clinkx 0.3.0 → 1.1.0

package/dist/elaris/types.js

@@ -0,0 +1,252 @@
+import { z } from "zod";
+export const ELARIS_RAW_MAX_DEPTH = 5;
+export const ELARIS_RAW_MAX_BYTES = 16384;
+export const ElarisRawStatusSchema = z.enum([
+    "queued",
+    "provisioning",
+    "provisioning_failed",
+    "running",
+    "succeeded",
+    "failed",
+    "timed_out",
+    "cancelling",
+    "cancelled",
+    "orphaned",
+]);
+export const ElarisFailureClassSchema = z.enum([
+    "execution_failed",
+    "timeout",
+    "cancelled",
+    "provisioning_failed",
+    "internal",
+]);
+export const ElarisPermissionModeSchema = z.enum([
+    "plan",
+    "acceptEdits",
+    "auto",
+    "fullAccess",
+]);
+export const ElarisEffortLevelSchema = z.enum([
+    "low",
+    "medium",
+    "high",
+    "xhigh",
+    "max",
+]);
+export const ElarisMetadataScalarSchema = z.union([
+    z.string(),
+    z.number().finite(),
+    z.boolean(),
+    z.null(),
+]);
+export const ElarisMetadataSchema = z.record(ElarisMetadataScalarSchema);
+export const ElarisRawPassthroughSchema = z.record(z.unknown());
+const uuidSchema = z.string().uuid();
+const dateTimeSchema = z.string().datetime({ offset: true });
+const nullableDateTimeSchema = dateTimeSchema.nullable();
+const urlPathSchema = z.string().min(1);
+function capRaw(value, depth = 0) {
+    if (depth >= ELARIS_RAW_MAX_DEPTH)
+        return "[MaxDepth]";
+    if (value == null)
+        return value;
+    if (typeof value === "string")
+        return value.length > 1024 ? `${value.slice(0, 1024)}...[truncated]` : value;
+    if (typeof value === "number" || typeof value === "boolean")
+        return value;
+    if (Array.isArray(value))
+        return value.slice(0, 50).map((item) => capRaw(item, depth + 1));
+    if (typeof value === "object") {
+        const capped = {};
+        for (const [key, item] of Object.entries(value).slice(0, 50)) {
+            capped[key] = capRaw(item, depth + 1);
+        }
+        return capped;
+    }
+    return String(value);
+}
+function enforceRawByteCap(raw) {
+    const capped = capRaw(raw);
+    const encoded = JSON.stringify(capped);
+    if (encoded.length <= ELARIS_RAW_MAX_BYTES)
+        return capped;
+    return {
+        _truncated: true,
+        _reason: "raw_passthrough_exceeded_cap",
+    };
+}
+function withRaw(schema) {
+    const knownKeys = new Set(Object.keys(schema.shape));
+    return schema.passthrough().transform((value) => {
+        const known = {};
+        const raw = {};
+        for (const [key, item] of Object.entries(value)) {
+            if (knownKeys.has(key))
+                known[key] = item;
+            else
+                raw[key] = item;
+        }
+        if (Object.keys(raw).length === 0)
+            return known;
+        return {
+            ...known,
+            raw: enforceRawByteCap(raw),
+        };
+    });
+}
+export const AgentSessionCreateRequestSchema = z.object({
+    prompt: z.string().min(1).max(100000),
+    model_id: z.string().min(1).max(100),
+    permission_mode: ElarisPermissionModeSchema.default("auto"),
+    effort_level: ElarisEffortLevelSchema.nullish(),
+    github_repo: z.record(z.unknown()).nullish(),
+    metadata: ElarisMetadataSchema.nullish(),
+    run_id: z.string().min(1).max(64).regex(/^[A-Za-z0-9_-]+$/),
+    keep_alive: z.boolean().default(false),
+}).strict();
+export const AgentSessionMessageRequestSchema = z.object({
+    prompt: z.string().min(1).max(100000),
+    model_id: z.string().min(1).max(100).nullish(),
+    permission_mode: ElarisPermissionModeSchema.default("auto"),
+    effort_level: ElarisEffortLevelSchema.nullish(),
+    metadata: ElarisMetadataSchema.nullish(),
+    idempotency_key: z.string().min(1).max(128).regex(/^[A-Za-z0-9_.:-]+$/),
+}).strict();
+export const AgentSessionMessageResponseSchema = withRaw(z.object({
+    session_id: uuidSchema,
+    turn_id: uuidSchema,
+    status: ElarisRawStatusSchema,
+    idempotent_replay: z.boolean().default(false),
+    status_url: urlPathSchema,
+    result_url: urlPathSchema,
+}));
+export const AgentSessionURLResponseSchema = withRaw(z.object({
+    run_id: z.string().min(1),
+    session_id: uuidSchema,
+    chat_id: uuidSchema,
+    status: ElarisRawStatusSchema,
+    cleaned_up_at: nullableDateTimeSchema,
+    artifacts_available: z.boolean().default(true),
+    status_url: urlPathSchema,
+    result_url: urlPathSchema,
+    events_url: urlPathSchema,
+    logs_url: urlPathSchema,
+    artifacts_url: urlPathSchema,
+}));
+export const AgentSessionStageSchema = withRaw(z.object({
+    stage_id: z.string().default("run"),
+    total_calls: z.number().int().nonnegative().default(1),
+    completed_calls: z.number().int().nonnegative(),
+    failed_calls: z.number().int().nonnegative(),
+    call_id: uuidSchema.nullable().default(null),
+    retry_count: z.number().int().nonnegative().default(0),
+    duration_ms: z.number().int().nonnegative().nullable().default(null),
+}));
+export const AgentSessionErrorSummarySchema = withRaw(z.object({
+    code: z.string().nullable().default(null),
+    detail: z.string().nullable().default(null),
+}));
+export const AgentSessionStatusResponseSchema = withRaw(z.object({
+    run_id: z.string().min(1),
+    status: ElarisRawStatusSchema,
+    status_reason: z.string().nullable().default(null),
+    started_at: nullableDateTimeSchema,
+    completed_at: nullableDateTimeSchema,
+    cleanup_due_at: nullableDateTimeSchema,
+    progress: z.number().min(0).max(1).nullable().default(null),
+    result_available: z.boolean(),
+    result_bytes: z.number().int().nonnegative().nullable().default(null),
+    stages: z.array(AgentSessionStageSchema).default([]),
+    error: AgentSessionErrorSummarySchema.nullable().default(null),
+    failure_class: ElarisFailureClassSchema.nullable().default(null),
+    cleaned_up_at: nullableDateTimeSchema,
+    artifacts_available: z.boolean(),
+}));
+export const AgentSessionUsageSchema = withRaw(z.object({
+    input_tokens: z.number().int().nonnegative().nullable().default(null),
+    cached_input_tokens: z.number().int().nonnegative().nullable().default(null),
+    output_tokens: z.number().int().nonnegative().nullable().default(null),
+    reasoning_output_tokens: z.number().int().nonnegative().nullable().default(null),
+    total_tokens: z.number().int().nonnegative().nullable().default(null),
+    total_cost_usd: z.number().nonnegative().nullable().default(null),
+    usage_json: z.record(z.unknown()).nullable().default(null),
+}));
+export const AgentSessionToolCallSummarySchema = withRaw(z.object({
+    id: z.string().nullable().default(null),
+    name: z.string().nullable().default(null),
+    title: z.string().nullable().default(null),
+    status: z.union([z.enum(["started", "completed", "failed"]), z.string()]),
+}));
+export const AgentSessionFileChangeSchema = withRaw(z.object({
+    path: z.string(),
+}));
+export const AgentSessionResultMetadataSchema = withRaw(z.object({
+    run_id: z.string().min(1),
+    text: z.string(),
+    result_bytes: z.number().int().nonnegative(),
+    truncated: z.boolean().default(false),
+    content_url: z.string().nullable().default(null),
+    usage: AgentSessionUsageSchema,
+    stream_status: z.string(),
+    message_id: uuidSchema,
+    tool_calls_summary: z.array(AgentSessionToolCallSummarySchema).default([]),
+    files_changed: z.array(AgentSessionFileChangeSchema).default([]),
+    redaction_count: z.number().int().nonnegative().optional(),
+}));
+export const AgentSessionResultContentSchema = withRaw(z.object({
+    text: z.string(),
+    content_type: z.string().nullable().default(null),
+    bytes_returned: z.number().int().nonnegative(),
+    result_bytes: z.number().int().nonnegative().nullable().default(null),
+    truncated: z.boolean().default(false),
+    redaction_count: z.number().int().nonnegative().optional(),
+}));
+export const AgentSessionLogItemSchema = z.record(z.unknown());
+export const AgentSessionLogsPageSchema = withRaw(z.object({
+    run_id: z.string().min(1).optional(),
+    session_id: uuidSchema.optional(),
+    items: z.array(AgentSessionLogItemSchema),
+    next_cursor: z.string().nullable().default(null),
+    redaction_count: z.number().int().nonnegative().optional(),
+}));
+export const AgentSessionArtifactManifestItemSchema = withRaw(z.object({
+    path: z.string(),
+    size: z.number().int().nonnegative(),
+    mtime: nullableDateTimeSchema.default(null),
+    type: z.enum(["file", "directory", "symlink", "other"]).default("file"),
+}));
+export const AgentSessionArtifactsPageSchema = withRaw(z.object({
+    run_id: z.string().min(1),
+    session_id: uuidSchema,
+    artifacts_available: z.boolean(),
+    items: z.array(AgentSessionArtifactManifestItemSchema),
+    next_cursor: z.string().nullable().default(null),
+    redaction_count: z.number().int().nonnegative().optional(),
+}));
+export const AgentSessionRawArtifactMetadataSchema = withRaw(z.object({
+    status_code: z.number().int(),
+    content_type: z.string().nullable().default(null),
+    content_length: z.number().int().nonnegative().nullable().default(null),
+    content_range: z.string().nullable().default(null),
+    accept_ranges: z.string().nullable().default(null),
+    bytes_returned: z.number().int().nonnegative(),
+    truncated: z.boolean().default(false),
+    encoding: z.enum(["text", "base64"]),
+    text: z.string().optional(),
+    data_base64: z.string().optional(),
+    // Fail-closed body-withholding markers (first-class, not `.raw` passthrough):
+    // set when a credential is detected in the inline text or decoded bytes.
+    withheld: z.literal("credential_detected").optional(),
+    redaction_count: z.number().int().nonnegative().optional(),
+}));
+export const AgentSessionCancelResponseSchema = AgentSessionStatusResponseSchema;
+export const AgentSessionCleanupResponseSchema = AgentSessionStatusResponseSchema;
+export const AgentSessionErrorEnvelopeSchema = withRaw(z.object({
+    error: z.string(),
+    detail: z.string(),
+    request_id: z.string(),
+    failure_class: ElarisFailureClassSchema.optional(),
+    run_id: z.string().optional(),
+    details: z.record(z.unknown()).optional(),
+}));
+//# sourceMappingURL=types.js.map

package/dist/elaris/types.js.map

@@ -0,0 +1 @@
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package/dist/errors.d.ts

@@ -21,6 +21,22 @@ export declare class InvalidParamsError extends ClinkxError {
  * These are NOT JSON-RPC errors; they are valid tool responses that signal failure.
  */
 export declare class ExecutionError extends ClinkxError {
+    /**
+     * Optional retry-classification marker consumed by cross-package readers
+     * (the clinkx-workflows engine reads it structurally, not by instanceof).
+     * Producers set "transient" for failures a retry can plausibly fix (e.g. a
+     * context-builder delegate timeout). Absent means the consumer's default
+     * classification applies. Additive and optional: the constructor is
+     * unchanged and existing throw sites are unaffected.
+     */
+    failureClass?: "transient" | "permanent";
+    constructor(message: string);
+}
+/**
+ * Startup/configuration failure — escapes createServer() and is logged by the
+ * process entrypoint, not converted to a request-scoped JSON-RPC error.
+ */
+export declare class ConfigError extends ClinkxError {
     constructor(message: string);
 }
 /**

package/dist/errors.js

@@ -27,11 +27,30 @@ export class InvalidParamsError extends ClinkxError {
  * These are NOT JSON-RPC errors; they are valid tool responses that signal failure.
  */
 export class ExecutionError extends ClinkxError {
+    /**
+     * Optional retry-classification marker consumed by cross-package readers
+     * (the clinkx-workflows engine reads it structurally, not by instanceof).
+     * Producers set "transient" for failures a retry can plausibly fix (e.g. a
+     * context-builder delegate timeout). Absent means the consumer's default
+     * classification applies. Additive and optional: the constructor is
+     * unchanged and existing throw sites are unaffected.
+     */
+    failureClass;
     constructor(message) {
         super(message);
         this.name = "ExecutionError";
     }
 }
+/**
+ * Startup/configuration failure — escapes createServer() and is logged by the
+ * process entrypoint, not converted to a request-scoped JSON-RPC error.
+ */
+export class ConfigError extends ClinkxError {
+    constructor(message) {
+        super(message);
+        this.name = "ConfigError";
+    }
+}
 /**
  * Convert an InvalidParamsError to an MCP SDK McpError (-32602).
  *

package/dist/errors.js.map

@@ -1 +1 @@
-{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AAEzE;;GAEG;AACH,MAAM,OAAO,WAAY,SAAQ,KAAK;IACpC,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,aAAa,CAAC;IAC5B,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,kBAAmB,SAAQ,WAAW;IACjD,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,oBAAoB,CAAC;IACnC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,cAAe,SAAQ,WAAW;IAC7C,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,gBAAgB,CAAC;IAC/B,CAAC;CACF;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAAC,GAAuB;IACxD,OAAO,IAAI,QAAQ,CAAC,SAAS,CAAC,aAAa,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;AAC5D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CAAC,GAAmB;IAIrD,OAAO;QACL,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,CAAC,OAAO,EAAE,CAAC;QAC9C,OAAO,EAAE,IAAI;KACd,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,OAAO,iBAAkB,SAAQ,WAAW;IAChD;QACE,KAAK,CAAC,mBAAmB,CAAC,CAAC;QAC3B,IAAI,CAAC,IAAI,GAAG,mBAAmB,CAAC;IAClC,CAAC;CACF;AAED;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAY;IAI1C,IAAI,GAAG,YAAY,kBAAkB,EAAE,CAAC;QACtC,MAAM,kBAAkB,CAAC,GAAG,CAAC,CAAC;IAChC,CAAC;IACD,IAAI,GAAG,YAAY,cAAc,EAAE,CAAC;QAClC,OAAO,mBAAmB,CAAC,GAAG,CAAC,CAAC;IAClC,CAAC;IACD,MAAM,OAAO,GACX,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,yBAAyB,CAAC;IACjE,OAAO;QACL,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;QAC1C,OAAO,EAAE,IAAI;KACd,CAAC;AACJ,CAAC"}
+{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,MAAM,oCAAoC,CAAC;AAEzE;;GAEG;AACH,MAAM,OAAO,WAAY,SAAQ,KAAK;IACpC,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,aAAa,CAAC;IAC5B,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,kBAAmB,SAAQ,WAAW;IACjD,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,oBAAoB,CAAC;IACnC,CAAC;CACF;AAED;;;;;GAKG;AACH,MAAM,OAAO,cAAe,SAAQ,WAAW;IAC7C;;;;;;;OAOG;IACH,YAAY,CAA6B;IAEzC,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,gBAAgB,CAAC;IAC/B,CAAC;CACF;AAED;;;GAGG;AACH,MAAM,OAAO,WAAY,SAAQ,WAAW;IAC1C,YAAY,OAAe;QACzB,KAAK,CAAC,OAAO,CAAC,CAAC;QACf,IAAI,CAAC,IAAI,GAAG,aAAa,CAAC;IAC5B,CAAC;CACF;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAAC,GAAuB;IACxD,OAAO,IAAI,QAAQ,CAAC,SAAS,CAAC,aAAa,EAAE,GAAG,CAAC,OAAO,CAAC,CAAC;AAC5D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,mBAAmB,CAAC,GAAmB;IAIrD,OAAO;QACL,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,CAAC,OAAO,EAAE,CAAC;QAC9C,OAAO,EAAE,IAAI;KACd,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,OAAO,iBAAkB,SAAQ,WAAW;IAChD;QACE,KAAK,CAAC,mBAAmB,CAAC,CAAC;QAC3B,IAAI,CAAC,IAAI,GAAG,mBAAmB,CAAC;IAClC,CAAC;CACF;AAED;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAAC,GAAY;IAI1C,IAAI,GAAG,YAAY,kBAAkB,EAAE,CAAC;QACtC,MAAM,kBAAkB,CAAC,GAAG,CAAC,CAAC;IAChC,CAAC;IACD,IAAI,GAAG,YAAY,cAAc,EAAE,CAAC;QAClC,OAAO,mBAAmB,CAAC,GAAG,CAAC,CAAC;IAClC,CAAC;IACD,MAAM,OAAO,GACX,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,yBAAyB,CAAC;IACjE,OAAO;QACL,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;QAC1C,OAAO,EAAE,IAAI;KACd,CAAC;AACJ,CAAC"}

package/dist/handler.d.ts

@@ -1,5 +1,7 @@
 import { AdapterRegistry } from "./registry.js";
 import type { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import type { ActivityJournal } from "./activity-journal.js";
+import type { SessionLogOwnerV1 } from "../clinkx-workflows/dist/dashboard/session-log-contract.js";
 /**
  * Handle a clink tool invocation.
  *
@@ -14,6 +16,8 @@ export declare function handleClink(rawInput: unknown, options?: {
         token: string | number;
     };
     registry?: AdapterRegistry;
+    activityJournal?: ActivityJournal;
+    sessionLogOwner?: SessionLogOwnerV1;
 }): Promise<{
     content: Array<{
         type: "text";

package/dist/handler.js

@@ -35,12 +35,25 @@ export async function handleClink(rawInput, options) {
     const input = parseResult.data;
     logger.debug({ cli_name: input.cli_name, role: input.role }, "clink invoked");
     const effectiveRegistry = options?.registry ?? getRegistry();
-    const pipelineOptions = options?.signal != null || options?.progress != null
+    const pipelineOptions = options?.signal != null ||
+        options?.progress != null ||
+        options?.activityJournal != null ||
+        options?.sessionLogOwner != null
         ? {
             ...(options?.signal != null ? { signal: options.signal } : {}),
             ...(options?.progress != null ? { progress: options.progress } : {}),
+            ...(options?.activityJournal != null
+                ? { activityJournal: options.activityJournal }
+                : {}),
+            ...(options?.sessionLogOwner != null
+                ? { sessionLogOwner: options.sessionLogOwner }
+                : {}),
         }
         : undefined;
-    return await executePipeline(input, effectiveRegistry, pipelineOptions);
+    const result = await executePipeline(input, effectiveRegistry, pipelineOptions);
+    return {
+        content: result.content,
+        ...(result.isError === undefined ? {} : { isError: result.isError }),
+    };
 }
 //# sourceMappingURL=handler.js.map

package/dist/handler.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,13 +1,31 @@
 #!/usr/bin/env node
 import { Writable } from "node:stream";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { type StdioActivity } from "./stdio-activity.js";
 interface ShutdownServer {
     close(): Promise<void> | void;
 }
 interface ShutdownOnceOptions {
-    killAllActiveFn?: () => Promise<void>;
+    killAllActiveFn?: (reason: string) => Promise<void>;
+    latchSubprocessAdmissionFn?: () => void;
+    latchAppServerAdmissionFn?: (reason: string) => void;
+    beginWorkflowShutdownFn?: (reason: string) => void;
+    clearWorkflowActivityObserverFn?: () => void;
+    clearAppServerActivityObserverFn?: () => void;
+    stopWatchdogFn?: () => void;
     exitFn?: (exitCode: number) => void;
 }
+export interface RootCleanupOptions {
+    killAllActiveFn?: (reason: string) => Promise<void>;
+    shutdownAppServerRegistryFn?: (reason: string) => Promise<void>;
+    shutdownWorkflowCoordinatorFn?: (reason: string) => Promise<void>;
+}
+/**
+ * Run every root-owned cleanup surface, preserving later cleanup when an
+ * earlier surface fails. The first failure is rethrown after all surfaces have
+ * had their bounded opportunity to clean up.
+ */
+export declare function createRootCleanup(options?: RootCleanupOptions): (reason: string) => Promise<void>;
 export declare function createShutdownOnce(server: ShutdownServer, options?: ShutdownOnceOptions): (reason: string, exitCode: number) => Promise<void>;
-export declare function patchTransportSend(transport: StdioServerTransport, stdout?: Writable, onBrokenStdout?: () => void): void;
+export declare function patchTransportSend(transport: StdioServerTransport, stdout?: Writable, onBrokenStdout?: () => void, activity?: StdioActivity): void;
 export {};

package/dist/index.js

@@ -6,13 +6,80 @@ import { serializeMessage } from "@modelcontextprotocol/sdk/shared/stdio.js";
 import { createServer } from "./server.js";
 import { logger, assertStderrLogger } from "./logger.js";
 import { assertNotRootDir } from "./paths.js";
-import { activeProcesses, killAllActive } from "./runner.js";
+import { activeProcesses, killAllActive, latchSubprocessAdmissionForShutdown, } from "./runner.js";
+import { latchAppServerAdmissionForShutdown, setAppServerActivityObserver, shutdownAppServerRegistry, } from "./codex/app-server-registry.js";
+import { createRootStdioActivity } from "./stdio-activity.js";
+import { setWorkflowActivityObserver, } from "../clinkx-workflows/dist/workflow-tools.js";
+import { shutdownCoordinator } from "../clinkx-workflows/dist/shutdown.js";
+import { createStdioWatchdog } from "../clinkx-workflows/dist/stdio-watchdog.js";
 const SHUTDOWN_DEADLINE_MS = 10_000;
 const SEND_TIMEOUT_MS = 30_000;
 const patchedTransports = new WeakSet();
+/**
+ * Run every root-owned cleanup surface, preserving later cleanup when an
+ * earlier surface fails. The first failure is rethrown after all surfaces have
+ * had their bounded opportunity to clean up.
+ */
+export function createRootCleanup(options = {}) {
+    const cleanups = [
+        {
+            name: "killAllActive",
+            run: options.killAllActiveFn ?? (async () => {
+                await killAllActive();
+            }),
+        },
+        {
+            name: "shutdownAppServerRegistry",
+            run: options.shutdownAppServerRegistryFn ?? shutdownAppServerRegistry,
+        },
+        {
+            name: "shutdownWorkflowCoordinator",
+            run: options.shutdownWorkflowCoordinatorFn ?? ((reason) => shutdownCoordinator.shutdown(reason)),
+        },
+    ];
+    return async (reason) => {
+        let failed = false;
+        let firstError;
+        const recordFailure = (cleanupName, err) => {
+            failed = true;
+            firstError ??= err;
+            try {
+                logger.error({
+                    reason,
+                    cleanup: cleanupName,
+                    err: err instanceof Error ? err.message : String(err),
+                }, "shutdown cleanup surface failed");
+            }
+            catch {
+                // A broken logger must not prevent the remaining cleanup surfaces from
+                // settling or replace the cleanup failure being reported.
+            }
+        };
+        const pending = [];
+        for (const cleanup of cleanups) {
+            try {
+                // Invoke each surface before awaiting any result. Workflow shutdown
+                // must latch active runs even if generic process cleanup is draining.
+                pending.push(Promise.resolve(cleanup.run(reason)).catch((err) => {
+                    recordFailure(cleanup.name, err);
+                }));
+            }
+            catch (err) {
+                recordFailure(cleanup.name, err);
+            }
+        }
+        await Promise.all(pending);
+        if (failed) {
+            throw firstError instanceof Error
+                ? firstError
+                : new Error("one or more shutdown cleanup surfaces failed");
+        }
+    };
+}
 export function createShutdownOnce(server, options = {}) {
     let shuttingDown = false;
     const killAllActiveFn = options.killAllActiveFn ?? killAllActive;
+    const latchSubprocessAdmissionFn = options.latchSubprocessAdmissionFn ?? latchSubprocessAdmissionForShutdown;
     const exitFn = options.exitFn ?? ((exitCode) => {
         process.exit(exitCode);
     });
@@ -20,6 +87,58 @@ export function createShutdownOnce(server, options = {}) {
         if (shuttingDown)
             return;
         shuttingDown = true;
+        // Synchronous and first: no generic request may cross into spawn while
+        // cleanup drains the registry or before server.close stops new requests.
+        latchSubprocessAdmissionFn();
+        try {
+            // Close singleton app-server admission before any asynchronous cleanup
+            // can observe or replace the current registry.
+            options.latchAppServerAdmissionFn?.(reason);
+        }
+        catch (err) {
+            logger.error({
+                reason,
+                err: err instanceof Error ? err.message : String(err),
+            }, "app-server shutdown latch failed");
+        }
+        try {
+            // The workflow coordinator must latch its own admission before any
+            // asynchronous cleanup surface begins to drain.
+            options.beginWorkflowShutdownFn?.(reason);
+        }
+        catch (err) {
+            logger.error({
+                reason,
+                err: err instanceof Error ? err.message : String(err),
+            }, "workflow shutdown latch failed");
+        }
+        try {
+            options.clearWorkflowActivityObserverFn?.();
+        }
+        catch (err) {
+            logger.error({
+                reason,
+                err: err instanceof Error ? err.message : String(err),
+            }, "workflow activity observer clear failed");
+        }
+        try {
+            options.clearAppServerActivityObserverFn?.();
+        }
+        catch (err) {
+            logger.error({
+                reason,
+                err: err instanceof Error ? err.message : String(err),
+            }, "app-server activity observer clear failed");
+        }
+        try {
+            options.stopWatchdogFn?.();
+        }
+        catch (err) {
+            logger.error({
+                reason,
+                err: err instanceof Error ? err.message : String(err),
+            }, "shutdown watchdog stop failed");
+        }
         const deadline = new Promise((_, reject) => {
             setTimeout(() => reject(new Error("shutdown deadline exceeded")), SHUTDOWN_DEADLINE_MS).unref();
         });
@@ -30,7 +149,7 @@ export function createShutdownOnce(server, options = {}) {
                     logger.info({ reason, activeProcesses: activeProcesses.size, writableLength: process.stdout.writableLength }, "clinkx:shutdown");
                     logger.info({ reason, exit_code: exitCode }, "shutdown requested, cleaning up");
                     try {
-                        await killAllActiveFn();
+                        await killAllActiveFn(reason);
                     }
                     catch (err) {
                         effectiveExitCode = 1;
@@ -103,7 +222,7 @@ function extractRpcMeta(msg) {
         return { id: msg.id };
     return {};
 }
-export function patchTransportSend(transport, stdout = process.stdout, onBrokenStdout) {
+export function patchTransportSend(transport, stdout = process.stdout, onBrokenStdout, activity) {
     if (patchedTransports.has(transport))
         return;
     patchedTransports.add(transport);
@@ -207,8 +326,12 @@ export function patchTransportSend(transport, stdout = process.stdout, onBrokenS
         });
     }
     transport.send = (message) => {
+        const releaseSend = activity?.beginSend();
         const send = sendChain.then(() => sendOne(message), () => sendOne(message));
         sendChain = send.catch(() => undefined);
+        if (releaseSend !== undefined) {
+            void send.then(() => releaseSend(), () => releaseSend());
+        }
         return send;
     };
 }
@@ -235,14 +358,39 @@ async function main() {
     assertStderrLogger();
     // Startup safety guard: refuse running from filesystem root unless explicitly allowlisted
     assertNotRootDir();
-    const server = createServer();
+    const activity = createRootStdioActivity();
+    const server = createServer({ activity });
     const transport = new StdioServerTransport();
     logger.info("ClinkX MCP server starting (STDIO transport)");
     logger.info({ pid: process.pid, ppid: process.ppid }, "clinkx:startup");
-    const shutdownOnce = createShutdownOnce(server);
+    let watchdog;
+    const shutdownOnce = createShutdownOnce(server, {
+        killAllActiveFn: createRootCleanup(),
+        latchAppServerAdmissionFn: (reason) => latchAppServerAdmissionForShutdown(reason),
+        beginWorkflowShutdownFn: (reason) => shutdownCoordinator.beginShutdown(reason),
+        clearWorkflowActivityObserverFn: () => setWorkflowActivityObserver(undefined),
+        clearAppServerActivityObserverFn: () => setAppServerActivityObserver(undefined),
+        stopWatchdogFn: () => watchdog?.stop(),
+    });
+    watchdog = createStdioWatchdog({
+        isBusy: activity.isBusy,
+        onShutdown: (reason, exitCode) => {
+            runShutdown(shutdownOnce, reason, exitCode);
+        },
+    });
+    activity.attachWatchdog(watchdog.recordActivity);
+    setWorkflowActivityObserver(activity.recordActivity);
+    setAppServerActivityObserver(activity.recordActivity);
+    const previousOnMessage = transport.onmessage;
+    transport.onmessage = (message) => {
+        activity.recordActivity();
+        previousOnMessage?.(message);
+    };
+    // The transport patch must retain activity until the SDK's response send or
+    // stdout drain settles; otherwise an idle timer can race the handler return.
     patchTransportSend(transport, process.stdout, () => {
         runShutdown(shutdownOnce, "stdout:error", 1);
-    });
+    }, activity);
     process.once("SIGTERM", () => runShutdown(shutdownOnce, "SIGTERM", 0));
     process.once("SIGINT", () => runShutdown(shutdownOnce, "SIGINT", 0));
     process.once("SIGHUP", () => runShutdown(shutdownOnce, "SIGHUP", 0));