@darkiceinteractive/mcp-conductor 1.1.0 → 2.0.0-alpha.1

package/dist/index.js

@@ -26,6 +26,7 @@ import { MCPExecutorServer } from './server/index.js';
 import { loadConfig } from './config/index.js';
 import { LIFECYCLE_TIMEOUTS } from './config/defaults.js';
 import { logger } from './utils/index.js';
+import { startOrphanWatch } from './utils/orphan-watch.js';
 import { BUILD_STRING } from './version.js';
 /**
  * Main entry point
@@ -42,10 +43,15 @@ async function main() {
     const server = new MCPExecutorServer(config);
     // Handle shutdown gracefully with timeout guard
     let isShuttingDown = false;
+    let orphanWatch = null;
     const shutdown = async () => {
         if (isShuttingDown)
             return; // Prevent double-shutdown
         isShuttingDown = true;
+        // Stop the orphan watchdog first so normal SIGTERM cleanup doesn't
+        // race with an "oh no, parent is gone" false positive.
+        orphanWatch?.stop();
+        orphanWatch = null;
         logger.info('Shutting down...');
         // Safety: force exit if shutdown hangs
         const shutdownTimeout = setTimeout(() => {
@@ -74,6 +80,12 @@ async function main() {
     });
     try {
         await server.start();
+        // Orphan watchdog: if the MCP client that spawned us dies, our
+        // parent PID changes (usually to 1 on POSIX). Poll for that and
+        // trigger shutdown so Deno children / bridge timers don't leak.
+        orphanWatch = startOrphanWatch({
+            onOrphaned: () => shutdown(),
+        });
         // Periodic memory logging for diagnostics
         const memLog = setInterval(() => {
             const m = process.memoryUsage();

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AAEH,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAC;AACtD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,MAAM,EAAE,MAAM,kBAAkB,CAAC;AAC1C,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAE5C;;GAEG;AACH,KAAK,UAAU,IAAI;IACjB,qBAAqB;IACrB,MAAM,MAAM,GAAG,UAAU,EAAE,CAAC;IAE5B,MAAM,CAAC,IAAI,CAAC,0BAA0B,YAAY,EAAE,EAAE;QACpD,IAAI,EAAE,MAAM,CAAC,SAAS,CAAC,IAAI;QAC3B,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI;QAC9B,OAAO,EAAE,MAAM,CAAC,SAAS,CAAC,gBAAgB;KAC3C,CAAC,CAAC;IAEH,0BAA0B;IAC1B,MAAM,MAAM,GAAG,IAAI,iBAAiB,CAAC,MAAM,CAAC,CAAC;IAE7C,gDAAgD;IAChD,IAAI,cAAc,GAAG,KAAK,CAAC;IAC3B,IAAI,WAAW,GAA4B,IAAI,CAAC;IAChD,MAAM,QAAQ,GAAG,KAAK,IAAI,EAAE;QAC1B,IAAI,cAAc;YAAE,OAAO,CAAC,0BAA0B;QACtD,cAAc,GAAG,IAAI,CAAC;QAEtB,mEAAmE;QACnE,uDAAuD;QACvD,WAAW,EAAE,IAAI,EAAE,CAAC;QACpB,WAAW,GAAG,IAAI,CAAC;QAEnB,MAAM,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC;QAEhC,uCAAuC;QACvC,MAAM,eAAe,GAAG,UAAU,CAAC,GAAG,EAAE;YACtC,MAAM,CAAC,KAAK,CAAC,4BAA4B,kBAAkB,CAAC,mBAAmB,kBAAkB,CAAC,CAAC;YACnG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC,EAAE,kBAAkB,CAAC,mBAAmB,CAAC,CAAC;QAC3C,eAAe,CAAC,KAAK,EAAE,CAAC,CAAC,+CAA+C;QAExE,IAAI,CAAC;YACH,MAAM,MAAM,CAAC,IAAI,EAAE,CAAC;QACtB,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,CAAC,KAAK,CAAC,uBAAuB,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAClE,CAAC;QAED,YAAY,CAAC,eAAe,CAAC,CAAC;QAC9B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC,CAAC;IAEF,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;IAC/B,OAAO,CAAC,EAAE,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;IAEhC,iDAAiD;IACjD,OAAO,CAAC,EAAE,CAAC,mBAAmB,EAAE,CAAC,KAAK,EAAE,EAAE;QACxC,MAAM,CAAC,KAAK,CAAC,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QACjF,QAAQ,EAAE,CAAC;IACb,CAAC,CAAC,CAAC;IAEH,OAAO,CAAC,EAAE,CAAC,oBAAoB,EAAE,CAAC,MAAM,EAAE,EAAE;QAC1C,MAAM,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IAClE,CAAC,CAAC,CAAC;IAEH,IAAI,CAAC;QACH,MAAM,MAAM,CAAC,KAAK,EAAE,CAAC;QAErB,+DAA+D;QAC/D,gEAAgE;QAChE,gEAAgE;QAChE,WAAW,GAAG,gBAAgB,CAAC;YAC7B,UAAU,EAAE,GAAG,EAAE,CAAC,QAAQ,EAAE;SAC7B,CAAC,CAAC;QAEH,0CAA0C;QAC1C,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,EAAE;YAC9B,MAAM,CAAC,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC;YAChC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE;gBACpB,MAAM,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,GAAG,IAAI,GAAG,IAAI,CAAC;gBAC5C,KAAK,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,GAAG,IAAI,CAAC;aACvC,CAAC,CAAC;QACL,CAAC,EAAE,kBAAkB,CAAC,sBAAsB,CAAC,CAAC;QAC9C,MAAM,CAAC,KAAK,EAAE,CAAC;IACjB,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,MAAM,CAAC,KAAK,CAAC,wBAAwB,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACjE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC;AAED,MAAM;AACN,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE;IACrB,OAAO,CAAC,KAAK,CAAC,cAAc,EAAE,KAAK,CAAC,CAAC;IACrC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC"}

package/dist/runtime/executor.d.ts

@@ -29,6 +29,18 @@ export interface ExecutionOptions {
     servers: string[];
     /** Enable streaming mode for real-time progress updates */
     stream?: boolean;
+    /**
+     * AbortSignal tied to the caller's request. When the signal fires we
+     * terminate the Deno process via the same SIGTERM→SIGKILL path used for
+     * shutdown. Surfaces MCP cancellation from the client side.
+     */
+    signal?: AbortSignal;
+    /**
+     * Caller-provided execution id. Lets the MCP server preallocate the id
+     * and subscribe to the matching ExecutionStream *before* Deno spawns, so
+     * we never miss the first progress event.
+     */
+    executionId?: string;
 }
 /**
  * Deno Sandbox Executor

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

@@ -1 +1 @@
-{"version":3,"file":"executor.d.ts","sourceRoot":"","sources":["../../src/runtime/executor.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAOH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAGxD,MAAM,WAAW,eAAe;IAC9B,qDAAqD;IACrD,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE;QACN,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,SAAS,GAAG,UAAU,CAAC;QACpD,OAAO,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,IAAI,CAAC,EAAE,MAAM,CAAC;KACf,CAAC;IACF,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,OAAO,EAAE;QACP,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,kBAAkB,EAAE,MAAM,CAAC;QAC3B,eAAe,EAAE,MAAM,CAAC;KACzB,CAAC;CACH;AAED,MAAM,WAAW,gBAAgB;IAC/B,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,2DAA2D;IAC3D,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AA+aD;;GAEG;AACH,qBAAa,YAAY;IACvB,OAAO,CAAC,MAAM,CAAgB;IAC9B,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,eAAe,CAAwC;IAC/D,OAAO,CAAC,sBAAsB,CAAS;IACvC,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,aAAa,CAAwB;gBAEjC,MAAM,EAAE,aAAa;IAejC;;;;;;;;OAQG;IACH,OAAO,CAAC,qBAAqB;IA2B7B;;OAEG;IACG,SAAS,IAAI,OAAO,CAAC,OAAO,CAAC;IAgBnC;;OAEG;IACG,QAAQ,IAAI,OAAO,CAAC,IAAI,CAAC;IAwC/B;;OAEG;IACH,qBAAqB,IAAI,MAAM;IAI/B;;OAEG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC,eAAe,CAAC;IA6DhF;;OAEG;IACH,mBAAmB,IAAI,MAAM;IAI7B;;OAEG;IACH,OAAO,CAAC,OAAO;CAmQhB"}
+{"version":3,"file":"executor.d.ts","sourceRoot":"","sources":["../../src/runtime/executor.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAOH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAGxD,MAAM,WAAW,eAAe;IAC9B,qDAAqD;IACrD,WAAW,EAAE,MAAM,CAAC;IACpB,OAAO,EAAE,OAAO,CAAC;IACjB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,KAAK,CAAC,EAAE;QACN,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,SAAS,GAAG,UAAU,CAAC;QACpD,OAAO,EAAE,MAAM,CAAC;QAChB,KAAK,CAAC,EAAE,MAAM,CAAC;QACf,IAAI,CAAC,EAAE,MAAM,CAAC;KACf,CAAC;IACF,IAAI,EAAE,MAAM,EAAE,CAAC;IACf,OAAO,EAAE;QACP,eAAe,EAAE,MAAM,CAAC;QACxB,SAAS,EAAE,MAAM,CAAC;QAClB,kBAAkB,EAAE,MAAM,CAAC;QAC3B,eAAe,EAAE,MAAM,CAAC;KACzB,CAAC;CACH;AAED,MAAM,WAAW,gBAAgB;IAC/B,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,2DAA2D;IAC3D,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB;;;;OAIG;IACH,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB;;;;OAIG;IACH,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AA+aD;;GAEG;AACH,qBAAa,YAAY;IACvB,OAAO,CAAC,MAAM,CAAgB;IAC9B,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,eAAe,CAAwC;IAC/D,OAAO,CAAC,sBAAsB,CAAS;IACvC,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,cAAc,CAAS;IAC/B,OAAO,CAAC,aAAa,CAAwB;gBAEjC,MAAM,EAAE,aAAa;IAejC;;;;;;;;OAQG;IACH,OAAO,CAAC,qBAAqB;IA2B7B;;OAEG;IACG,SAAS,IAAI,OAAO,CAAC,OAAO,CAAC;IAgBnC;;OAEG;IACG,QAAQ,IAAI,OAAO,CAAC,IAAI,CAAC;IAwC/B;;OAEG;IACH,qBAAqB,IAAI,MAAM;IAI/B;;OAEG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC,eAAe,CAAC;IA8EhF;;OAEG;IACH,mBAAmB,IAAI,MAAM;IAI7B;;OAEG;IACH,OAAO,CAAC,OAAO;CAkUhB"}

package/dist/runtime/executor.js

@@ -558,9 +558,19 @@ export class DenoExecutor {
      * Execute code in the Deno sandbox
      */
     async execute(code, options) {
-        const executionId = generateExecutionId();
+        const executionId = options.executionId ?? generateExecutionId();
         const startTime = Date.now();
         const streamEnabled = options.stream ?? false;
+        // Short-circuit if the caller already cancelled before we started.
+        if (options.signal?.aborted) {
+            return {
+                executionId,
+                success: false,
+                error: { type: 'runtime', message: 'Execution cancelled before start' },
+                logs: [],
+                metrics: { executionTimeMs: 0, toolCalls: 0, dataProcessedBytes: 0, resultSizeBytes: 0 },
+            };
+        }
         logger.debug('Starting execution', { executionId, streamEnabled });
         // Validate Deno is available
         const hasDenoAvailable = await this.checkDeno();
@@ -587,7 +597,7 @@ export class DenoExecutor {
         const tempFile = join(this.tempDir, `exec_${executionId}.ts`);
         writeFileSync(tempFile, sandboxCode);
         try {
-            const result = await this.runDeno(tempFile, options.timeoutMs, executionId, options.bridgeUrl);
+            const result = await this.runDeno(tempFile, options.timeoutMs, executionId, options.bridgeUrl, options.signal);
             return {
                 ...result,
                 executionId,
@@ -617,7 +627,7 @@ export class DenoExecutor {
     /**
      * Run Deno subprocess
      */
-    runDeno(filePath, timeoutMs, executionId, bridgeUrl) {
+    runDeno(filePath, timeoutMs, executionId, bridgeUrl, signal) {
         return new Promise((resolve) => {
             // Reject if shutting down
             if (this.isShuttingDown) {
@@ -693,6 +703,35 @@ export class DenoExecutor {
                 killed = true;
                 proc.kill('SIGKILL');
             }, timeoutMs);
+            // Honour MCP cancellation (RequestHandlerExtra.signal). We kill the
+            // process and flag cancellation so the close handler returns the
+            // dedicated error type instead of a timeout / runtime error.
+            let cancelled = false;
+            const onAbort = () => {
+                cancelled = true;
+                killed = true;
+                logger.info('Execution cancelled by client', { executionId });
+                try {
+                    proc.kill('SIGTERM');
+                    // Escalate to SIGKILL if the process doesn't exit in the grace window.
+                    setTimeout(() => {
+                        if (this.activeProcesses.has(executionId)) {
+                            proc.kill('SIGKILL');
+                        }
+                    }, LIFECYCLE_TIMEOUTS.PROCESS_FORCE_KILL_MS).unref?.();
+                }
+                catch {
+                    // Process may already be gone.
+                }
+            };
+            if (signal) {
+                if (signal.aborted) {
+                    onAbort();
+                }
+                else {
+                    signal.addEventListener('abort', onAbort, { once: true });
+                }
+            }
             // Bounded stdout/stderr buffering
             const stdoutChunks = [];
             let stdoutLen = 0;
@@ -731,8 +770,29 @@ export class DenoExecutor {
             proc.on('close', (code) => {
                 clearTimeout(timer);
                 this.activeProcesses.delete(executionId);
+                if (signal) {
+                    signal.removeEventListener('abort', onAbort);
+                }
                 const stdout = Buffer.concat(stdoutChunks).toString('utf-8');
                 const stderr = Buffer.concat(stderrChunks).toString('utf-8');
+                if (cancelled) {
+                    resolve({
+                        executionId,
+                        success: false,
+                        error: {
+                            type: 'runtime',
+                            message: 'Execution cancelled by client',
+                        },
+                        logs: [],
+                        metrics: {
+                            executionTimeMs: 0,
+                            toolCalls: 0,
+                            dataProcessedBytes: 0,
+                            resultSizeBytes: 0,
+                        },
+                    });
+                    return;
+                }
                 if (killed) {
                     resolve({
                         executionId,
@@ -836,6 +896,13 @@ export class DenoExecutor {
             proc.on('error', (error) => {
                 clearTimeout(timer);
                 this.activeProcesses.delete(executionId);
+                // Symmetric with the close handler — without this the abort
+                // listener stays attached to the AbortSignal until the SDK GCs
+                // the request, leaking closure refs across repeated spawn
+                // failures (EAGAIN/EMFILE/ENOENT).
+                if (signal) {
+                    signal.removeEventListener('abort', onAbort);
+                }
                 // Reset deno check cache on spawn failure
                 if (error.message.includes('ENOENT')) {
                     this.denoAvailable = null;

package/dist/runtime/executor.js.map

@@ -1 +1 @@
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package/dist/server/mcp-server.d.ts

@@ -30,6 +30,11 @@ export declare class MCPExecutorServer {
     /**
      * Register all MCP tools
      */
+    /**
+     * Record metrics + shape the execute_code tool response. Extracted so the
+     * progress/cancel wiring in the handler stays readable.
+     */
+    private finaliseExecuteCodeResult;
     private registerTools;
     /**
      * Start the server

package/dist/server/mcp-server.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"mcp-server.d.ts","sourceRoot":"","sources":["../../src/server/mcp-server.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,OAAO,EAAE,MAAM,EAAE,MAAM,iBAAiB,CAAC;AAQzC,OAAO,KAAK,EAAE,iBAAiB,EAAkC,MAAM,oBAAoB,CAAC;AAI5F;;GAEG;AACH,qBAAa,iBAAiB;IAC5B,OAAO,CAAC,MAAM,CAAY;IAC1B,OAAO,CAAC,MAAM,CAAa;IAC3B,OAAO,CAAC,QAAQ,CAAe;IAC/B,OAAO,CAAC,GAAG,CAAS;IACpB,OAAO,CAAC,MAAM,CAA6B;IAC3C,OAAO,CAAC,WAAW,CAAc;IACjC,OAAO,CAAC,gBAAgB,CAAmB;IAC3C,OAAO,CAAC,MAAM,CAAoB;IAClC,OAAO,CAAC,cAAc,CAAU;IAChC,OAAO,CAAC,WAAW,CAAgB;IAGnC,OAAO,CAAC,WAAW,CAAmF;gBAE1F,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE;QAAE,cAAc,CAAC,EAAE,OAAO,CAAA;KAAE;IAiE7E;;OAEG;IACH,OAAO,CAAC,gBAAgB;IAoBxB;;OAEG;IACH;;;OAGG;IACH,OAAO,CAAC,yBAAyB;IA8CjC,OAAO,CAAC,aAAa;IA0wCrB;;OAEG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAqH5B;;OAEG;IACG,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC;IAuB3B;;OAEG;IACH,MAAM,IAAI,MAAM;IAIhB;;OAEG;IACG,aAAa,IAAI,OAAO,CAAC;QAAE,KAAK,EAAE,MAAM,EAAE,CAAC;QAAC,OAAO,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;IAOtE;;;;OAIG;IACH,kBAAkB,IAAI,GAAG,CAAC,MAAM,EAAE;QAAE,OAAO,EAAE,CAAC,MAAM,EAAE,OAAO,KAAK,OAAO,CAAC,OAAO,CAAC,CAAA;KAAE,CAAC;CActF"}

package/dist/server/mcp-server.js

@@ -17,6 +17,7 @@ import { shutdownMetricsCollector } from '../metrics/index.js';
 import { shutdownModeHandler } from '../modes/index.js';
 import { shutdownSkillsEngine } from '../skills/index.js';
 import { loadConductorConfig, saveConductorConfig, getDefaultConductorConfigPath } from '../config/index.js';
+import { VERSION } from '../version.js';
 /**
  * MCP Executor Server
  */
@@ -49,7 +50,7 @@ export class MCPExecutorServer {
         this.server = new McpServer({
             name: 'mcp-conductor',
             title: 'MCP Conductor',
-            version: '0.1.0',
+            version: VERSION,
             websiteUrl: 'https://github.com/darkiceinteractive/mcp-conductor',
             icons: [
                 {
@@ -113,6 +114,46 @@ export class MCPExecutorServer {
     /**
      * Register all MCP tools
      */
+    /**
+     * Record metrics + shape the execute_code tool response. Extracted so the
+     * progress/cancel wiring in the handler stays readable.
+     */
+    finaliseExecuteCodeResult(result, code, servers, verbose) {
+        const executionMetrics = this.metricsCollector.recordExecution({
+            executionId: result.executionId,
+            code,
+            result: result.result,
+            success: result.success,
+            durationMs: result.metrics.executionTimeMs,
+            toolCalls: result.metrics.toolCalls,
+            dataProcessedBytes: result.metrics.dataProcessedBytes,
+            resultSizeBytes: result.metrics.resultSizeBytes,
+            mode: 'execution',
+            serversUsed: servers || [],
+            errorType: result.error?.type,
+        });
+        this.modeHandler.recordExecutionCall(executionMetrics.estimatedTokensSaved);
+        const output = {
+            success: result.success,
+            result: result.result,
+            error: result.error,
+        };
+        if (verbose) {
+            output.metrics = {
+                execution_time_ms: result.metrics.executionTimeMs,
+                tool_calls: result.metrics.toolCalls,
+                data_processed_bytes: result.metrics.dataProcessedBytes,
+                result_size_bytes: result.metrics.resultSizeBytes,
+                estimated_tokens_saved: executionMetrics.estimatedTokensSaved,
+                savings_percent: executionMetrics.savingsPercent,
+            };
+            output.logs = result.logs;
+        }
+        return {
+            content: [{ type: 'text', text: JSON.stringify(output) }],
+            structuredContent: output,
+        };
+    }
     registerTools() {
         // Register execute_code tool
         this.server.registerTool('execute_code', {
@@ -126,6 +167,14 @@ export class MCPExecutorServer {
 **Example:** \`const files = await mcp.filesystem.call('list_directory', { path: '/src' }); return files;\`
 
 Use passthrough_call only for debugging - it has HIGH token cost.`,
+            annotations: {
+                // execute_code proxies arbitrary code that can call any backend MCP
+                // tool, so it inherits the most permissive capability surface.
+                readOnlyHint: false,
+                destructiveHint: true,
+                idempotentHint: false,
+                openWorldHint: true,
+            },
             inputSchema: {
                 code: z.string().describe('TypeScript/JavaScript code to execute. Must include a return statement.'),
                 servers: z.array(z.string()).optional().describe('Optional: List of MCP server names to load.'),
@@ -151,60 +200,87 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
                 }).optional(),
                 logs: z.array(z.string()).optional(),
             },
-        }, async ({ code, servers, timeout_ms, stream, verbose }) => {
+        }, async ({ code, servers, timeout_ms, stream, verbose }, extra) => {
             const timeoutMs = Math.min(timeout_ms || this.config.execution.defaultTimeoutMs, this.config.execution.maxTimeoutMs);
             logger.info('Executing code', {
                 codeLength: code.length,
                 timeout: timeoutMs,
                 servers: servers || 'all',
             });
-            const result = await this.executor.execute(code, {
-                timeoutMs,
-                bridgeUrl: this.bridge.getUrl(),
-                servers: servers || [],
-            });
-            // Record execution with enhanced metrics collector
-            const executionMetrics = this.metricsCollector.recordExecution({
-                executionId: result.executionId,
-                code,
-                result: result.result,
-                success: result.success,
-                durationMs: result.metrics.executionTimeMs,
-                toolCalls: result.metrics.toolCalls,
-                dataProcessedBytes: result.metrics.dataProcessedBytes,
-                resultSizeBytes: result.metrics.resultSizeBytes,
-                mode: 'execution',
-                serversUsed: servers || [],
-                errorType: result.error?.type,
-            });
-            // Track with mode handler
-            this.modeHandler.recordExecutionCall(executionMetrics.estimatedTokensSaved);
-            const output = {
-                success: result.success,
-                result: result.result,
-                error: result.error,
+            // If the client supplied a progressToken in _meta, forward sandbox
+            // progress() calls as MCP notifications/progress. We preallocate the
+            // execution id + stream so we never miss the first event.
+            const progressToken = extra?._meta?.progressToken;
+            const wantProgress = progressToken !== undefined;
+            const wantStream = stream || wantProgress;
+            const executionId = wantStream ? this.executor.generateExecutionId() : undefined;
+            const execStream = executionId ? this.bridge.createStream(executionId) : undefined;
+            const forwardProgress = (percent, message) => {
+                if (!wantProgress || !extra?.sendNotification)
+                    return;
+                void extra
+                    .sendNotification({
+                    method: 'notifications/progress',
+                    params: {
+                        progressToken,
+                        progress: percent,
+                        total: 100,
+                        ...(message ? { message } : {}),
+                    },
+                })
+                    .catch((err) => {
+                    logger.debug('Failed to forward progress notification', { error: String(err) });
+                });
             };
-            // Only include metrics when verbose is true (saves ~150-300 tokens per response)
-            if (verbose) {
-                output.metrics = {
-                    execution_time_ms: result.metrics.executionTimeMs,
-                    tool_calls: result.metrics.toolCalls,
-                    data_processed_bytes: result.metrics.dataProcessedBytes,
-                    result_size_bytes: result.metrics.resultSizeBytes,
-                    estimated_tokens_saved: executionMetrics.estimatedTokensSaved,
-                    savings_percent: executionMetrics.savingsPercent,
-                };
-                output.logs = result.logs;
+            if (execStream && wantProgress) {
+                execStream.on('progress', (ev) => {
+                    forwardProgress(ev.data.percent, ev.data.message);
+                });
+            }
+            let result;
+            try {
+                result = await this.executor.execute(code, {
+                    timeoutMs,
+                    bridgeUrl: this.bridge.getUrl(),
+                    servers: servers || [],
+                    stream: wantStream,
+                    signal: extra?.signal,
+                    executionId,
+                });
+                return this.finaliseExecuteCodeResult(result, code, servers, verbose);
+            }
+            finally {
+                if (execStream) {
+                    // Flip the stream out of `running` so StreamManager's normal
+                    // 5/10-min cleanup applies instead of the 15-min stuck-stream
+                    // sweep. Only fire complete() if we actually got a result —
+                    // if execute() threw, the stream will time out via the stuck
+                    // path which is the right safety net.
+                    if (result) {
+                        execStream.complete({
+                            success: result.success,
+                            result: result.result,
+                            error: result.error,
+                            metrics: {
+                                executionTimeMs: result.metrics.executionTimeMs,
+                                toolCalls: result.metrics.toolCalls,
+                                dataProcessedBytes: result.metrics.dataProcessedBytes,
+                            },
+                        });
+                    }
+                    execStream.removeAllListeners('progress');
+                }
             }
-            return {
-                content: [{ type: 'text', text: JSON.stringify(output) }],
-                structuredContent: output,
-            };
         });
         // Register list_servers tool
         this.server.registerTool('list_servers', {
             title: 'List Servers',
             description: 'List all MCP servers connected through MCP Executor.',
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 include_tools: z.boolean().optional().describe('If true, include list of tool names.'),
             },
@@ -253,6 +329,11 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
         this.server.registerTool('discover_tools', {
             title: 'Discover Tools',
             description: 'Search for available tools across all connected MCP servers.',
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 query: z.string().optional().describe('Search query. Matches against tool names and descriptions.'),
                 server: z.string().optional().describe('Optional: limit search to a specific server.'),
@@ -334,6 +415,11 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
         this.server.registerTool('get_metrics', {
             title: 'Get Metrics',
             description: 'Get detailed aggregated metrics for the current session including token savings, performance, and usage patterns.',
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 reset: z.boolean().optional().describe('Reset metrics after returning.'),
                 include_details: z.boolean().optional().describe('Include detailed breakdowns (servers, tools, recent executions).'),
@@ -443,6 +529,13 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
 - execution: All requests go through the code executor (default, maximum token savings)
 - passthrough: Direct tool calls without code execution (for debugging/comparison)
 - hybrid: Automatic selection based on task complexity`,
+            annotations: {
+                // Changes global server behaviour; future tool calls take the new path.
+                readOnlyHint: false,
+                destructiveHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 mode: z.enum(['execution', 'passthrough', 'hybrid']).describe('The operation mode to switch to.'),
             },
@@ -469,6 +562,11 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
         this.server.registerTool('reload_servers', {
             title: 'Reload Servers',
             description: 'Reload MCP server configurations. Useful after modifying claude_desktop_config.json.',
+            annotations: {
+                destructiveHint: true,
+                idempotentHint: false,
+                openWorldHint: true,
+            },
             inputSchema: {},
             outputSchema: {
                 added: z.array(z.string()),
@@ -493,6 +591,11 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
         this.server.registerTool('get_capabilities', {
             title: 'Get Capabilities',
             description: 'Get detailed information about MCP Executor capabilities and configuration.',
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {},
             outputSchema: {
                 version: z.string(),
@@ -522,7 +625,7 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
                 ? { loaded: this.skills.getSkillCount(), categories: this.skills.getCategories() }
                 : { loaded: 0, categories: [] };
             const output = {
-                version: '0.1.0',
+                version: VERSION,
                 current_mode: this.currentMode,
                 features: {
                     streaming: this.config.execution.streamingEnabled,
@@ -550,6 +653,11 @@ Use passthrough_call only for debugging - it has HIGH token cost.`,
             title: 'Compare Modes',
             description: `Analyse how a task would be handled in different modes.
 Returns estimated token usage and approach for each mode.`,
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 task_description: z.string().describe('Description of the task to analyse.'),
                 estimated_tool_calls: z.number().optional().describe('Estimated number of tool calls needed.'),
@@ -628,6 +736,14 @@ Returns estimated token usage and approach for each mode.`,
             description: `⚠️ DEBUGGING TOOL - Direct MCP tool call. HIGH TOKEN COST (10-100x vs execute_code).
 
 Only use for debugging raw tool input/output. Use execute_code for all normal operations.`,
+            annotations: {
+                // Proxies into a backend MCP server so the effect depends on the
+                // downstream tool. Conservative defaults: assume external + mutable.
+                readOnlyHint: false,
+                destructiveHint: true,
+                idempotentHint: false,
+                openWorldHint: true,
+            },
             inputSchema: {
                 server: z.string().describe('Name of the MCP server to call.'),
                 tool: z.string().describe('Name of the tool to invoke.'),
@@ -773,6 +889,11 @@ Only use for debugging raw tool input/output. Use execute_code for all normal op
             description: `Web search via Brave Search API. Uses 90% fewer tokens than native WebSearch.
 
 Routes to brave-search MCP server internally. Requires brave-search server to be configured.`,
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: false, // Web results change between calls
+                openWorldHint: true,
+            },
             inputSchema: {
                 query: z.string().describe('Search query (max 400 chars, 50 words).'),
                 count: z.number().optional().describe('Number of results (1-20, default 10).'),
@@ -834,6 +955,12 @@ Routes to brave-search MCP server internally. Requires brave-search server to be
 
 Saves the server configuration to ~/.mcp-conductor.json and triggers a reload.
 Use this to dynamically add servers without restarting Claude.`,
+            annotations: {
+                readOnlyHint: false,
+                destructiveHint: false, // Adds a new server; not destructive by itself
+                idempotentHint: false, // Re-adding the same name returns an error
+                openWorldHint: false,
+            },
             inputSchema: {
                 name: z.string().describe('Unique server name (e.g., "github", "filesystem").'),
                 command: z.string().describe('Command to run the server (e.g., "npx", "node", "python").'),
@@ -921,6 +1048,12 @@ Use this to dynamically add servers without restarting Claude.`,
 
 Removes the server configuration from ~/.mcp-conductor.json and triggers a reload.
 Use this to dynamically remove servers without restarting Claude.`,
+            annotations: {
+                readOnlyHint: false,
+                destructiveHint: true,
+                idempotentHint: true, // Removing an already-gone server is a safe no-op
+                openWorldHint: false,
+            },
             inputSchema: {
                 name: z.string().describe('Name of the server to remove.'),
             },
@@ -1006,6 +1139,12 @@ Use this to dynamically remove servers without restarting Claude.`,
 
 Use this to update API keys or other settings without removing and re-adding the server.
 Triggers a reload to apply changes immediately.`,
+            annotations: {
+                readOnlyHint: false,
+                destructiveHint: true, // Overwrites existing config; may disconnect/reconnect
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {
                 name: z.string().describe('Name of the server to update.'),
                 command: z.string().optional().describe('New command (optional, keeps existing if not provided).'),
@@ -1124,6 +1263,11 @@ Triggers a reload to apply changes immediately.`,
         this.server.registerTool('get_memory_stats', {
             title: 'Get Memory Stats',
             description: 'Returns live memory usage and resource counts for the conductor process. Use this to diagnose memory issues.',
+            annotations: {
+                readOnlyHint: true,
+                idempotentHint: true,
+                openWorldHint: false,
+            },
             inputSchema: {},
             outputSchema: {
                 heap_used_mb: z.number(),