@opengsd/gsd-pi 1.2.0 → 1.3.0-dev.eed73bea

package/packages/mcp-server/dist/pid-registry.js

@@ -0,0 +1,459 @@
+/**
+ * MCP server PID registry — tracks running instances per project so new
+ * launches can kill stale ones. Mirrors web-mode's web-instances.json pattern.
+ */
+import { execFileSync } from 'node:child_process';
+import { readFileSync, writeFileSync, mkdirSync, renameSync } from 'node:fs';
+import { homedir } from 'node:os';
+import { dirname, join, resolve } from 'node:path';
+const REGISTRY_PATH = join(process.env.GSD_HOME || join(homedir(), '.gsd'), 'mcp-instances.json');
+// A live PID is only treated as "our" stale server if its OS start time is no
+// later than the moment we recorded the registry entry (plus a small skew for
+// clock granularity / start-vs-register delay). A PID that started materially
+// later has been recycled by a different process and must not be signalled.
+const STALE_PID_START_SKEW_MS = 60_000;
+export function readMcpRegistry(registryPath = REGISTRY_PATH) {
+    let raw;
+    try {
+        raw = readFileSync(registryPath, 'utf8');
+    }
+    catch (err) {
+        // A missing file is the normal first-run case — start with an empty
+        // registry silently. Any other read error is worth surfacing.
+        if (err.code !== 'ENOENT') {
+            process.stderr.write(`[gsd-mcp-server] failed to read MCP registry ${registryPath}: ${err instanceof Error ? err.message : String(err)}\n`);
+        }
+        return {};
+    }
+    try {
+        const parsed = JSON.parse(raw);
+        if (parsed && typeof parsed === 'object' && !Array.isArray(parsed)) {
+            return parsed;
+        }
+        throw new Error('registry is not a JSON object');
+    }
+    catch (err) {
+        // The file exists but is unparseable. Returning {} here means the next
+        // registerMcpInstance would overwrite the file and silently drop every
+        // other project's entry. The corrupt bytes can't be recovered, but we
+        // preserve them for forensics and warn loudly instead of dropping them
+        // without a trace.
+        const backup = `${registryPath}.corrupt-${Date.now()}`;
+        try {
+            renameSync(registryPath, backup);
+            process.stderr.write(`[gsd-mcp-server] MCP registry ${registryPath} was corrupt (${err instanceof Error ? err.message : String(err)}); preserved as ${backup}\n`);
+        }
+        catch {
+            process.stderr.write(`[gsd-mcp-server] MCP registry ${registryPath} was corrupt (${err instanceof Error ? err.message : String(err)}) and could not be preserved\n`);
+        }
+        return {};
+    }
+}
+function writeMcpRegistry(registry, registryPath = REGISTRY_PATH) {
+    mkdirSync(dirname(registryPath), { recursive: true });
+    writeFileSync(registryPath, JSON.stringify(registry, null, 2), 'utf8');
+}
+function defaultGetProcessCommand(pid) {
+    try {
+        if (process.platform === 'win32') {
+            // `ps` does not exist on Windows; query the process command line via CIM
+            // so stale same-project cleanup is not silently disabled there.
+            const out = execFileSync('powershell.exe', [
+                '-NoProfile',
+                '-NonInteractive',
+                '-Command',
+                `(Get-CimInstance Win32_Process -Filter "ProcessId=${pid}").CommandLine`,
+            ], { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+            return out || null;
+        }
+        const command = execFileSync('ps', ['-p', String(pid), '-o', 'command='], {
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            env: { ...process.env, LC_ALL: 'C' },
+        }).trim();
+        return command || null;
+    }
+    catch {
+        return null;
+    }
+}
+function defaultGetProcessStartTime(pid) {
+    try {
+        if (process.platform === 'win32') {
+            const out = execFileSync('powershell.exe', [
+                '-NoProfile',
+                '-NonInteractive',
+                '-Command',
+                `$p = Get-CimInstance Win32_Process -Filter "ProcessId=${pid}"; if ($p) { [int64](($p.CreationDate.ToUniversalTime() - [datetime]'1970-01-01T00:00:00Z').TotalMilliseconds) }`,
+            ], { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+            const ms = Number(out);
+            return Number.isFinite(ms) && ms > 0 ? ms : null;
+        }
+        // `lstart` is supported by both Linux (procps) and macOS (BSD) ps. Force
+        // the C locale so the timestamp is parseable regardless of the user's LANG.
+        const lstart = execFileSync('ps', ['-p', String(pid), '-o', 'lstart='], {
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            env: { ...process.env, LC_ALL: 'C' },
+        }).trim();
+        if (!lstart)
+            return null;
+        const ms = new Date(lstart).getTime();
+        return Number.isFinite(ms) ? ms : null;
+    }
+    catch {
+        return null;
+    }
+}
+function normalizeProcessCwd(value) {
+    return value.startsWith('\\\\?\\') ? value.slice(4) : value;
+}
+function defaultGetProcessCwd(pid) {
+    if (process.platform === 'win32') {
+        try {
+            const out = execFileSync('powershell.exe', [
+                '-NoProfile',
+                '-NonInteractive',
+                '-Command',
+                `$pid=${pid};$t=@'
+using System;using System.Runtime.InteropServices;using System.Text;
+public static class GsdProcCwd{
+ [DllImport("kernel32.dll")] public static extern IntPtr OpenProcess(int a,bool b,int p);
+ [DllImport("kernel32.dll")] public static extern bool CloseHandle(IntPtr h);
+ [DllImport("kernel32.dll")] public static extern bool ReadProcessMemory(IntPtr h,IntPtr a,byte[] b,int l,out int r);
+ [DllImport("ntdll.dll")] public static extern int NtQueryInformationProcess(IntPtr h,int c,byte[] i,int l,out int o);
+ public static string G(int pid){
+  IntPtr h=OpenProcess(0x1010,false,pid);if(h==IntPtr.Zero)return null;
+  try{bool x=IntPtr.Size==8;int n=IntPtr.Size*6;byte[] pbi=new byte[n];int o;
+  if(NtQueryInformationProcess(h,0,pbi,n,out o)!=0)return null;
+  IntPtr peb=x?(IntPtr)BitConverter.ToInt64(pbi,IntPtr.Size):(IntPtr)BitConverter.ToInt32(pbi,4);
+  byte[] ptr=new byte[IntPtr.Size];int rd;
+  if(!ReadProcessMemory(h,IntPtr.Add(peb,x?0x20:0x10),ptr,ptr.Length,out rd))return null;
+  IntPtr pp=x?(IntPtr)BitConverter.ToInt64(ptr,0):(IntPtr)BitConverter.ToInt32(ptr,0);
+  byte[] us=new byte[16];
+  if(!ReadProcessMemory(h,IntPtr.Add(pp,x?0x38:0x24),us,us.Length,out rd))return null;
+  int len=BitConverter.ToUInt16(us,0);if(len<=0||len>32766)return null;
+  IntPtr buf=x?(IntPtr)BitConverter.ToInt64(us,8):(IntPtr)BitConverter.ToInt32(us,4);
+  byte[] ch=new byte[len];
+  if(!ReadProcessMemory(h,buf,ch,ch.Length,out rd))return null;
+  return Encoding.Unicode.GetString(ch,0,len);}finally{CloseHandle(h);}}
+}
+'@;Add-Type -TypeDefinition $t -ErrorAction Stop;[GsdProcCwd]::G($pid)`,
+            ], { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+            if (!out)
+                return null;
+            return normalizeProcessCwd(out);
+        }
+        catch {
+            return null;
+        }
+    }
+    try {
+        const out = execFileSync('lsof', ['-a', '-p', String(pid), '-d', 'cwd', '-Fn'], {
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            env: { ...process.env, LC_ALL: 'C' },
+        });
+        const cwd = out.split('\n').find((line) => line.startsWith('n'))?.slice(1).trim();
+        if (cwd)
+            return cwd;
+    }
+    catch {
+    }
+    try {
+        const out = execFileSync('pwdx', [String(pid)], {
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            env: { ...process.env, LC_ALL: 'C' },
+        }).trim();
+        const match = /^\d+:\s+(.+)$/.exec(out);
+        return match?.[1]?.trim() || null;
+    }
+    catch {
+        return null;
+    }
+}
+function isSafePid(pid) {
+    return typeof pid === 'number' && Number.isSafeInteger(pid) && pid > 1;
+}
+function isMcpServerCommand(command) {
+    if (!command)
+        return false;
+    const normalized = command.replace(/\\/g, '/');
+    return (command.includes('gsd-mcp-server') ||
+        command.includes('@opengsd/mcp-server') ||
+        normalized.includes('/packages/mcp-server/'));
+}
+function defaultListProcesses() {
+    if (process.platform === 'win32') {
+        try {
+            const out = execFileSync('powershell.exe', [
+                '-NoProfile',
+                '-NonInteractive',
+                '-Command',
+                'Get-CimInstance Win32_Process | Select-Object ProcessId,ParentProcessId,CommandLine | ConvertTo-Json -Compress',
+            ], { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] }).trim();
+            if (!out)
+                return [];
+            const parsed = JSON.parse(out);
+            const rows = Array.isArray(parsed) ? parsed : [parsed];
+            return rows.flatMap((row) => {
+                if (!row || typeof row !== 'object')
+                    return [];
+                const record = row;
+                const pid = Number(record.ProcessId);
+                const ppid = Number(record.ParentProcessId);
+                const command = typeof record.CommandLine === 'string' ? record.CommandLine : '';
+                if (!Number.isSafeInteger(pid) || !Number.isSafeInteger(ppid))
+                    return [];
+                return [{ pid, ppid, command }];
+            });
+        }
+        catch {
+            return [];
+        }
+    }
+    try {
+        const out = execFileSync('ps', ['-axo', 'pid=,ppid=,command='], {
+            encoding: 'utf8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+            env: { ...process.env, LC_ALL: 'C' },
+        });
+        return out.split('\n').flatMap((line) => {
+            const match = /^\s*(\d+)\s+(\d+)\s+(.+)$/.exec(line);
+            if (!match)
+                return [];
+            return [{
+                    pid: Number(match[1]),
+                    ppid: Number(match[2]),
+                    command: match[3],
+                }];
+        });
+    }
+    catch {
+        return [];
+    }
+}
+function defaultWaitForExit() {
+    const shared = new Int32Array(new SharedArrayBuffer(4));
+    Atomics.wait(shared, 0, 0, 250);
+}
+function escapeRegExp(value) {
+    return value.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+}
+function normalizeCommandPath(value) {
+    return value.replace(/\\/g, '/');
+}
+function resolveComparableProjectPath(projectDir) {
+    if (/^[A-Za-z]:[\\/]/.test(projectDir) ||
+        projectDir.startsWith('\\\\') ||
+        projectDir.startsWith('/')) {
+        // Already an absolute path (Windows drive-letter, UNC, or POSIX). Do NOT
+        // call path.resolve(), which would prepend the current drive letter on
+        // Windows and turn a POSIX path like /workspace/project into
+        // C:/workspace/project, breaking command-path matching when the process
+        // command still contains the raw POSIX prefix.
+        return normalizeCommandPath(projectDir);
+    }
+    return normalizeCommandPath(resolve(projectDir));
+}
+function projectRegistryKeys(projectDir) {
+    return [...new Set([
+            resolveComparableProjectPath(projectDir),
+            resolve(projectDir),
+            projectDir,
+        ])];
+}
+function commandContainsProjectPath(command, projectDir) {
+    const normalizedProject = resolveComparableProjectPath(projectDir);
+    const normalizedCommand = normalizeCommandPath(command);
+    const pattern = new RegExp(`(^|[\\s"'])${escapeRegExp(normalizedProject)}(?=$|[/\\s"'])`);
+    return pattern.test(normalizedCommand);
+}
+function isSameProjectMcpProcess(command, cwd, projectDir) {
+    if (!isMcpServerCommand(command))
+        return false;
+    if (cwd && resolveComparableProjectPath(normalizeProcessCwd(cwd)) === resolveComparableProjectPath(projectDir))
+        return true;
+    return commandContainsProjectPath(command, projectDir);
+}
+function isPidAlive(pid, sendSignal) {
+    try {
+        sendSignal(pid, 0);
+        return true;
+    }
+    catch (error) {
+        return !(error instanceof Error &&
+            'code' in error &&
+            error.code === 'ESRCH');
+    }
+}
+function isOrphanedMcpProcess(proc, sendSignal) {
+    if (process.platform === 'win32') {
+        // Windows does not reparent orphans to PID 1; the PPID usually still
+        // points at the dead parent, so treat a missing parent as orphaned.
+        if (!isSafePid(proc.ppid))
+            return false;
+        return !isPidAlive(proc.ppid, sendSignal);
+    }
+    return proc.ppid === 1;
+}
+export function sweepProjectOrphanMcpServers(projectDir, options = {}) {
+    const sendSignal = options.kill ?? ((targetPid, signal) => process.kill(targetPid, signal));
+    const getProcessCwd = options.getProcessCwd ?? defaultGetProcessCwd;
+    const listProcesses = options.listProcesses ?? defaultListProcesses;
+    const isOrphaned = options.isOrphaned ?? ((proc) => isOrphanedMcpProcess(proc, sendSignal));
+    const waitForExit = options.waitForExit ?? defaultWaitForExit;
+    const result = {
+        matched: [],
+        terminated: [],
+        forceKilled: [],
+        skipped: [],
+    };
+    for (const proc of listProcesses()) {
+        if (!isSafePid(proc.pid) || proc.pid === process.pid)
+            continue;
+        if (!isOrphaned(proc))
+            continue;
+        if (!isMcpServerCommand(proc.command))
+            continue;
+        const cwd = commandContainsProjectPath(proc.command, projectDir) ? null : getProcessCwd(proc.pid);
+        if (!isSameProjectMcpProcess(proc.command, cwd, projectDir))
+            continue;
+        result.matched.push(proc.pid);
+        if (!isPidAlive(proc.pid, sendSignal)) {
+            result.skipped.push(proc.pid);
+            continue;
+        }
+        try {
+            sendSignal(proc.pid, 'SIGTERM');
+            result.terminated.push(proc.pid);
+        }
+        catch {
+            result.skipped.push(proc.pid);
+        }
+    }
+    if (result.terminated.length > 0)
+        waitForExit();
+    for (const pid of result.terminated) {
+        if (!isPidAlive(pid, sendSignal))
+            continue;
+        try {
+            sendSignal(pid, 'SIGKILL');
+            result.forceKilled.push(pid);
+        }
+        catch {
+            result.skipped.push(pid);
+        }
+    }
+    return result;
+}
+function killPid(pid, projectDir, startedAt, options = {}) {
+    if (!isSafePid(pid))
+        return 'invalid';
+    const sendSignal = options.kill ?? ((targetPid, signal) => process.kill(targetPid, signal));
+    const getProcessCommand = options.getProcessCommand ?? defaultGetProcessCommand;
+    const getProcessCwd = options.getProcessCwd ?? defaultGetProcessCwd;
+    const getProcessStartTime = options.getProcessStartTime ?? defaultGetProcessStartTime;
+    const waitForExit = options.waitForExit ?? defaultWaitForExit;
+    try {
+        sendSignal(pid, 0);
+    }
+    catch (error) {
+        const isAlreadyDead = error instanceof Error && 'code' in error && error.code === 'ESRCH';
+        if (isAlreadyDead)
+            return 'already-dead';
+        return { error: error instanceof Error ? error.message : String(error) };
+    }
+    const command = getProcessCommand(pid);
+    if (!command || !isMcpServerCommand(command))
+        return 'unverified';
+    const cwd = getProcessCwd(pid);
+    const recordedMs = startedAt ? Date.parse(startedAt) : NaN;
+    const actualStartMs = getProcessStartTime(pid);
+    // Guard against PID reuse: a recycled PID can belong to a *different* live
+    // MCP server (even for another project). If we can determine when the live
+    // process actually started and it began materially after we recorded this
+    // entry, the original server is gone and this PID is not ours — refuse to
+    // signal it.
+    if (Number.isFinite(recordedMs) &&
+        actualStartMs !== null &&
+        actualStartMs > recordedMs + STALE_PID_START_SKEW_MS) {
+        return 'unverified';
+    }
+    // Confirm the live MCP server is the one we registered for this project via
+    // the process cwd or an embedded project path. Start time alone is not enough
+    // to authorize a signal when cwd is unavailable — another project's global
+    // install can share the same command line and a coincidentally aligned start.
+    const sameProject = isSameProjectMcpProcess(command, cwd, projectDir);
+    if (!sameProject)
+        return 'unverified';
+    try {
+        sendSignal(pid, 'SIGTERM');
+        waitForExit();
+        if (!isPidAlive(pid, sendSignal))
+            return 'killed';
+        sendSignal(pid, 'SIGKILL');
+        return 'force-killed';
+    }
+    catch (error) {
+        const isAlreadyDead = error instanceof Error && 'code' in error && error.code === 'ESRCH';
+        if (isAlreadyDead)
+            return 'already-dead';
+        return { error: error instanceof Error ? error.message : String(error) };
+    }
+}
+/**
+ * Kill any existing MCP server for this project, then register our PID.
+ */
+export function registerMcpInstance(projectDir, registryPath = REGISTRY_PATH, options = {}) {
+    const registry = readMcpRegistry(registryPath);
+    const keys = projectRegistryKeys(projectDir);
+    const key = keys[0];
+    const existingKey = keys.find((candidate) => candidate in registry);
+    const existing = existingKey ? registry[existingKey] : undefined;
+    if (existing && existing.pid !== process.pid) {
+        const result = killPid(existing.pid, key, existing.startedAt, options);
+        const label = result === 'killed'
+            ? `killed stale pid=${existing.pid}`
+            : result === 'force-killed'
+                ? `force-killed stale pid=${existing.pid}`
+                : result === 'already-dead'
+                    ? `stale pid=${existing.pid} already dead`
+                    : result === 'invalid'
+                        ? `ignored invalid stale pid=${String(existing.pid)}`
+                        : result === 'unverified'
+                            ? `ignored unverified stale pid=${existing.pid}`
+                            : `failed to kill pid=${existing.pid}: ${result.error}`;
+        process.stderr.write(`[gsd-mcp-server] ${label} for ${key}\n`);
+        if (result === 'unverified')
+            return false;
+    }
+    if (existingKey && existingKey !== key)
+        delete registry[existingKey];
+    registry[key] = {
+        pid: process.pid,
+        projectDir: key,
+        startedAt: new Date().toISOString(),
+    };
+    writeMcpRegistry(registry, registryPath);
+    return true;
+}
+/**
+ * Remove our PID from the registry on shutdown.
+ */
+export function unregisterMcpInstance(projectDir, registryPath = REGISTRY_PATH) {
+    const keys = projectRegistryKeys(projectDir);
+    const registry = readMcpRegistry(registryPath);
+    let changed = false;
+    for (const key of keys) {
+        if (registry[key]?.pid === process.pid) {
+            delete registry[key];
+            changed = true;
+        }
+    }
+    if (changed) {
+        writeMcpRegistry(registry, registryPath);
+    }
+}
+//# sourceMappingURL=pid-registry.js.map

package/packages/mcp-server/dist/pid-registry.js.map

@@ -0,0 +1 @@
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* MCP server PID registry — tracks running instances per project so new\n * launches can kill stale ones. Mirrors web-mode's web-instances.json pattern.\n */\n\nimport { execFileSync } from 'node:child_process';\nimport { readFileSync, writeFileSync, mkdirSync, renameSync } from 'node:fs';\nimport { homedir } from 'node:os';\nimport { dirname, join, resolve } from 'node:path';\n\nexport interface McpInstanceEntry {\n  pid: number;\n  projectDir: string;\n  startedAt: string;\n}\n\nexport type McpInstanceRegistry = Record<string, McpInstanceEntry>;\n\nexport interface RegisterMcpInstanceOptions {\n  kill?: (pid: number, signal?: NodeJS.Signals | 0) => void;\n  getProcessCommand?: (pid: number) => string | null;\n  getProcessCwd?: (pid: number) => string | null;\n  getProcessStartTime?: (pid: number) => number | null;\n  waitForExit?: () => void;\n}\n\nexport interface McpProcessSnapshot {\n  pid: number;\n  ppid: number;\n  command: string;\n}\n\nexport interface SweepProjectOrphanMcpServersOptions {\n  kill?: (pid: number, signal?: NodeJS.Signals | 0) => void;\n  getProcessCwd?: (pid: number) => string | null;\n  listProcesses?: () => McpProcessSnapshot[];\n  isOrphaned?: (proc: McpProcessSnapshot) => boolean;\n  waitForExit?: () => void;\n}\n\nexport interface SweepProjectOrphanMcpServersResult {\n  matched: number[];\n  terminated: number[];\n  forceKilled: number[];\n  skipped: number[];\n}\n\nconst REGISTRY_PATH = join(\n  process.env.GSD_HOME || join(homedir(), '.gsd'),\n  'mcp-instances.json',\n);\n\n// A live PID is only treated as \"our\" stale server if its OS start time is no\n// later than the moment we recorded the registry entry (plus a small skew for\n// clock granularity / start-vs-register delay). A PID that started materially\n// later has been recycled by a different process and must not be signalled.\nconst STALE_PID_START_SKEW_MS = 60_000;\n\nexport function readMcpRegistry(registryPath = REGISTRY_PATH): McpInstanceRegistry {\n  let raw: string;\n  try {\n    raw = readFileSync(registryPath, 'utf8');\n  } catch (err) {\n    // A missing file is the normal first-run case — start with an empty\n    // registry silently. Any other read error is worth surfacing.\n    if ((err as NodeJS.ErrnoException).code !== 'ENOENT') {\n      process.stderr.write(\n        `[gsd-mcp-server] failed to read MCP registry ${registryPath}: ${err instanceof Error ? err.message : String(err)}\\n`,\n      );\n    }\n    return {};\n  }\n\n  try {\n    const parsed = JSON.parse(raw) as unknown;\n    if (parsed && typeof parsed === 'object' && !Array.isArray(parsed)) {\n      return parsed as McpInstanceRegistry;\n    }\n    throw new Error('registry is not a JSON object');\n  } catch (err) {\n    // The file exists but is unparseable. Returning {} here means the next\n    // registerMcpInstance would overwrite the file and silently drop every\n    // other project's entry. The corrupt bytes can't be recovered, but we\n    // preserve them for forensics and warn loudly instead of dropping them\n    // without a trace.\n    const backup = `${registryPath}.corrupt-${Date.now()}`;\n    try {\n      renameSync(registryPath, backup);\n      process.stderr.write(\n        `[gsd-mcp-server] MCP registry ${registryPath} was corrupt (${err instanceof Error ? err.message : String(err)}); preserved as ${backup}\\n`,\n      );\n    } catch {\n      process.stderr.write(\n        `[gsd-mcp-server] MCP registry ${registryPath} was corrupt (${err instanceof Error ? err.message : String(err)}) and could not be preserved\\n`,\n      );\n    }\n    return {};\n  }\n}\n\nfunction writeMcpRegistry(registry: McpInstanceRegistry, registryPath = REGISTRY_PATH): void {\n  mkdirSync(dirname(registryPath), { recursive: true });\n  writeFileSync(registryPath, JSON.stringify(registry, null, 2), 'utf8');\n}\n\nfunction defaultGetProcessCommand(pid: number): string | null {\n  try {\n    if (process.platform === 'win32') {\n      // `ps` does not exist on Windows; query the process command line via CIM\n      // so stale same-project cleanup is not silently disabled there.\n      const out = execFileSync(\n        'powershell.exe',\n        [\n          '-NoProfile',\n          '-NonInteractive',\n          '-Command',\n          `(Get-CimInstance Win32_Process -Filter \"ProcessId=${pid}\").CommandLine`,\n        ],\n        { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] },\n      ).trim();\n      return out || null;\n    }\n    const command = execFileSync('ps', ['-p', String(pid), '-o', 'command='], {\n      encoding: 'utf8',\n      stdio: ['ignore', 'pipe', 'ignore'],\n      env: { ...process.env, LC_ALL: 'C' },\n    }).trim();\n    return command || null;\n  } catch {\n    return null;\n  }\n}\n\nfunction defaultGetProcessStartTime(pid: number): number | null {\n  try {\n    if (process.platform === 'win32') {\n      const out = execFileSync(\n        'powershell.exe',\n        [\n          '-NoProfile',\n          '-NonInteractive',\n          '-Command',\n          `$p = Get-CimInstance Win32_Process -Filter \"ProcessId=${pid}\"; if ($p) { [int64](($p.CreationDate.ToUniversalTime() - [datetime]'1970-01-01T00:00:00Z').TotalMilliseconds) }`,\n        ],\n        { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] },\n      ).trim();\n      const ms = Number(out);\n      return Number.isFinite(ms) && ms > 0 ? ms : null;\n    }\n    // `lstart` is supported by both Linux (procps) and macOS (BSD) ps. Force\n    // the C locale so the timestamp is parseable regardless of the user's LANG.\n    const lstart = execFileSync('ps', ['-p', String(pid), '-o', 'lstart='], {\n      encoding: 'utf8',\n      stdio: ['ignore', 'pipe', 'ignore'],\n      env: { ...process.env, LC_ALL: 'C' },\n    }).trim();\n    if (!lstart) return null;\n    const ms = new Date(lstart).getTime();\n    return Number.isFinite(ms) ? ms : null;\n  } catch {\n    return null;\n  }\n}\n\nfunction normalizeProcessCwd(value: string): string {\n  return value.startsWith('\\\\\\\\?\\\\') ? value.slice(4) : value;\n}\n\nfunction defaultGetProcessCwd(pid: number): string | null {\n  if (process.platform === 'win32') {\n    try {\n      const out = execFileSync(\n        'powershell.exe',\n        [\n          '-NoProfile',\n          '-NonInteractive',\n          '-Command',\n          `$pid=${pid};$t=@'\nusing System;using System.Runtime.InteropServices;using System.Text;\npublic static class GsdProcCwd{\n [DllImport(\"kernel32.dll\")] public static extern IntPtr OpenProcess(int a,bool b,int p);\n [DllImport(\"kernel32.dll\")] public static extern bool CloseHandle(IntPtr h);\n [DllImport(\"kernel32.dll\")] public static extern bool ReadProcessMemory(IntPtr h,IntPtr a,byte[] b,int l,out int r);\n [DllImport(\"ntdll.dll\")] public static extern int NtQueryInformationProcess(IntPtr h,int c,byte[] i,int l,out int o);\n public static string G(int pid){\n  IntPtr h=OpenProcess(0x1010,false,pid);if(h==IntPtr.Zero)return null;\n  try{bool x=IntPtr.Size==8;int n=IntPtr.Size*6;byte[] pbi=new byte[n];int o;\n  if(NtQueryInformationProcess(h,0,pbi,n,out o)!=0)return null;\n  IntPtr peb=x?(IntPtr)BitConverter.ToInt64(pbi,IntPtr.Size):(IntPtr)BitConverter.ToInt32(pbi,4);\n  byte[] ptr=new byte[IntPtr.Size];int rd;\n  if(!ReadProcessMemory(h,IntPtr.Add(peb,x?0x20:0x10),ptr,ptr.Length,out rd))return null;\n  IntPtr pp=x?(IntPtr)BitConverter.ToInt64(ptr,0):(IntPtr)BitConverter.ToInt32(ptr,0);\n  byte[] us=new byte[16];\n  if(!ReadProcessMemory(h,IntPtr.Add(pp,x?0x38:0x24),us,us.Length,out rd))return null;\n  int len=BitConverter.ToUInt16(us,0);if(len<=0||len>32766)return null;\n  IntPtr buf=x?(IntPtr)BitConverter.ToInt64(us,8):(IntPtr)BitConverter.ToInt32(us,4);\n  byte[] ch=new byte[len];\n  if(!ReadProcessMemory(h,buf,ch,ch.Length,out rd))return null;\n  return Encoding.Unicode.GetString(ch,0,len);}finally{CloseHandle(h);}}\n}\n'@;Add-Type -TypeDefinition $t -ErrorAction Stop;[GsdProcCwd]::G($pid)`,\n        ],\n        { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] },\n      ).trim();\n      if (!out) return null;\n      return normalizeProcessCwd(out);\n    } catch {\n      return null;\n    }\n  }\n\n  try {\n    const out = execFileSync('lsof', ['-a', '-p', String(pid), '-d', 'cwd', '-Fn'], {\n      encoding: 'utf8',\n      stdio: ['ignore', 'pipe', 'ignore'],\n      env: { ...process.env, LC_ALL: 'C' },\n    });\n    const cwd = out.split('\\n').find((line) => line.startsWith('n'))?.slice(1).trim();\n    if (cwd) return cwd;\n  } catch {\n  }\n\n  try {\n    const out = execFileSync('pwdx', [String(pid)], {\n      encoding: 'utf8',\n      stdio: ['ignore', 'pipe', 'ignore'],\n      env: { ...process.env, LC_ALL: 'C' },\n    }).trim();\n    const match = /^\\d+:\\s+(.+)$/.exec(out);\n    return match?.[1]?.trim() || null;\n  } catch {\n    return null;\n  }\n}\n\nfunction isSafePid(pid: unknown): pid is number {\n  return typeof pid === 'number' && Number.isSafeInteger(pid) && pid > 1;\n}\n\nfunction isMcpServerCommand(command: string | null): boolean {\n  if (!command) return false;\n  const normalized = command.replace(/\\\\/g, '/');\n  return (\n    command.includes('gsd-mcp-server') ||\n    command.includes('@opengsd/mcp-server') ||\n    normalized.includes('/packages/mcp-server/')\n  );\n}\n\nfunction defaultListProcesses(): McpProcessSnapshot[] {\n  if (process.platform === 'win32') {\n    try {\n      const out = execFileSync(\n        'powershell.exe',\n        [\n          '-NoProfile',\n          '-NonInteractive',\n          '-Command',\n          'Get-CimInstance Win32_Process | Select-Object ProcessId,ParentProcessId,CommandLine | ConvertTo-Json -Compress',\n        ],\n        { encoding: 'utf8', stdio: ['ignore', 'pipe', 'ignore'] },\n      ).trim();\n      if (!out) return [];\n      const parsed = JSON.parse(out) as unknown;\n      const rows = Array.isArray(parsed) ? parsed : [parsed];\n      return rows.flatMap((row) => {\n        if (!row || typeof row !== 'object') return [];\n        const record = row as Record<string, unknown>;\n        const pid = Number(record.ProcessId);\n        const ppid = Number(record.ParentProcessId);\n        const command = typeof record.CommandLine === 'string' ? record.CommandLine : '';\n        if (!Number.isSafeInteger(pid) || !Number.isSafeInteger(ppid)) return [];\n        return [{ pid, ppid, command }];\n      });\n    } catch {\n      return [];\n    }\n  }\n\n  try {\n    const out = execFileSync('ps', ['-axo', 'pid=,ppid=,command='], {\n      encoding: 'utf8',\n      stdio: ['ignore', 'pipe', 'ignore'],\n      env: { ...process.env, LC_ALL: 'C' },\n    });\n    return out.split('\\n').flatMap((line) => {\n      const match = /^\\s*(\\d+)\\s+(\\d+)\\s+(.+)$/.exec(line);\n      if (!match) return [];\n      return [{\n        pid: Number(match[1]),\n        ppid: Number(match[2]),\n        command: match[3],\n      }];\n    });\n  } catch {\n    return [];\n  }\n}\n\nfunction defaultWaitForExit(): void {\n  const shared = new Int32Array(new SharedArrayBuffer(4));\n  Atomics.wait(shared, 0, 0, 250);\n}\n\nfunction escapeRegExp(value: string): string {\n  return value.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n\nfunction normalizeCommandPath(value: string): string {\n  return value.replace(/\\\\/g, '/');\n}\n\nfunction resolveComparableProjectPath(projectDir: string): string {\n  if (\n    /^[A-Za-z]:[\\\\/]/.test(projectDir) ||\n    projectDir.startsWith('\\\\\\\\') ||\n    projectDir.startsWith('/')\n  ) {\n    // Already an absolute path (Windows drive-letter, UNC, or POSIX). Do NOT\n    // call path.resolve(), which would prepend the current drive letter on\n    // Windows and turn a POSIX path like /workspace/project into\n    // C:/workspace/project, breaking command-path matching when the process\n    // command still contains the raw POSIX prefix.\n    return normalizeCommandPath(projectDir);\n  }\n  return normalizeCommandPath(resolve(projectDir));\n}\n\nfunction projectRegistryKeys(projectDir: string): string[] {\n  return [...new Set([\n    resolveComparableProjectPath(projectDir),\n    resolve(projectDir),\n    projectDir,\n  ])];\n}\n\nfunction commandContainsProjectPath(command: string, projectDir: string): boolean {\n  const normalizedProject = resolveComparableProjectPath(projectDir);\n  const normalizedCommand = normalizeCommandPath(command);\n  const pattern = new RegExp(`(^|[\\\\s\"'])${escapeRegExp(normalizedProject)}(?=$|[/\\\\s\"'])`);\n  return pattern.test(normalizedCommand);\n}\n\nfunction isSameProjectMcpProcess(command: string, cwd: string | null, projectDir: string): boolean {\n  if (!isMcpServerCommand(command)) return false;\n  if (cwd && resolveComparableProjectPath(normalizeProcessCwd(cwd)) === resolveComparableProjectPath(projectDir)) return true;\n  return commandContainsProjectPath(command, projectDir);\n}\n\nfunction isPidAlive(\n  pid: number,\n  sendSignal: (pid: number, signal?: NodeJS.Signals | 0) => void,\n): boolean {\n  try {\n    sendSignal(pid, 0);\n    return true;\n  } catch (error) {\n    return !(\n      error instanceof Error &&\n      'code' in error &&\n      (error as NodeJS.ErrnoException).code === 'ESRCH'\n    );\n  }\n}\n\nfunction isOrphanedMcpProcess(\n  proc: McpProcessSnapshot,\n  sendSignal: (pid: number, signal?: NodeJS.Signals | 0) => void,\n): boolean {\n  if (process.platform === 'win32') {\n    // Windows does not reparent orphans to PID 1; the PPID usually still\n    // points at the dead parent, so treat a missing parent as orphaned.\n    if (!isSafePid(proc.ppid)) return false;\n    return !isPidAlive(proc.ppid, sendSignal);\n  }\n  return proc.ppid === 1;\n}\n\nexport function sweepProjectOrphanMcpServers(\n  projectDir: string,\n  options: SweepProjectOrphanMcpServersOptions = {},\n): SweepProjectOrphanMcpServersResult {\n  const sendSignal = options.kill ?? ((targetPid, signal) => process.kill(targetPid, signal));\n  const getProcessCwd = options.getProcessCwd ?? defaultGetProcessCwd;\n  const listProcesses = options.listProcesses ?? defaultListProcesses;\n  const isOrphaned = options.isOrphaned ?? ((proc: McpProcessSnapshot) => isOrphanedMcpProcess(proc, sendSignal));\n  const waitForExit = options.waitForExit ?? defaultWaitForExit;\n\n  const result: SweepProjectOrphanMcpServersResult = {\n    matched: [],\n    terminated: [],\n    forceKilled: [],\n    skipped: [],\n  };\n\n  for (const proc of listProcesses()) {\n    if (!isSafePid(proc.pid) || proc.pid === process.pid) continue;\n    if (!isOrphaned(proc)) continue;\n    if (!isMcpServerCommand(proc.command)) continue;\n    const cwd = commandContainsProjectPath(proc.command, projectDir) ? null : getProcessCwd(proc.pid);\n    if (!isSameProjectMcpProcess(proc.command, cwd, projectDir)) continue;\n    result.matched.push(proc.pid);\n\n    if (!isPidAlive(proc.pid, sendSignal)) {\n      result.skipped.push(proc.pid);\n      continue;\n    }\n\n    try {\n      sendSignal(proc.pid, 'SIGTERM');\n      result.terminated.push(proc.pid);\n    } catch {\n      result.skipped.push(proc.pid);\n    }\n  }\n\n  if (result.terminated.length > 0) waitForExit();\n\n  for (const pid of result.terminated) {\n    if (!isPidAlive(pid, sendSignal)) continue;\n    try {\n      sendSignal(pid, 'SIGKILL');\n      result.forceKilled.push(pid);\n    } catch {\n      result.skipped.push(pid);\n    }\n  }\n\n  return result;\n}\n\nfunction killPid(\n  pid: unknown,\n  projectDir: string,\n  startedAt: string | undefined,\n  options: RegisterMcpInstanceOptions = {},\n): 'killed' | 'force-killed' | 'already-dead' | 'invalid' | 'unverified' | { error: string } {\n  if (!isSafePid(pid)) return 'invalid';\n\n  const sendSignal = options.kill ?? ((targetPid, signal) => process.kill(targetPid, signal));\n  const getProcessCommand = options.getProcessCommand ?? defaultGetProcessCommand;\n  const getProcessCwd = options.getProcessCwd ?? defaultGetProcessCwd;\n  const getProcessStartTime = options.getProcessStartTime ?? defaultGetProcessStartTime;\n  const waitForExit = options.waitForExit ?? defaultWaitForExit;\n\n  try {\n    sendSignal(pid, 0);\n  } catch (error) {\n    const isAlreadyDead =\n      error instanceof Error && 'code' in error && (error as NodeJS.ErrnoException).code === 'ESRCH';\n    if (isAlreadyDead) return 'already-dead';\n    return { error: error instanceof Error ? error.message : String(error) };\n  }\n\n  const command = getProcessCommand(pid);\n  if (!command || !isMcpServerCommand(command)) return 'unverified';\n\n  const cwd = getProcessCwd(pid);\n  const recordedMs = startedAt ? Date.parse(startedAt) : NaN;\n  const actualStartMs = getProcessStartTime(pid);\n\n  // Guard against PID reuse: a recycled PID can belong to a *different* live\n  // MCP server (even for another project). If we can determine when the live\n  // process actually started and it began materially after we recorded this\n  // entry, the original server is gone and this PID is not ours — refuse to\n  // signal it.\n  if (\n    Number.isFinite(recordedMs) &&\n    actualStartMs !== null &&\n    actualStartMs > recordedMs + STALE_PID_START_SKEW_MS\n  ) {\n    return 'unverified';\n  }\n\n  // Confirm the live MCP server is the one we registered for this project via\n  // the process cwd or an embedded project path. Start time alone is not enough\n  // to authorize a signal when cwd is unavailable — another project's global\n  // install can share the same command line and a coincidentally aligned start.\n  const sameProject = isSameProjectMcpProcess(command, cwd, projectDir);\n  if (!sameProject) return 'unverified';\n\n  try {\n    sendSignal(pid, 'SIGTERM');\n    waitForExit();\n    if (!isPidAlive(pid, sendSignal)) return 'killed';\n    sendSignal(pid, 'SIGKILL');\n    return 'force-killed';\n  } catch (error) {\n    const isAlreadyDead =\n      error instanceof Error && 'code' in error && (error as NodeJS.ErrnoException).code === 'ESRCH';\n    if (isAlreadyDead) return 'already-dead';\n    return { error: error instanceof Error ? error.message : String(error) };\n  }\n}\n\n/**\n * Kill any existing MCP server for this project, then register our PID.\n */\nexport function registerMcpInstance(\n  projectDir: string,\n  registryPath = REGISTRY_PATH,\n  options: RegisterMcpInstanceOptions = {},\n): boolean {\n  const registry = readMcpRegistry(registryPath);\n  const keys = projectRegistryKeys(projectDir);\n  const key = keys[0];\n  const existingKey = keys.find((candidate) => candidate in registry);\n\n  const existing = existingKey ? registry[existingKey] : undefined;\n  if (existing && existing.pid !== process.pid) {\n    const result = killPid(existing.pid, key, existing.startedAt, options);\n    const label = result === 'killed'\n      ? `killed stale pid=${existing.pid}`\n      : result === 'force-killed'\n        ? `force-killed stale pid=${existing.pid}`\n      : result === 'already-dead'\n        ? `stale pid=${existing.pid} already dead`\n        : result === 'invalid'\n          ? `ignored invalid stale pid=${String(existing.pid)}`\n          : result === 'unverified'\n            ? `ignored unverified stale pid=${existing.pid}`\n            : `failed to kill pid=${existing.pid}: ${result.error}`;\n    process.stderr.write(`[gsd-mcp-server] ${label} for ${key}\\n`);\n    if (result === 'unverified') return false;\n  }\n  if (existingKey && existingKey !== key) delete registry[existingKey];\n\n  registry[key] = {\n    pid: process.pid,\n    projectDir: key,\n    startedAt: new Date().toISOString(),\n  };\n  writeMcpRegistry(registry, registryPath);\n  return true;\n}\n\n/**\n * Remove our PID from the registry on shutdown.\n */\nexport function unregisterMcpInstance(projectDir: string, registryPath = REGISTRY_PATH): void {\n  const keys = projectRegistryKeys(projectDir);\n  const registry = readMcpRegistry(registryPath);\n  let changed = false;\n  for (const key of keys) {\n    if (registry[key]?.pid === process.pid) {\n      delete registry[key];\n      changed = true;\n    }\n  }\n  if (changed) {\n    writeMcpRegistry(registry, registryPath);\n  }\n}\n"]}

package/packages/mcp-server/dist/probe-mode.d.ts

@@ -0,0 +1,4 @@
+/** When set, stdio MCP is a short-lived tools/list probe — skip PID registry side effects. */
+export declare const GSD_MCP_PROBE_ENV = "GSD_MCP_PROBE";
+export declare function isMcpProbeSession(env?: NodeJS.ProcessEnv): boolean;
+//# sourceMappingURL=probe-mode.d.ts.map

package/packages/mcp-server/dist/probe-mode.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"probe-mode.d.ts","sourceRoot":"","sources":["../src/probe-mode.ts"],"names":[],"mappings":"AAAA,8FAA8F;AAC9F,eAAO,MAAM,iBAAiB,kBAAkB,CAAC;AAEjD,wBAAgB,iBAAiB,CAAC,GAAG,GAAE,MAAM,CAAC,UAAwB,GAAG,OAAO,CAK/E"}

package/packages/mcp-server/dist/probe-mode.js

@@ -0,0 +1,10 @@
+/** When set, stdio MCP is a short-lived tools/list probe — skip PID registry side effects. */
+export const GSD_MCP_PROBE_ENV = 'GSD_MCP_PROBE';
+export function isMcpProbeSession(env = process.env) {
+    const value = env[GSD_MCP_PROBE_ENV];
+    if (!value)
+        return false;
+    const normalized = value.trim().toLowerCase();
+    return normalized === '1' || normalized === 'true' || normalized === 'yes';
+}
+//# sourceMappingURL=probe-mode.js.map

package/packages/mcp-server/dist/probe-mode.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"probe-mode.js","sourceRoot":"","sources":["../src/probe-mode.ts"],"names":[],"mappings":"AAAA,8FAA8F;AAC9F,MAAM,CAAC,MAAM,iBAAiB,GAAG,eAAe,CAAC;AAEjD,MAAM,UAAU,iBAAiB,CAAC,MAAyB,OAAO,CAAC,GAAG;IACpE,MAAM,KAAK,GAAG,GAAG,CAAC,iBAAiB,CAAC,CAAC;IACrC,IAAI,CAAC,KAAK;QAAE,OAAO,KAAK,CAAC;IACzB,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IAC9C,OAAO,UAAU,KAAK,GAAG,IAAI,UAAU,KAAK,MAAM,IAAI,UAAU,KAAK,KAAK,CAAC;AAC7E,CAAC","sourcesContent":["/** When set, stdio MCP is a short-lived tools/list probe — skip PID registry side effects. */\nexport const GSD_MCP_PROBE_ENV = 'GSD_MCP_PROBE';\n\nexport function isMcpProbeSession(env: NodeJS.ProcessEnv = process.env): boolean {\n  const value = env[GSD_MCP_PROBE_ENV];\n  if (!value) return false;\n  const normalized = value.trim().toLowerCase();\n  return normalized === '1' || normalized === 'true' || normalized === 'yes';\n}\n"]}

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

@@ -93,6 +93,18 @@ interface AskUserQuestionsRoundResult {
     endInterview: false;
     answers: Record<string, AskUserQuestionsRoundResultAnswer>;
 }
+interface AskUserQuestionsStructuredContent {
+    questions: AskUserQuestion[];
+    response: AskUserQuestionsRoundResult | null;
+    cancelled: boolean;
+    /**
+     * True when the host elicitation timed out before the user answered.
+     * Distinct from `cancelled` (deliberate user dismissal): a timeout must not
+     * be laundered into a re-ask loop, so the gate hook treats it as "waiting"
+     * and pauses auto-mode (#852).
+     */
+    timed_out?: boolean;
+}
 interface AskUserQuestionsWriteGateModule {
     isGateQuestionId(questionId: string): boolean;
     isDepthConfirmationAnswer(selected: unknown, options?: Array<{
@@ -103,9 +115,23 @@ interface AskUserQuestionsWriteGateModule {
     markDepthVerified(milestoneId?: string | null, basePath?: string): void;
     clearPendingGate(basePath: string): void;
     extractDepthVerificationMilestoneId(questionId: string): string | null;
+    applyAskUserQuestionsGateResult?(options: {
+        basePath: string;
+        questions: AskUserQuestion[];
+        details: AskUserQuestionsStructuredContent;
+    }): unknown;
 }
 export declare function buildAskUserQuestionsElicitRequest(questions: AskUserQuestion[]): AskUserQuestionsElicitRequest;
 export declare function formatAskUserQuestionsElicitResult(questions: AskUserQuestion[], result: AskUserQuestionsElicitResult): string;
+/**
+ * Format the user-visible message returned when the host elicitation times out
+ * before the user answers. The message is LLM-facing: it tells the model the
+ * question was not answered, that it must NOT re-ask in the same turn, and that
+ * auto-mode is paused until the user responds. The gate hook routes this to a
+ * `timed_out` verdict so the depth-verification gate stays pending (fail-closed)
+ * without becoming a permanent block (#852).
+ */
+export declare function formatAskUserQuestionsTimeoutMessage(err: unknown): string;
 /**
  * Normalize an MCP elicitation form result into the `RoundResult` shape the
  * GSD discussion-gate hook reads from `tool_result` `details.response`. The
@@ -121,6 +147,19 @@ interface AskUserQuestionsHandlerDeps {
     writeGate?: AskUserQuestionsWriteGateModule | null;
     writeGateBasePath?: string;
 }
+/**
+ * Detect an elicitation-side timeout error so the handler returns a clean
+ * "timed_out" result rather than a raw error the model will retry.
+ *
+ * The Claude Agent SDK enforces its own ~60s elicitation timeout
+ * (`MCP error -32001: Request timed out`); `withElicitTimeout` enforces a
+ * longer 10-minute timeout (`… timed out after … minutes`). Both surface as
+ * elicitation fallback errors that should never become a raw `errorContent`
+ * response — without recognition they re-throw, skip
+ * `recordAskUserQuestionsGateResult`, leave the depth-verification gate
+ * pending, and the model loops on the blocked call (#852).
+ */
+export declare function isLocalElicitTimeoutError(err: unknown): boolean;
 export declare function askUserQuestionsHandler(questions: AskUserQuestion[], extra: McpToolExtra | undefined, deps: AskUserQuestionsHandlerDeps): Promise<ToolContent>;
 export type ElicitInputFn = (params: {
     message: string;
@@ -147,7 +186,7 @@ type ToolContent = {
     }>;
     structuredContent?: Record<string, unknown>;
 };
-export declare function secureEnvCollectHandler(args: Record<string, unknown>, elicitInput: ElicitInputFn): Promise<ToolContent>;
+export declare function secureEnvCollectHandler(args: Record<string, unknown>, elicitInput: ElicitInputFn, signal?: AbortSignal): Promise<ToolContent>;
 /**
  * Create and configure an MCP server with session, read-only, and workflow tools.
  *