@stigmer/runner 3.12.4 → 3.12.6

package/dist/shared/skill-writer.js

@@ -1,5 +1,5 @@
 /**
- * Skill writing and prompt generation for the deep-agent execution path.
+ * Skill mounting and prompt generation for the deep-agent execution path.
  *
  * Follows the Agent Skills specification progressive disclosure model:
  *
@@ -10,13 +10,23 @@
  * 3. Resources (on demand) — scripts, references, and assets are
  *    loaded by the agent only when required.
  *
- * Skills live under `.stigmer/skills/{name}/` relative to the workspace root.
- * Returned paths are workspace-relative so that the agent's sandbox backend
- * resolves them correctly regardless of mount strategy.
+ * Skills physically live in the session's platform directory
+ * (`{platformDir}/skills/{name}/` — the SAME location the Cursor harness
+ * mounts into), and the agent sees them as `.stigmer/skills/{name}/`
+ * through the per-turn workspace symlink (see workspace/stigmer-link.ts).
+ * Returned paths are the agent-visible `.stigmer/…` form.
+ *
+ * Mounts are cached by the skill's content-addressed version hash via the
+ * shared skill-mount mechanics (issue #337, mirroring the Cursor harness's
+ * #672 fix): metadata is fetched every execution — a pushed skill update
+ * still lands on the very next message — but an unchanged skill skips the
+ * artifact download and rewrite entirely.
  */
-import { extractZipFileEntries } from "./zip-extract.js";
-const SKILLS_RELATIVE_BASE = ".stigmer/skills";
-const SCRIPT_EXTENSIONS = new Set([".sh", ".py", ".js", ".ts", ".rb", ".pl"]);
+import { join } from "node:path";
+import { SKILLS_SUBDIR, mountIsFresh, downloadArtifact, writeSkillMount, } from "./skill-mount.js";
+import { STIGMER_LOCAL_STATE_DIR } from "./workspace/stigmer-link.js";
+/** Agent-visible base of the skills tree (via the workspace `.stigmer` symlink). */
+const SKILLS_RELATIVE_BASE = `${STIGMER_LOCAL_STATE_DIR}/${SKILLS_SUBDIR}`;
 // ─── Fetch ───────────────────────────────────────────────────────────────
 /**
  * Merge skill refs from agent and session specs (union, dedup by slug,
@@ -59,87 +69,80 @@ export async function fetchSkillsByRefs(client, refs) {
     }
     return results;
 }
-// ─── Write ───────────────────────────────────────────────────────────────
+// ─── Mount ───────────────────────────────────────────────────────────────
 /**
- * Write skill artifacts to the workspace. Returns a map of
- * skill-id -> workspace-relative directory path.
+ * Mount skills into the session's platform directory, downloading each
+ * skill's artifact only on a version-hash cache miss (see skill-mount.ts
+ * for the marker mechanics). Returns a map of skill-id -> agent-visible
+ * directory path.
+ *
+ * The returned map is a NAMING function, not a success record: every skill
+ * gets its path entry so prompt generation stays total, while mount
+ * failures degrade that one skill (loud log, no throw) — one broken skill
+ * must never kill the run.
  *
- * For each skill:
- * - If a ZIP artifact is available, extract it to .stigmer/skills/{name}/
- * - Otherwise, write just the SKILL.md from the spec
- * - Make scripts executable
+ * Skills mount in parallel (each owns an independent directory), EXCEPT
+ * when two skills resolve to the same directory name (same `spec.name`
+ * from different orgs): concurrent remove-and-rewrite passes on one
+ * directory would corrupt the mount, so only the first claimant mounts and
+ * the collision is logged loudly. (The sequential code this replaced
+ * silently let the last writer win — no better, just quieter.)
  */
-export async function writeSkills(skills, workspaceBackend, artifacts) {
+export async function mountSkills(client, skills, platformDir) {
     const paths = new Map();
+    const claims = new Map();
     for (const skill of skills) {
         const name = skill.spec?.name || skill.metadata?.slug || "unknown";
         const skillId = skill.metadata?.id ?? name;
-        const relativeDir = `${SKILLS_RELATIVE_BASE}/${name}`;
-        paths.set(skillId, relativeDir);
-        const artifactBytes = artifacts.get(skillId);
-        if (skill.spec?.skillMd) {
-            const skillMdPath = `${relativeDir}/SKILL.md`;
-            await workspaceBackend.writeFile(skillMdPath, skill.spec.skillMd);
-            if (artifactBytes && artifactBytes.length > 0) {
-                await extractZipToWorkspaceExcluding(artifactBytes, "SKILL.md", relativeDir, workspaceBackend);
-            }
+        paths.set(skillId, `${SKILLS_RELATIVE_BASE}/${name}`);
+        // Impossible through the push pipeline (push.go hard-fails a ZIP
+        // without an extractable SKILL.md and always populates spec.skill_md),
+        // so an empty skillMd means a broken resource — skip, same as Cursor.
+        if (!skill.spec?.skillMd) {
+            console.warn(`[skill-writer] skill ${name} (${skillId}) has no skillMd content — skipping mount`);
+            continue;
         }
-        else if (artifactBytes && artifactBytes.length > 0) {
-            await extractZipToWorkspace(artifactBytes, relativeDir, workspaceBackend);
+        const prev = claims.get(name);
+        if (prev) {
+            console.warn(`[skill-writer] mount directory collision on '${name}': ` +
+                `${prev.metadata?.org}/${prev.metadata?.slug} already claims it, ` +
+                `skipping ${skill.metadata?.org}/${skill.metadata?.slug}`);
+            continue;
         }
-        await makeScriptsExecutable(relativeDir, workspaceBackend);
+        claims.set(name, skill);
     }
+    await Promise.all([...claims.entries()].map(async ([name, skill]) => {
+        const skillDir = join(platformDir, SKILLS_SUBDIR, name);
+        try {
+            const versionHash = skill.status?.versionHash ?? "";
+            const wantsArtifact = Boolean(skill.status?.artifactStorageKey);
+            if (versionHash !== "" && (await mountIsFresh(skillDir, versionHash, wantsArtifact))) {
+                console.log(`[skill-writer] mount cache hit: ${name} (version ${versionHash.slice(0, 12)}) — skipping artifact transfer`);
+                return;
+            }
+            let artifactBytes;
+            if (wantsArtifact) {
+                try {
+                    artifactBytes = await downloadArtifact(client, skill.status.artifactStorageKey);
+                }
+                catch (err) {
+                    // Deliberate degradation, but LOUD (#675): the run still gets
+                    // SKILL.md, and the marker records artifactMounted=false so the
+                    // next execution retries the download.
+                    console.error(`[skill-writer] artifact download FAILED for ${name} ` +
+                        `(key=${skill.status.artifactStorageKey}) — mounting SKILL.md WITHOUT the skill's ` +
+                        `supporting files (scripts/references will be missing): ${err instanceof Error ? err.message : err}`);
+                }
+            }
+            await writeSkillMount(skill, skillDir, artifactBytes);
+            console.log(`[skill-writer] wrote skill mount: ${name}`);
+        }
+        catch (err) {
+            console.warn(`[skill-writer] failed to mount skill ${name}: ${err instanceof Error ? err.message : err}`);
+        }
+    }));
     return { paths };
 }
-/**
- * Compute skill paths without writing anything (for resume integrity checks).
- */
-export function computeSkillPaths(skills) {
-    const paths = new Map();
-    for (const skill of skills) {
-        const name = skill.spec?.name || skill.metadata?.slug || "unknown";
-        const skillId = skill.metadata?.id ?? name;
-        paths.set(skillId, `${SKILLS_RELATIVE_BASE}/${name}`);
-    }
-    return paths;
-}
-/**
- * Check workspace integrity for resume fast-path.
- * Returns true if the sentinel SKILL.md file exists for the first skill.
- */
-export async function checkSkillIntegrity(skills, workspaceBackend) {
-    if (skills.length === 0)
-        return true;
-    const paths = computeSkillPaths(skills);
-    const firstPath = paths.values().next().value;
-    if (!firstPath)
-        return true;
-    const sentinel = `${firstPath}/SKILL.md`;
-    return workspaceBackend.exists(sentinel);
-}
-// ─── ZIP extraction ──────────────────────────────────────────────────────
-async function extractZipToWorkspace(zipBytes, targetDir, backend) {
-    const entries = await extractZipFileEntries(zipBytes);
-    for (const entry of entries) {
-        await backend.writeFileBuffer(`${targetDir}/${entry.path}`, Buffer.from(entry.content));
-    }
-}
-async function extractZipToWorkspaceExcluding(zipBytes, excludeName, targetDir, backend) {
-    const entries = await extractZipFileEntries(zipBytes, { exclude: [excludeName] });
-    for (const entry of entries) {
-        await backend.writeFileBuffer(`${targetDir}/${entry.path}`, Buffer.from(entry.content));
-    }
-}
-async function makeScriptsExecutable(relativeDir, backend) {
-    const extensions = [...SCRIPT_EXTENSIONS].map(ext => `-name '*${ext}'`).join(" -o ");
-    const cmd = `find ${relativeDir} -type f \\( ${extensions} \\) -exec chmod +x {} \\; 2>/dev/null || true`;
-    try {
-        await backend.execute(cmd);
-    }
-    catch {
-        // Non-fatal: scripts may not be executable in all environments
-    }
-}
 // ─── Prompt generation ───────────────────────────────────────────────────
 /**
  * Generate the system prompt section following the Agent Skills spec
@@ -201,30 +204,4 @@ export function generateAlsoAvailableSection(excludedNames) {
         "If you determine one of them is relevant to your task, " +
         "read its SKILL.md at `.stigmer/skills/<name>/SKILL.md` to activate it.\n");
 }
-// ─── Artifact fetching ───────────────────────────────────────────────────
-/**
- * Download skill artifacts for all skills that have a storage key.
- * Returns a map from skill ID to artifact bytes.
- */
-export async function fetchSkillArtifacts(client, skills) {
-    const artifacts = new Map();
-    const fetches = skills
-        .filter(s => s.status?.artifactStorageKey)
-        .map(async (skill) => {
-        const key = skill.status.artifactStorageKey;
-        const skillId = skill.metadata?.id ?? skill.spec?.name ?? "unknown";
-        try {
-            const response = await client.getSkillArtifact(key);
-            if (response.artifact && response.artifact.length > 0) {
-                artifacts.set(skillId, response.artifact);
-            }
-        }
-        catch (err) {
-            console.warn(`[skill-writer] Failed to download artifact for ${skill.spec?.name}: ` +
-                `${err instanceof Error ? err.message : String(err)}. Falling back to SKILL.md only.`);
-        }
-    });
-    await Promise.all(fetches);
-    return artifacts;
-}
 //# sourceMappingURL=skill-writer.js.map

package/dist/shared/skill-writer.js.map

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package/dist/shared/thinking-mode.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Harness-neutral thinking-mode semantics (stigmer/stigmer#772) — the
+ * second variant dimension alongside `shared/service-tier.ts`.
+ *
+ * The platform contract mirrors the service tier's: the thinking pin is
+ * ALWAYS explicit by the time a provider request leaves the runner.
+ * UNSPECIFIED resolves to DISABLED here and ONLY here — every upstream
+ * layer preserves the caller's raw enum so "user chose disabled" stays
+ * distinguishable from "platform default" all the way to the ledger.
+ *
+ * Unlike the fast tier, thinking is NOT separately priced: Cursor bills
+ * thinking variants at base per-token rates (ledger-verified 2026-08-15 —
+ * 277 events at exactly base; thinking+fast at exactly the fast rate).
+ * The cost of ENABLED is the extra reasoning tokens, billed as output.
+ * Selection is therefore capability-gated (registry capabilities.thinking)
+ * rather than pricing-gated, and the estimate/billing paths need no
+ * thinking-specific rates.
+ *
+ * v1 translates thinking on the Cursor harness only (the explicit
+ * `thinking` variant parameter, `execute-cursor/service-tier.ts`). No
+ * native wire mapping exists yet — create-time validation refuses ENABLED
+ * for native-harness models, mirroring the tier's #361 posture.
+ */
+import { ThinkingMode } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/enum_pb";
+/**
+ * The effective mode after platform-default resolution: never UNSPECIFIED.
+ */
+export type EffectiveThinkingMode = ThinkingMode.DISABLED | ThinkingMode.ENABLED;
+/**
+ * Resolve the configured mode to its effective value. The single place in
+ * the platform where UNSPECIFIED becomes DISABLED.
+ */
+export declare function resolveEffectiveThinkingMode(configured: ThinkingMode | undefined): EffectiveThinkingMode;
+/** Human-readable mode label for logs and error messages. */
+export declare function thinkingModeLabel(mode: ThinkingMode): string;

package/dist/shared/thinking-mode.js

@@ -0,0 +1,43 @@
+/**
+ * Harness-neutral thinking-mode semantics (stigmer/stigmer#772) — the
+ * second variant dimension alongside `shared/service-tier.ts`.
+ *
+ * The platform contract mirrors the service tier's: the thinking pin is
+ * ALWAYS explicit by the time a provider request leaves the runner.
+ * UNSPECIFIED resolves to DISABLED here and ONLY here — every upstream
+ * layer preserves the caller's raw enum so "user chose disabled" stays
+ * distinguishable from "platform default" all the way to the ledger.
+ *
+ * Unlike the fast tier, thinking is NOT separately priced: Cursor bills
+ * thinking variants at base per-token rates (ledger-verified 2026-08-15 —
+ * 277 events at exactly base; thinking+fast at exactly the fast rate).
+ * The cost of ENABLED is the extra reasoning tokens, billed as output.
+ * Selection is therefore capability-gated (registry capabilities.thinking)
+ * rather than pricing-gated, and the estimate/billing paths need no
+ * thinking-specific rates.
+ *
+ * v1 translates thinking on the Cursor harness only (the explicit
+ * `thinking` variant parameter, `execute-cursor/service-tier.ts`). No
+ * native wire mapping exists yet — create-time validation refuses ENABLED
+ * for native-harness models, mirroring the tier's #361 posture.
+ */
+import { ThinkingMode } from "@stigmer/protos/ai/stigmer/agentic/agentexecution/v1/enum_pb";
+/**
+ * Resolve the configured mode to its effective value. The single place in
+ * the platform where UNSPECIFIED becomes DISABLED.
+ */
+export function resolveEffectiveThinkingMode(configured) {
+    return configured === ThinkingMode.ENABLED ? ThinkingMode.ENABLED : ThinkingMode.DISABLED;
+}
+/** Human-readable mode label for logs and error messages. */
+export function thinkingModeLabel(mode) {
+    switch (mode) {
+        case ThinkingMode.ENABLED:
+            return "enabled";
+        case ThinkingMode.DISABLED:
+            return "disabled";
+        default:
+            return "unspecified";
+    }
+}
+//# sourceMappingURL=thinking-mode.js.map

package/dist/shared/thinking-mode.js.map

@@ -0,0 +1 @@
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package/dist/shared/worker-shutdown.d.ts

@@ -0,0 +1,67 @@
+/**
+ * Per-task-queue worker-shutdown signals — the classification channel that
+ * lets an in-flight activity distinguish "my worker is shutting down" from
+ * "the orchestrator cancelled me" (a user pause).
+ *
+ * The signal carries NO lifecycle authority: aborting it never stops a
+ * worker or an activity (Temporal's own drain does that). It exists purely
+ * so the activity's cancellation handling can classify the interruption
+ * honestly — a shutdown is not a pause, and must surface as the
+ * worker-shutdown failure shape the control planes recognize (issue #776).
+ *
+ * Ownership contract:
+ *   - whoever creates a Worker registers a signal for its queue BEFORE the
+ *     worker starts polling;
+ *   - whoever initiates a full shutdown (SIGTERM handler, desktop quit)
+ *     aborts the signal BEFORE calling worker.shutdown(), so activities
+ *     cancelled by the drain observe it already aborted;
+ *   - a graceful single-worker teardown (view close, deferred teardown in
+ *     the runner-manager) must NOT abort — those paths only run once no
+ *     activity is in flight, and aborting earlier is exactly the regression
+ *     that killed running activities on a view close.
+ *
+ * Module-level (not per-manager) because activities resolve their signal by
+ * task-queue name via {@link getShutdownSignalForQueue} without a handle to
+ * the runner/manager instance that created their worker.
+ */
+/**
+ * Register a fresh shutdown signal for a task queue, replacing any previous
+ * registration (a re-created worker on a reused queue must not observe the
+ * old worker's aborted signal). Returns the controller so the worker's owner
+ * can abort it at shutdown.
+ */
+export declare function registerWorkerShutdownSignal(taskQueue: string): AbortController;
+/** The signal an activity on `taskQueue` should observe, if one is registered. */
+export declare function getShutdownSignalForQueue(taskQueue: string): AbortSignal | undefined;
+/**
+ * Abort the queue's signal, marking any in-flight activity's imminent
+ * cancellation as a worker shutdown. Idempotent; no-op for an unknown queue.
+ */
+export declare function signalWorkerShutdown(taskQueue: string): void;
+/** Drop the registration once the queue's worker is fully torn down. */
+export declare function unregisterWorkerShutdownSignal(taskQueue: string): void;
+/** The evidence a turn's post-stream classification weighs (see below). */
+export interface TurnInterruptionEvidence {
+    /** The periodic heartbeat threw CancelledFailure with no shutdown signal. */
+    heartbeatCancelled: boolean;
+    /** The periodic heartbeat threw CancelledFailure with the signal aborted. */
+    heartbeatWorkerShutdown: boolean;
+    /** Temporal delivered cancellation to the activity. */
+    cancellationSignalAborted: boolean;
+    /** This queue's worker-shutdown signal is aborted. */
+    shutdownSignalAborted: boolean;
+}
+/**
+ * Classify how (whether) a turn's stream was interrupted, from the evidence
+ * available after the stream ends. Pure so the decision table is directly
+ * testable — the activities feed it their heartbeat flags and signals.
+ *
+ * The load-bearing rule is the grace-window guard (#776): an aborted
+ * shutdown signal ALONE is "none", because a run that completes normally
+ * inside the drain grace window reaches the classification with the signal
+ * already aborted and nothing actually interrupted. Shutdown requires
+ * interruption evidence (a heartbeat CancelledFailure or a delivered
+ * cancellation) alongside the signal; a heartbeat cancellation with no
+ * shutdown signal is the orchestrator's pause.
+ */
+export declare function classifyTurnInterruption(evidence: TurnInterruptionEvidence): "worker-shutdown" | "pause" | "none";

package/dist/shared/worker-shutdown.js

@@ -0,0 +1,79 @@
+/**
+ * Per-task-queue worker-shutdown signals — the classification channel that
+ * lets an in-flight activity distinguish "my worker is shutting down" from
+ * "the orchestrator cancelled me" (a user pause).
+ *
+ * The signal carries NO lifecycle authority: aborting it never stops a
+ * worker or an activity (Temporal's own drain does that). It exists purely
+ * so the activity's cancellation handling can classify the interruption
+ * honestly — a shutdown is not a pause, and must surface as the
+ * worker-shutdown failure shape the control planes recognize (issue #776).
+ *
+ * Ownership contract:
+ *   - whoever creates a Worker registers a signal for its queue BEFORE the
+ *     worker starts polling;
+ *   - whoever initiates a full shutdown (SIGTERM handler, desktop quit)
+ *     aborts the signal BEFORE calling worker.shutdown(), so activities
+ *     cancelled by the drain observe it already aborted;
+ *   - a graceful single-worker teardown (view close, deferred teardown in
+ *     the runner-manager) must NOT abort — those paths only run once no
+ *     activity is in flight, and aborting earlier is exactly the regression
+ *     that killed running activities on a view close.
+ *
+ * Module-level (not per-manager) because activities resolve their signal by
+ * task-queue name via {@link getShutdownSignalForQueue} without a handle to
+ * the runner/manager instance that created their worker.
+ */
+const registry = new Map();
+/**
+ * Register a fresh shutdown signal for a task queue, replacing any previous
+ * registration (a re-created worker on a reused queue must not observe the
+ * old worker's aborted signal). Returns the controller so the worker's owner
+ * can abort it at shutdown.
+ */
+export function registerWorkerShutdownSignal(taskQueue) {
+    const controller = new AbortController();
+    registry.set(taskQueue, controller);
+    return controller;
+}
+/** The signal an activity on `taskQueue` should observe, if one is registered. */
+export function getShutdownSignalForQueue(taskQueue) {
+    return registry.get(taskQueue)?.signal;
+}
+/**
+ * Abort the queue's signal, marking any in-flight activity's imminent
+ * cancellation as a worker shutdown. Idempotent; no-op for an unknown queue.
+ */
+export function signalWorkerShutdown(taskQueue) {
+    registry.get(taskQueue)?.abort();
+}
+/** Drop the registration once the queue's worker is fully torn down. */
+export function unregisterWorkerShutdownSignal(taskQueue) {
+    registry.delete(taskQueue);
+}
+/**
+ * Classify how (whether) a turn's stream was interrupted, from the evidence
+ * available after the stream ends. Pure so the decision table is directly
+ * testable — the activities feed it their heartbeat flags and signals.
+ *
+ * The load-bearing rule is the grace-window guard (#776): an aborted
+ * shutdown signal ALONE is "none", because a run that completes normally
+ * inside the drain grace window reaches the classification with the signal
+ * already aborted and nothing actually interrupted. Shutdown requires
+ * interruption evidence (a heartbeat CancelledFailure or a delivered
+ * cancellation) alongside the signal; a heartbeat cancellation with no
+ * shutdown signal is the orchestrator's pause.
+ */
+export function classifyTurnInterruption(evidence) {
+    const interrupted = evidence.heartbeatCancelled ||
+        evidence.heartbeatWorkerShutdown ||
+        evidence.cancellationSignalAborted;
+    if (!interrupted) {
+        return "none";
+    }
+    if (evidence.heartbeatWorkerShutdown || evidence.shutdownSignalAborted) {
+        return "worker-shutdown";
+    }
+    return evidence.heartbeatCancelled ? "pause" : "none";
+}
+//# sourceMappingURL=worker-shutdown.js.map

package/dist/shared/worker-shutdown.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"worker-shutdown.js","sourceRoot":"","sources":["../../src/shared/worker-shutdown.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AAEH,MAAM,QAAQ,GAAG,IAAI,GAAG,EAA2B,CAAC;AAEpD;;;;;GAKG;AACH,MAAM,UAAU,4BAA4B,CAAC,SAAiB;IAC5D,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAC;IACzC,QAAQ,CAAC,GAAG,CAAC,SAAS,EAAE,UAAU,CAAC,CAAC;IACpC,OAAO,UAAU,CAAC;AACpB,CAAC;AAED,kFAAkF;AAClF,MAAM,UAAU,yBAAyB,CAAC,SAAiB;IACzD,OAAO,QAAQ,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,MAAM,CAAC;AACzC,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,oBAAoB,CAAC,SAAiB;IACpD,QAAQ,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,CAAC;AACnC,CAAC;AAED,wEAAwE;AACxE,MAAM,UAAU,8BAA8B,CAAC,SAAiB;IAC9D,QAAQ,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;AAC7B,CAAC;AAcD;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,wBAAwB,CACtC,QAAkC;IAElC,MAAM,WAAW,GACf,QAAQ,CAAC,kBAAkB;QAC3B,QAAQ,CAAC,uBAAuB;QAChC,QAAQ,CAAC,yBAAyB,CAAC;IACrC,IAAI,CAAC,WAAW,EAAE,CAAC;QACjB,OAAO,MAAM,CAAC;IAChB,CAAC;IACD,IAAI,QAAQ,CAAC,uBAAuB,IAAI,QAAQ,CAAC,qBAAqB,EAAE,CAAC;QACvE,OAAO,iBAAiB,CAAC;IAC3B,CAAC;IACD,OAAO,QAAQ,CAAC,kBAAkB,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC;AACxD,CAAC"}

package/dist/shared/workspace/types.d.ts

@@ -36,8 +36,9 @@ export declare class WorkspaceProvisionError extends Error {
 /**
  * Abstraction for executing commands inside a workspace.
  *
- * In local mode, commands run via child_process. In cloud mode (Phase 3),
- * commands route through the Daytona sandbox proxy.
+ * Commands run via child_process in both modes: in cloud mode the runner
+ * itself lives inside the sandbox, so "local" execution is already
+ * sandbox-scoped there.
  *
  * When `platformDir` is set, paths under `.stigmer/` are transparently
  * routed to the platform directory instead of the workspace root, keeping

package/dist/workflow-engine/loader.js

@@ -449,11 +449,13 @@ function parseAgentCallRunConfig(raw) {
         throw new Error("call:agent 'run_config' must be a mapping");
     }
     const obj = raw;
-    const known = new Set(["model_name", "max_cost_usd", "max_tool_rounds", "service_tier"]);
+    const known = new Set([
+        "model_name", "max_cost_usd", "max_tool_rounds", "service_tier", "thinking_mode",
+    ]);
     for (const key of Object.keys(obj)) {
         if (!known.has(key)) {
             throw new Error(`call:agent 'run_config' has unknown field '${key}' ` +
-                `(expected: model_name, max_cost_usd, max_tool_rounds, service_tier)`);
+                `(expected: model_name, max_cost_usd, max_tool_rounds, service_tier, thinking_mode)`);
         }
     }
     const modelName = obj.model_name;
@@ -469,11 +471,13 @@ function parseAgentCallRunConfig(raw) {
         throw new Error("call:agent 'run_config.max_tool_rounds' must be a number >= 0");
     }
     const serviceTier = parseServiceTier(obj.service_tier);
+    const thinkingMode = parseThinkingMode(obj.thinking_mode);
     return {
         model_name: modelName,
         max_cost_usd: maxCostUsd,
         max_tool_rounds: maxToolRounds,
         service_tier: serviceTier,
+        thinking_mode: thinkingMode,
     };
 }
 /**
@@ -500,6 +504,63 @@ function parseServiceTier(raw) {
     }
     return canonical;
 }
+/**
+ * Maps YAML thinking-mode shorthands to canonical enum names, mirroring
+ * SERVICE_TIER_SHORTHANDS (stigmer/stigmer#772). Unknown values are
+ * authoring errors: the mode exists to make the served variant
+ * deterministic, so a typo must never silently fall back to the default.
+ */
+const THINKING_MODE_SHORTHANDS = {
+    disabled: "THINKING_MODE_DISABLED",
+    enabled: "THINKING_MODE_ENABLED",
+};
+function parseThinkingMode(raw) {
+    if (raw === undefined || raw === null)
+        return undefined;
+    if (typeof raw !== "string") {
+        throw new Error("call:agent 'run_config.thinking_mode' must be a string");
+    }
+    const canonical = THINKING_MODE_SHORTHANDS[raw.toLowerCase()] ??
+        (Object.values(THINKING_MODE_SHORTHANDS).includes(raw) ? raw : undefined);
+    if (!canonical) {
+        throw new Error(`call:agent 'run_config.thinking_mode' has unknown value '${raw}' ` +
+            `(expected: disabled, enabled)`);
+    }
+    return canonical;
+}
+/**
+ * Maps on_timeout values to the runner's internal policy words, mirroring
+ * SERVICE_TIER_SHORTHANDS. The persisted CNCF YAML carries the proto enum
+ * NAMES (the server converter emits `HumanInputTimeoutPolicy.String()`),
+ * while hand-written fixtures use the lowercase words — both are accepted.
+ * Unknown values are authoring errors: a timeout policy must never silently
+ * fall back to fail (stigmer/stigmer#779 — the unvalidated cast let every
+ * enum-name policy reach the orchestrator unrecognized, so gates configured
+ * to auto-approve/deny failed at their first real timeout instead).
+ */
+const ON_TIMEOUT_VOCABULARY = {
+    fail: "fail",
+    approve: "approve",
+    deny: "deny",
+    escalate: "escalate",
+    HUMAN_INPUT_TIMEOUT_FAIL: "fail",
+    HUMAN_INPUT_TIMEOUT_APPROVE: "approve",
+    HUMAN_INPUT_TIMEOUT_DENY: "deny",
+    HUMAN_INPUT_TIMEOUT_ESCALATE: "escalate",
+};
+function parseOnTimeout(taskName, raw) {
+    if (raw === undefined || raw === null)
+        return undefined;
+    if (typeof raw !== "string") {
+        throw new Error(`human_input task '${taskName}': 'on_timeout' must be a string`);
+    }
+    const policy = ON_TIMEOUT_VOCABULARY[raw];
+    if (!policy) {
+        throw new Error(`human_input task '${taskName}': unknown on_timeout value '${raw}' ` +
+            `(expected: fail, approve, deny, escalate, or a HUMAN_INPUT_TIMEOUT_* enum name)`);
+    }
+    return policy;
+}
 function parseHumanInputConfig(taskName, raw) {
     if (!raw || typeof raw !== "object") {
         throw new Error(`human_input task '${taskName}' requires a 'with' configuration block`);
@@ -508,11 +569,26 @@ function parseHumanInputConfig(taskName, raw) {
     if (typeof obj.prompt !== "string" || !obj.prompt) {
         throw new Error(`human_input task '${taskName}' requires 'prompt' in 'with'`);
     }
+    const outcomes = Array.isArray(obj.outcomes) && obj.outcomes.length > 0
+        ? obj.outcomes.map((o) => ({ name: o.name, label: o.label, then: o.then }))
+        : undefined;
+    const onTimeout = parseOnTimeout(taskName, obj.on_timeout);
+    // The escalate policy's outcome-by-name contract (stigmer/stigmer#781):
+    // a timeout resolves to the outcome NAMED "escalate", so that outcome must
+    // exist and declare where the escalation branch goes. Checked at load so a
+    // misconfigured gate fails before it ever waits on a reviewer — the server
+    // validator enforces the same shape at apply; this covers hand-written YAML.
+    if (onTimeout === "escalate") {
+        const escalation = outcomes?.find((o) => o.name === "escalate");
+        if (!escalation || !escalation.then) {
+            throw new Error(`human_input task '${taskName}': on_timeout policy 'escalate' requires ` +
+                `an outcome named 'escalate' with 'then' set (the timeout resolves to ` +
+                `that outcome and follows its 'then' branch)`);
+        }
+    }
     return {
         prompt: obj.prompt,
-        outcomes: Array.isArray(obj.outcomes) && obj.outcomes.length > 0
-            ? obj.outcomes.map((o) => ({ name: o.name, label: o.label, then: o.then }))
-            : undefined,
+        outcomes,
         formSchema: obj.form_schema && typeof obj.form_schema === "object"
             ? obj.form_schema
             : undefined,
@@ -520,7 +596,7 @@ function parseHumanInputConfig(taskName, raw) {
             ? obj.approvers.filter((a) => typeof a === "string")
             : undefined,
         timeout: typeof obj.timeout === "number" ? obj.timeout : undefined,
-        onTimeout: obj.on_timeout ?? undefined,
+        onTimeout,
         // Any JSON shape is a valid payload (expression string, object, array),
         // so only null/undefined mean "no payload" here.
         payload: obj.payload ?? undefined,