feat: per-server tool-call timeout, on the server resource

Completes the plan's last item. The deadline shipped with a global default;
this makes it overridable per server, where the knowledge actually lives -- a
server with genuinely slow tools declares its own budget instead of forcing the
global up for everyone.

Source of truth is the server resource, following healthCheck exactly:
Prisma column + migration (NULL keeps today's behaviour, so no existing server
changes), zod validation on create and update, the repository, an
`--tool-call-timeout` flag mirroring `--health-check-timeout`, and the apply
schema so `apply -f` accepts what `get server -o yaml` emits.

That round-trip needed care: get emits `toolCallTimeoutSeconds: null` for every
server without an override, so the apply schema is nullable, not merely
optional -- otherwise the very first `get -o yaml | apply -f` on an untouched
server would have failed validation.

Bounded at one hour. A deadline exists so a wedged call answers instead of
hanging; a value beyond an hour is indistinguishable from having none.

It reaches mcplocal through server discovery rather than the project-scoped
serverOverrides map, and is applied on EVERY sync rather than only at first
registration -- raising a server's timeout should take effect at the next
refresh, not require the upstream to be dropped and rebuilt.

The endpoint sees the wire name (`docmost_search`), so it decodes to the
canonical `server/tool` before resolving. The override is keyed by server, so
every tool on that server inherits it without being enumerated, and the
failure message quotes the deadline actually applied rather than the global.

Smoke tests (tests/smoke/bounded-failures.smoke.test.ts) cover the two
production faults against the live proxy: a stale session recovers instead of
stranding the client on an uncorrelatable 404, every request is answered, and
`mcpctl trace` responds for an unknown code.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01GqMidYEGUJG5fxeoTELBu2

src/cli/src/commands/apply.ts

@@ -46,6 +46,9 @@ const ServerSpecSchema = z.object({
   volumes: z.array(VolumeSpecSchema).default([]),
   secretDelivery: z.enum(['env', 'injector']).optional(),
   entrypoint: z.array(z.string()).optional(),
+  // nullable: `get server -o yaml` emits null for servers with no override,
+  // and that YAML must apply back unchanged.
+  toolCallTimeoutSeconds: z.number().int().min(1).max(3600).nullable().optional(),
 });
 
 const SecretSpecSchema = z.object({
@@ -140,6 +143,9 @@ const TemplateSpecSchema = z.object({
   volumes: z.array(VolumeSpecSchema).default([]),
   secretDelivery: z.enum(['env', 'injector']).optional(),
   entrypoint: z.array(z.string()).optional(),
+  // nullable: `get server -o yaml` emits null for servers with no override,
+  // and that YAML must apply back unchanged.
+  toolCallTimeoutSeconds: z.number().int().min(1).max(3600).nullable().optional(),
 });
 
 const UserSpecSchema = z.object({

src/cli/src/commands/create.ts

@@ -251,6 +251,7 @@ export function createCreateCommand(deps: CreateCommandDeps): Command {
     .option('--health-check-args <json>', 'Readiness probe: JSON object of arguments for the probe tool')
     .option('--health-check-interval <seconds>', 'Readiness probe interval in seconds (default 60)')
     .option('--health-check-timeout <seconds>', 'Readiness probe timeout in seconds (default 10)')
+    .option('--tool-call-timeout <seconds>', 'Per-server tool-call deadline in seconds (default: mcplocal\'s global deadline)')
     .option('--health-check-failure-threshold <count>', 'Consecutive failures before the instance is marked unhealthy (default 3)')
     .option('--secret-delivery <mode>', 'How secret env reaches the container: env (default, value written into the pod spec) or injector (pod fetches its own secrets from OpenBao under a scoped identity)')
     .option('--entrypoint <argv>', 'Comma-separated argv to exec under the injector wrapper. Required for --secret-delivery injector on a dockerImage server, whose ENTRYPOINT mcpd cannot introspect')
@@ -331,6 +332,9 @@ export function createCreateCommand(deps: CreateCommandDeps): Command {
       if (opts.replicas) body.replicas = parseInt(opts.replicas, 10);
       if (opts.secretDelivery) body.secretDelivery = opts.secretDelivery;
       if (opts.entrypoint) body.entrypoint = (opts.entrypoint as string).split(',').map((a) => a.trim()).filter(Boolean);
+      if (opts.toolCallTimeout !== undefined) {
+        body.toolCallTimeoutSeconds = parsePositiveInt('--tool-call-timeout', opts.toolCallTimeout as string);
+      }
       if (opts.packageName) body.packageName = opts.packageName;
       if (opts.runtime) body.runtime = opts.runtime;
       if (opts.dockerImage) body.dockerImage = opts.dockerImage;