map

package/dist/activities/execute-deep-agent/cas-capture-backend.js.map

@@ -1 +1 @@
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+{"version":3,"file":"cas-capture-backend.js","sourceRoot":"","sources":["../../../src/activities/execute-deep-agent/cas-capture-backend.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AAEH,OAAO,EAAE,iBAAiB,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAYlE,MAAM,OAAO,2BAA4B,SAAQ,iBAAiB;IAC/C,QAAQ,CAAqB;IAE9C,YAAY,OAAiC,EAAE,IAAoB;QACjE,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAChC,CAAC;IAEQ,KAAK,CAAC,KAAK,CAAC,QAAgB,EAAE,OAAe;QACpD,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAC3C,OAAO,KAAK,CAAC,KAAK,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IACxC,CAAC;IAEQ,KAAK,CAAC,IAAI,CACjB,QAAgB,EAChB,SAAiB,EACjB,SAAiB,EACjB,UAAoB;QAEpB,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAC3C,OAAO,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAE,UAAU,CAAC,CAAC;IAChE,CAAC;CACF;AAED,MAAM,OAAO,sBAAuB,SAAQ,iBAAiB;IAC1C,QAAQ,CAAqB;IAE9C,YAAY,OAAiC,EAAE,IAAoB;QACjE,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAChC,CAAC;IAEQ,KAAK,CAAC,KAAK,CAAC,QAAgB,EAAE,OAAe;QACpD,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAC3C,OAAO,KAAK,CAAC,KAAK,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;IACxC,CAAC;IAEQ,KAAK,CAAC,IAAI,CACjB,QAAgB,EAChB,SAAiB,EACjB,SAAiB,EACjB,UAAoB;QAEpB,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAC;QAC3C,OAAO,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,SAAS,EAAE,SAAS,EAAE,UAAU,CAAC,CAAC;IAChE,CAAC;CACF;AAWD;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,uBAAuB,CAC3C,OAAuC;IAEvC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAC;IAEhD,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;QAC3B,MAAM,OAAO,GAAG,IAAI,sBAAsB,CACxC,EAAE,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,EAC1B,EAAE,QAAQ,EAAE,CACb,CAAC;QACF,MAAM,OAAO,CAAC,UAAU,EAAE,CAAC;QAC3B,OAAO,OAAO,CAAC;IACjB,CAAC;IAED,OAAO,IAAI,2BAA2B,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAC;AACpE,CAAC"}

package/dist/activities/execute-deep-agent/deepagents-profiles.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Stigmer-specific deepagents harness profile registrations.
+ *
+ * deepagents 1.10.x auto-injects a built-in `general-purpose` sub-agent into
+ * every `createDeepAgent()` call unless the caller supplies one with that name.
+ * The injected sub-agent carries only deepagents' built-in middleware — not our
+ * approval gate — so it is an ungated write/edit path today and would be an
+ * ungated `execute` path with a shell backend.
+ *
+ * Registrations merge additively with deepagents' built-in prompt profiles, so
+ * disabling auto-injection here does not alter model prompt overlays.
+ */
+/** Idempotent: safe to call from runner boot and from tests. */
+export declare function registerStigmerDeepagentsProfiles(): void;
+/** Test-only: reset the once guard so profile registration can be re-exercised. */
+export declare function resetStigmerDeepagentsProfilesForTests(): void;

package/dist/activities/execute-deep-agent/deepagents-profiles.js

@@ -0,0 +1,31 @@
+/**
+ * Stigmer-specific deepagents harness profile registrations.
+ *
+ * deepagents 1.10.x auto-injects a built-in `general-purpose` sub-agent into
+ * every `createDeepAgent()` call unless the caller supplies one with that name.
+ * The injected sub-agent carries only deepagents' built-in middleware — not our
+ * approval gate — so it is an ungated write/edit path today and would be an
+ * ungated `execute` path with a shell backend.
+ *
+ * Registrations merge additively with deepagents' built-in prompt profiles, so
+ * disabling auto-injection here does not alter model prompt overlays.
+ */
+import { registerHarnessProfile } from "deepagents";
+const PROVIDERS_WITH_GP_SUPPRESSION = ["anthropic", "openai"];
+let registered = false;
+/** Idempotent: safe to call from runner boot and from tests. */
+export function registerStigmerDeepagentsProfiles() {
+    if (registered)
+        return;
+    registered = true;
+    for (const provider of PROVIDERS_WITH_GP_SUPPRESSION) {
+        registerHarnessProfile(provider, {
+            generalPurposeSubagent: { enabled: false },
+        });
+    }
+}
+/** Test-only: reset the once guard so profile registration can be re-exercised. */
+export function resetStigmerDeepagentsProfilesForTests() {
+    registered = false;
+}
+//# sourceMappingURL=deepagents-profiles.js.map

package/dist/activities/execute-deep-agent/deepagents-profiles.js.map

@@ -0,0 +1 @@
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package/dist/activities/execute-deep-agent/setup.js

@@ -15,7 +15,8 @@ import { resolveMcpServers } from "../../shared/mcp-resolver.js";
 import { backfillMcpServersIfNeeded } from "../../shared/connect-backfill.js";
 import { WorkspaceProvisioner } from "../../shared/workspace/provisioner.js";
 import { LocalWorkspaceBackend } from "../../shared/workspace/local-backend.js";
-import { CasCaptureFilesystemBackend } from "./cas-capture-backend.js";
+import { createCasCaptureBackend } from "./cas-capture-backend.js";
+import { buildShellEnv } from "./shell-env.js";
 import { CasCaptureObserver } from "./cas-capture-observer.js";
 import { isGitWorkTree, isPathCapturable } from "../../shared/filereview/git-substrate.js";
 import { deriveCaptureMode } from "../../shared/filereview/capture.js";
@@ -217,6 +218,8 @@ export async function performSetup(deps) {
         await ensurePricingLoaded();
         const pricing = getModelPricing(modelName);
         const execConfig = execution.spec.executionConfig;
+        const isPlanMode = execConfig?.interactionMode === InteractionMode.PLAN;
+        const shellEnv = isPlanMode ? undefined : buildShellEnv(envResult.mergedEnvVars);
         const toolServerMap = new Map();
         if (mcpConnection) {
             for (const [serverName, serverTools] of Object.entries(mcpConnection.serverToolMap)) {
@@ -336,6 +339,9 @@ export async function performSetup(deps) {
                     stigmerToken: config.stigmerToken ?? undefined,
                     headerScope: { executionId },
                 })).model,
+                // Presence of shellEnv is the shell-capability switch for sub-agent
+                // backends too (undefined in plan mode; see buildShellEnv above).
+                shellEnv,
             });
         }
         // Step 12: Create the agent graph with middleware
@@ -351,7 +357,6 @@ export async function performSetup(deps) {
         // first-match-wins with a permissive default, so a single deny-all-writes
         // rule is sufficient. (The Cursor harness enforces plan mode via its prompt
         // prefix; the native harness enforces it here.)
-        const isPlanMode = execConfig?.interactionMode === InteractionMode.PLAN;
         const planModePermissions = [
             { operations: ["write"], paths: ["/**"], mode: "deny" },
         ];
@@ -361,7 +366,11 @@ export async function performSetup(deps) {
         // bytes of every CAS-owned path — .gitignored paths in a git work tree, all
         // touched paths in a non-git one — so the boundary can capture them into CAS.
         // It is gate-independent, so it holds even under the global bypass.
-        const fileBackend = new CasCaptureFilesystemBackend({ rootDir: workspaceBackend.rootDir }, { observer: casObserver });
+        const fileBackend = await createCasCaptureBackend({
+            rootDir: workspaceBackend.rootDir,
+            observer: casObserver,
+            shellEnv,
+        });
         const agentGraph = await createDeepAgent({
             model,
             checkpointer: checkpointer,

package/dist/activities/execute-deep-agent/setup.js.map

@@ -1 +1 @@
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package/dist/activities/execute-deep-agent/shell-env.d.ts

@@ -0,0 +1,16 @@
+/**
+ * Shell environment for the native harness `execute` tool.
+ *
+ * Per-execution snapshot: runner-manager rotates `STIGMER_TOKEN` in
+ * `process.env` at runtime, so this must run inside setup for each execution,
+ * never once at process start.
+ */
+/** Runner-internal keys that must never reach agent shell commands. */
+export declare const SHELL_ENV_DENYLIST: readonly string[];
+/**
+ * Build the environment map passed to deepagents' LocalShellBackend.
+ *
+ * Base: runner process env minus {@link SHELL_ENV_DENYLIST}, then overlay
+ * {@link mergedEnvVars} (ExecutionContext wins on conflict).
+ */
+export declare function buildShellEnv(mergedEnvVars: Readonly<Record<string, string>>, baseEnv?: NodeJS.ProcessEnv): Record<string, string>;

package/dist/activities/execute-deep-agent/shell-env.js

@@ -0,0 +1,36 @@
+/**
+ * Shell environment for the native harness `execute` tool.
+ *
+ * Per-execution snapshot: runner-manager rotates `STIGMER_TOKEN` in
+ * `process.env` at runtime, so this must run inside setup for each execution,
+ * never once at process start.
+ */
+/** Runner-internal keys that must never reach agent shell commands. */
+export const SHELL_ENV_DENYLIST = [
+    // Derives HITL approval fingerprints — an agent that reads this could forge receipts.
+    "STIGMER_RUNNER_HITL_SECRET",
+    // Cursor harness credential; shell commands do not need direct Cursor API access.
+    "CURSOR_API_KEY",
+    // Stigmer control-plane auth; shell commands use ExecutionContext overlay instead.
+    "STIGMER_TOKEN",
+];
+/**
+ * Build the environment map passed to deepagents' LocalShellBackend.
+ *
+ * Base: runner process env minus {@link SHELL_ENV_DENYLIST}, then overlay
+ * {@link mergedEnvVars} (ExecutionContext wins on conflict).
+ */
+export function buildShellEnv(mergedEnvVars, baseEnv = process.env) {
+    const deny = new Set(SHELL_ENV_DENYLIST);
+    const env = {};
+    for (const [key, value] of Object.entries(baseEnv)) {
+        if (deny.has(key) || value === undefined)
+            continue;
+        env[key] = value;
+    }
+    for (const [key, value] of Object.entries(mergedEnvVars)) {
+        env[key] = value;
+    }
+    return env;
+}
+//# sourceMappingURL=shell-env.js.map

package/dist/activities/execute-deep-agent/shell-env.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"shell-env.js","sourceRoot":"","sources":["../../../src/activities/execute-deep-agent/shell-env.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,uEAAuE;AACvE,MAAM,CAAC,MAAM,kBAAkB,GAAsB;IACnD,sFAAsF;IACtF,4BAA4B;IAC5B,kFAAkF;IAClF,gBAAgB;IAChB,mFAAmF;IACnF,eAAe;CAChB,CAAC;AAEF;;;;;GAKG;AACH,MAAM,UAAU,aAAa,CAC3B,aAA+C,EAC/C,UAA6B,OAAO,CAAC,GAAG;IAExC,MAAM,IAAI,GAAG,IAAI,GAAG,CAAC,kBAAkB,CAAC,CAAC;IACzC,MAAM,GAAG,GAA2B,EAAE,CAAC;IAEvC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC;QACnD,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,KAAK,KAAK,SAAS;YAAE,SAAS;QACnD,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;IACnB,CAAC;IAED,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,aAAa,CAAC,EAAE,CAAC;QACzD,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;IACnB,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC"}

package/dist/activities/execute-deep-agent/subagent-transformer.d.ts

@@ -11,6 +11,10 @@
  * - Filter parent MCP tools: no reconnection overhead, stateless servers are the norm
  * - Prompt injection for skills: FilesystemBackend incompatible with native skills field
  * - Built-in explore/shell subagents use prompt-based tool restriction
+ * - Built-in general-purpose replaces deepagents' auto-injected one (which carries
+ *   no approval gate — see deepagents-profiles.ts for the suppression half)
+ * - Sub-agent backends are shell-capable outside plan mode (issue #248), mirroring
+ *   the parent's backend selection in setup.ts
  * - Invalid configurations are logged and skipped (graceful degradation)
  * - Empty subagent list returns null (no subagents configured)
  */
@@ -71,19 +75,35 @@ export interface SubagentTransformOptions {
      * model name string is passed to deepagents directly.
      */
     readonly modelFactory?: (modelName: string) => Promise<BaseChatModel>;
+    /**
+     * Per-execution env for the sub-agent `execute` tool, snapshotted in setup
+     * (see shell-env.ts). Presence is the single switch for shell capability:
+     * undefined (plan mode) compiles sub-agents onto non-shell filesystem
+     * backends, exactly like the parent's backend selection.
+     */
+    readonly shellEnv?: Record<string, string>;
 }
 /**
- * Create built-in explore and shell subagent specifications.
+ * Create built-in explore, shell, and general-purpose subagent specifications.
  *
- * Built-in subagents receive:
- * - The full deepagents built-in tool set (from FilesystemBackend) restricted via prompt
+ * explore and shell receive:
+ * - The full deepagents built-in tool set restricted via prompt
  * - Purpose-built system prompts with explicit scope boundaries
  * - No skills, no MCP tools, no parent prompt inheritance
  *
+ * general-purpose is the gated replacement for the sub-agent deepagents would
+ * otherwise auto-inject WITHOUT our approval gate (suppressed process-wide in
+ * deepagents-profiles.ts; supplying our own under the same name is the
+ * documented override path). It uses deepagents' own description/prompt so the
+ * model's delegation behavior is unchanged, and receives the parent's MCP tools
+ * for capability parity with the injected original. Conscious simplification:
+ * the parent's skills prompt is NOT inherited — a sub-agent needing skills
+ * should be declared explicitly in the Agent spec.
+ *
  * Returns an empty array if no workspace is configured (subagents need
  * workspace tools to be useful).
  */
-export declare function createBuiltinSubagents(hasWorkspace: boolean): TransformedSubagent[];
+export declare function createBuiltinSubagents(hasWorkspace: boolean, parentMcpTools?: readonly StructuredTool[]): TransformedSubagent[];
 /**
  * Transform a single SubAgent proto into the intermediate representation.
  *
@@ -140,7 +160,8 @@ export declare function resolveSubagentSkillPrompt(subAgent: SubAgent, skillsByS
  * Compile transformed subagent specifications into CompiledSubAgent instances.
  *
  * Each subagent gets:
- * - Its own agent graph (via createDeepAgent with FilesystemBackend sharing the workspace)
+ * - Its own agent graph sharing the parent's workspace root (shell-capable
+ *   outside plan mode; see {@link buildSubagentBackend})
  * - Per-subagent middleware (loop detection, budget, truncation, cost cap view)
  * - Concurrency gating via shared SubAgentGate
  */
@@ -152,12 +173,14 @@ export declare function compileSubagents(transformed: readonly TransformedSubage
     /** Shared CAS observer (capture mode only); see {@link SubagentTransformOptions.casObserver}. */
     readonly casObserver?: CasCaptureObserver;
     readonly modelFactory?: (modelName: string) => Promise<BaseChatModel>;
+    /** Shell env for `execute`; see {@link SubagentTransformOptions.shellEnv}. */
+    readonly shellEnv?: Record<string, string>;
 }): Promise<CompiledSubAgent[]>;
 /**
  * Transform proto SubAgents and compile into CompiledSubAgent instances.
  *
  * This is the main entry point called from setup.ts. It orchestrates:
- * 1. Built-in subagent creation (explore + shell)
+ * 1. Built-in subagent creation (explore, shell, general-purpose)
  * 2. Per-subagent transformation (proto → TransformedSubagent)
  * 3. MCP tool filtering per subagent
  * 4. Skill resolution and prompt injection (Session 2)