@stigmer/cli 3.10.0 → 3.11.1-dev.20260812192248

package/resources/usage.js.map

@@ -1 +1 @@
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package/resources/validate.d.ts

@@ -1,5 +1,6 @@
 import { type DescMessage, type JsonValue } from "@bufbuild/protobuf";
 import { ApiResourceKind } from "@stigmer/protos/ai/stigmer/commons/apiresource/apiresourcekind/api_resource_kind_pb";
+export declare const VALIDATE_SCHEMAS: ReadonlyMap<ApiResourceKind, DescMessage>;
 export declare function schemaForValidate(kind: ApiResourceKind): DescMessage | undefined;
 /** Structurally validate a parsed YAML document against its proto schema. */
 export declare function validateDocument(schema: DescMessage, document: JsonValue): void;

package/resources/validate.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../../src/resources/validate.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,KAAK,WAAW,EAAY,KAAK,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAKhF,OAAO,EAAE,eAAe,EAAE,MAAM,qFAAqF,CAAC;AAWtH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,eAAe,GAAG,WAAW,GAAG,SAAS,CAEhF;AAED,6EAA6E;AAC7E,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,SAAS,GAAG,IAAI,CAI/E"}
+{"version":3,"file":"validate.d.ts","sourceRoot":"","sources":["../../src/resources/validate.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,KAAK,WAAW,EAAY,KAAK,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAKhF,OAAO,EAAE,eAAe,EAAE,MAAM,qFAAqF,CAAC;AAOtH,eAAO,MAAM,gBAAgB,EAAE,WAAW,CAAC,eAAe,EAAE,WAAW,CAMrE,CAAC;AAEH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,eAAe,GAAG,WAAW,GAAG,SAAS,CAEhF;AAED,6EAA6E;AAC7E,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,WAAW,EAAE,QAAQ,EAAE,SAAS,GAAG,IAAI,CAI/E"}

package/resources/validate.js

@@ -11,7 +11,11 @@ import { McpServerSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1
 import { WorkflowSchema } from "@stigmer/protos/ai/stigmer/agentic/workflow/v1/api_pb";
 import { ApiResourceKind } from "@stigmer/protos/ai/stigmer/commons/apiresource/apiresourcekind/api_resource_kind_pb";
 import { ProjectSchema } from "@stigmer/protos/ai/stigmer/tenancy/project/v1/api_pb";
-const VALIDATE_SCHEMAS = new Map([
+// Exported for the verb/dispatch conformance suite (registry/registry.test.ts),
+// which holds this map and the matrix's Verb.Validate promises to strict
+// bidirectional equality — the stigmer/stigmer#353 drift class. Command code
+// resolves schemas through `schemaForValidate`, never this map directly.
+export const VALIDATE_SCHEMAS = new Map([
     [ApiResourceKind.agent, AgentSchema],
     [ApiResourceKind.workflow, WorkflowSchema],
     [ApiResourceKind.mcp_server, McpServerSchema],

package/resources/validate.js.map

@@ -1 +1 @@
-{"version":3,"file":"validate.js","sourceRoot":"","sources":["../../src/resources/validate.ts"],"names":[],"mappings":"AAAA,4EAA4E;AAC5E,EAAE;AACF,gFAAgF;AAChF,8EAA8E;AAC9E,6EAA6E;AAC7E,qDAAqD;AAErD,OAAO,EAAoB,QAAQ,EAAkB,MAAM,oBAAoB,CAAC;AAChF,OAAO,EAAE,WAAW,EAAE,MAAM,oDAAoD,CAAC;AACjF,OAAO,EAAE,eAAe,EAAE,MAAM,wDAAwD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,wDAAwD,CAAC;AACzF,OAAO,EAAE,cAAc,EAAE,MAAM,uDAAuD,CAAC;AACvF,OAAO,EAAE,eAAe,EAAE,MAAM,qFAAqF,CAAC;AACtH,OAAO,EAAE,aAAa,EAAE,MAAM,sDAAsD,CAAC;AAErF,MAAM,gBAAgB,GAA8C,IAAI,GAAG,CAA+B;IACxG,CAAC,eAAe,CAAC,KAAK,EAAE,WAAW,CAAC;IACpC,CAAC,eAAe,CAAC,QAAQ,EAAE,cAAc,CAAC;IAC1C,CAAC,eAAe,CAAC,UAAU,EAAE,eAAe,CAAC;IAC7C,CAAC,eAAe,CAAC,OAAO,EAAE,aAAa,CAAC;IACxC,CAAC,eAAe,CAAC,SAAS,EAAE,eAAe,CAAC;CAC7C,CAAC,CAAC;AAEH,MAAM,UAAU,iBAAiB,CAAC,IAAqB;IACrD,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;AACpC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,gBAAgB,CAAC,MAAmB,EAAE,QAAmB;IACvE,6EAA6E;IAC7E,mEAAmE;IACnE,QAAQ,CAAC,MAAM,EAAE,QAAQ,EAAE,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAAC,CAAC;AAC5D,CAAC"}
+{"version":3,"file":"validate.js","sourceRoot":"","sources":["../../src/resources/validate.ts"],"names":[],"mappings":"AAAA,4EAA4E;AAC5E,EAAE;AACF,gFAAgF;AAChF,8EAA8E;AAC9E,6EAA6E;AAC7E,qDAAqD;AAErD,OAAO,EAAoB,QAAQ,EAAkB,MAAM,oBAAoB,CAAC;AAChF,OAAO,EAAE,WAAW,EAAE,MAAM,oDAAoD,CAAC;AACjF,OAAO,EAAE,eAAe,EAAE,MAAM,wDAAwD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,wDAAwD,CAAC;AACzF,OAAO,EAAE,cAAc,EAAE,MAAM,uDAAuD,CAAC;AACvF,OAAO,EAAE,eAAe,EAAE,MAAM,qFAAqF,CAAC;AACtH,OAAO,EAAE,aAAa,EAAE,MAAM,sDAAsD,CAAC;AAErF,gFAAgF;AAChF,yEAAyE;AACzE,6EAA6E;AAC7E,yEAAyE;AACzE,MAAM,CAAC,MAAM,gBAAgB,GAA8C,IAAI,GAAG,CAA+B;IAC/G,CAAC,eAAe,CAAC,KAAK,EAAE,WAAW,CAAC;IACpC,CAAC,eAAe,CAAC,QAAQ,EAAE,cAAc,CAAC;IAC1C,CAAC,eAAe,CAAC,UAAU,EAAE,eAAe,CAAC;IAC7C,CAAC,eAAe,CAAC,OAAO,EAAE,aAAa,CAAC;IACxC,CAAC,eAAe,CAAC,SAAS,EAAE,eAAe,CAAC;CAC7C,CAAC,CAAC;AAEH,MAAM,UAAU,iBAAiB,CAAC,IAAqB;IACrD,OAAO,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;AACpC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,gBAAgB,CAAC,MAAmB,EAAE,QAAmB;IACvE,6EAA6E;IAC7E,mEAAmE;IACnE,QAAQ,CAAC,MAAM,EAAE,QAAQ,EAAE,EAAE,mBAAmB,EAAE,IAAI,EAAE,CAAC,CAAC;AAC5D,CAAC"}

package/src/commands/connect.ts

@@ -26,7 +26,12 @@ export function registerConnect(program: Command): void {
   connect
     .command("mcp-server <slug-or-id>")
     .description("connect to an MCP server and discover its tools")
-    .option("--timeout <seconds>", "timeout for connection and discovery", String(DEFAULT_TIMEOUT_SECONDS))
+    .option(
+      "--timeout <seconds>",
+      "bound the wait for connection and discovery (always bounds --dry-run; " +
+        "bounds the server-side connect only when set explicitly)",
+      String(DEFAULT_TIMEOUT_SECONDS),
+    )
     .option("--dry-run", "discover and display results without pushing to the backend")
     .option(
       "--env <KEY=VALUE>",
@@ -39,6 +44,12 @@ export function registerConnect(program: Command): void {
 
 async function runConnect(reference: string, options: ConnectFlags, command: Command): Promise<void> {
   const timeoutMs = parseTimeout(options.timeout);
+  // The 30s default exists for --dry-run's local discovery. A real connect
+  // legitimately takes minutes (server-side sandbox boot + discovery + tool
+  // classification), so bounding it by the DEFAULT would fail healthy
+  // connects — the wait is bounded only when the user set --timeout
+  // explicitly (issue #239: the flag used to be silently ignored here).
+  const timeoutIsExplicit = command.getOptionValueSource("timeout") === "cli";
   const [{ connectBackend }, { connectMcpServer }, { renderConnectResult }] = await Promise.all([
     import("../backend.js"),
     import("../resources/connect/connect.js"),
@@ -67,6 +78,7 @@ async function runConnect(reference: string, options: ConnectFlags, command: Com
     reference,
     org,
     timeoutMs,
+    pushTimeoutMs: timeoutIsExplicit ? timeoutMs : undefined,
     dryRun: options.dryRun === true,
     envOverrides: options.env,
     backendType: client.config.backend.type,

package/src/commands/usage.ts

@@ -24,11 +24,11 @@ export function registerUsage(program: Command): void {
 
   usage
     .command("agent <agent-id>")
-    .description("view the aggregated usage report for an agent")
+    .description("view the aggregated usage report for an agent within your organization")
     .option("--from <date>", "start date (ISO 8601, e.g. 2026-03-01)")
     .option("--to <date>", "end date (ISO 8601, e.g. 2026-03-13)")
     .option("-o, --output <format>", "output format: table, json, or yaml")
-    .action((agentId: string, options: UsageFlags) => runAgentUsage(agentId, options));
+    .action((agentId: string, options: UsageFlags, command: Command) => runAgentUsage(agentId, options, command));
 
   usage
     .command("org")
@@ -48,13 +48,16 @@ async function runSessionUsage(sessionId: string, options: UsageFlags): Promise<
   process.stdout.write(usage.renderSessionUsage(report, readFormat(options)));
 }
 
-async function runAgentUsage(agentId: string, options: UsageFlags): Promise<void> {
+async function runAgentUsage(agentId: string, options: UsageFlags, command: Command): Promise<void> {
   const [{ connectBackend }, usage] = await Promise.all([import("../backend.js"), import("../resources/usage.js")]);
   const client = connectBackend();
   ensureAuthenticated(client.config);
+  // The report is org-scoped (usage of the agent within one org), so the org
+  // resolves exactly as `usage org` does: global --org flag or config default.
+  const org = resolveOrganization(client.config, globalOrg(command));
 
   const range = { from: options.from ?? "", to: options.to ?? "" };
-  const report = await usage.getAgentUsageReport(client.stigmer, agentId, range);
+  const report = await usage.getAgentUsageReport(client.stigmer, agentId, org, range);
   process.stdout.write(usage.renderAgentUsage(report, range, readFormat(options)));
 }
 

package/src/registry/registry.test.ts

@@ -4,6 +4,7 @@ import { APPLY_HANDLERS } from "../resources/apply/handlers.js";
 import { DELETE_HANDLERS } from "../resources/delete.js";
 import { GET_BINDINGS } from "../resources/get-bindings.js";
 import { LIST_HANDLERS, SEARCH_KINDS } from "../resources/list.js";
+import { VALIDATE_SCHEMAS } from "../resources/validate.js";
 import { defaultRegistry } from "./registry.js";
 import { Verb } from "./verbs.js";
 
@@ -167,6 +168,12 @@ describe("registry — verb/dispatch conformance", () => {
       wired: new Set([...LIST_HANDLERS.keys(), ...SEARCH_KINDS]),
       specialCases: new Map(),
     },
+    {
+      label: "validate",
+      verb: Verb.Validate,
+      wired: new Set(VALIDATE_SCHEMAS.keys()),
+      specialCases: new Map(),
+    },
     {
       label: "delete",
       verb: Verb.Delete,

package/src/resources/connect/connect.integration.test.ts

@@ -34,12 +34,17 @@ const openSessions = new Set<ServerHttp2Session>();
 
 let connectCalls: ConnectInput[] = [];
 let grantConnected = false;
+// Delay before the mock Connect RPC answers; lets the --timeout tests
+// simulate a long-running server-side connect. The timer is unref'd so a
+// still-pending delayed response can never hold the test process open.
+let connectDelayMs = 0;
 // The server returned by getByReference; mutated per test for auth scenarios.
 let servedSpec: ReturnType<typeof create<typeof McpServerSchema>>;
 
 beforeEach(() => {
   connectCalls = [];
   grantConnected = false;
+  connectDelayMs = 0;
   servedSpec = create(McpServerSchema, {
     metadata: { id: "mcp_1", name: "github", slug: "github", org: "acme" },
     spec: {
@@ -72,8 +77,11 @@ beforeAll(async () => {
       // Mirror the backend's protovalidate rule (org min_len=1): reject an empty
       // org so a regression that drops org fails loudly here instead of silently
       // passing (the mock adapter does not run protovalidate on its own).
-      connect: (req) => {
+      connect: async (req) => {
         if (req.org === "") throw new ConnectError("org – value length must be at least 1 characters", Code.InvalidArgument);
+        if (connectDelayMs > 0) {
+          await new Promise((resolve) => setTimeout(resolve, connectDelayMs).unref());
+        }
         connectCalls.push(req);
         return updatedServer;
       },
@@ -120,6 +128,42 @@ describe("connect push path", () => {
   });
 });
 
+describe("--timeout bounds the server-side connect (issue #239)", () => {
+  it("stops waiting with actionable guidance when pushTimeoutMs elapses", async () => {
+    connectDelayMs = 5_000;
+    await expect(
+      connectMcpServer(client, {
+        reference: "github",
+        org: "acme",
+        timeoutMs: 30_000,
+        pushTimeoutMs: 150,
+        dryRun: false,
+        envOverrides: ["GITHUB_TOKEN=ghp-x"],
+        backendType: "cloud",
+        interactive: false,
+      }),
+    ).rejects.toThrow(/Stopped waiting for the connect of MCP server 'github' after 0\.15s/);
+  });
+
+  it("does not bound the wait when pushTimeoutMs is unset (default --timeout)", async () => {
+    // The flag's 30s default is sized for --dry-run local discovery; a real
+    // connect legitimately outlives it, so only an explicit --timeout bounds
+    // the push. 200ms of server delay stands in for "longer than the bound
+    // would have been".
+    connectDelayMs = 200;
+    const result = await connectMcpServer(client, {
+      reference: "github",
+      org: "acme",
+      timeoutMs: 100,
+      dryRun: false,
+      envOverrides: ["GITHUB_TOKEN=ghp-x"],
+      backendType: "cloud",
+      interactive: false,
+    });
+    expect(result.updated?.metadata?.id).toBe("mcp_1");
+  });
+});
+
 describe("OAuth guidance gate", () => {
   beforeEach(() => {
     servedSpec.spec!.auth = create(McpServerAuthSchema, { targetEnvVar: "GITHUB_TOKEN" });

package/src/resources/connect/connect.ts

@@ -16,7 +16,7 @@ import type { DiscoveredCapabilities } from "@stigmer/protos/ai/stigmer/agentic/
 import { ApiResourceKind } from "@stigmer/protos/ai/stigmer/commons/apiresource/apiresourcekind/api_resource_kind_pb";
 import type { Stigmer } from "@stigmer/sdk";
 import type { BackendType } from "../../config/config.js";
-import { UsageError } from "../../errors/index.js";
+import { CliExitError, ExitCode, UsageError } from "../../errors/index.js";
 import { defaultRegistry } from "../../registry/index.js";
 import { PlaceholderResolutionError } from "../mcp/placeholder-resolver.js";
 import { buildRuntimeEnv } from "../mcp/runtime-env.js";
@@ -27,6 +27,15 @@ export interface ConnectOptions {
   readonly reference: string;
   readonly org: string;
   readonly timeoutMs: number;
+  /**
+   * Bound the wait on the server-side connect RPC. Unset by default: a real
+   * connect legitimately takes minutes (sandbox boot + discovery + tool
+   * classification), so only an EXPLICIT --timeout bounds it — the flag's
+   * 30s default is sized for --dry-run's local discovery and would fail
+   * healthy connects. The bound is soft (the CLI stops waiting; the backend
+   * finishes the connect on its own).
+   */
+  readonly pushTimeoutMs?: number;
   readonly dryRun: boolean;
   readonly envOverrides: readonly string[];
   /** Backend type, for resolving the OAuth web-console URL. */
@@ -66,16 +75,53 @@ export async function connectMcpServer(client: Stigmer, opts: ConnectOptions): P
 
   await ensureOAuthSatisfied(client, server, opts);
 
-  const updated = await client.mcpServer.connect(
+  const push = client.mcpServer.connect(
     create(ConnectInputSchema, {
       mcpServerId: server.metadata?.id ?? "",
       org: opts.org,
       runtimeEnv: buildRuntimeEnv(server, opts.envOverrides),
     }),
   );
+  const updated = opts.pushTimeoutMs === undefined
+    ? await push
+    : await boundedPush(push, opts.pushTimeoutMs, server);
   return { server, capabilities: updated.status?.discoveredCapabilities, updated };
 }
 
+// Soft timeout on the server-side connect (the client/client.ts idiom): races
+// the RPC against a timer without cancelling it — the backend's connect
+// workflow keeps running and persists its result on its own, so the message
+// says exactly that instead of implying the connect failed.
+async function boundedPush<T>(push: Promise<T>, timeoutMs: number, server: McpServer): Promise<T> {
+  const slug = server.metadata?.slug ?? server.metadata?.id ?? "the server";
+  let timer: NodeJS.Timeout | undefined;
+  const timeout = new Promise<never>((_, reject) => {
+    timer = setTimeout(
+      () =>
+        reject(
+          new CliExitError(
+            `Stopped waiting for the connect of MCP server '${slug}' after ${timeoutMs / 1000}s (--timeout)`,
+            ExitCode.Connection,
+            [
+              "The server-side connect is still running and will persist its result if it succeeds.",
+              `Check the outcome with: stigmer get mcp-server ${slug}`,
+              "Re-run without --timeout to wait for completion.",
+            ],
+          ),
+        ),
+      timeoutMs,
+    );
+  });
+  // The losing push may settle after the CLI has started exiting; swallow its
+  // late rejection so it cannot surface as an unhandled-rejection crash.
+  void push.catch(() => {});
+  try {
+    return await Promise.race([push, timeout]);
+  } finally {
+    if (timer !== undefined) clearTimeout(timer);
+  }
+}
+
 // Resolve a reference (id, org/slug, or bare slug) to an McpServer. Mirrors Go's
 // GetFromBackend.
 async function resolveMcpServer(client: Stigmer, reference: string, org: string): Promise<McpServer> {

package/src/resources/list.ts

@@ -7,8 +7,14 @@
 // registered in LIST_HANDLERS — the same map-dispatch shape as the get,
 // delete, and apply registries, so the conformance test in
 // registry/registry.test.ts can hold all four to the verb matrix.
+//
+// Handlers FETCH, the dispatcher RENDERS: every handler returns entries plus
+// its schema/table pair, and listResources alone applies --limit and renders.
+// That split is deliberate (stigmer/stigmer#312): when handlers owned
+// rendering, honoring --limit was per-handler discipline, and the two
+// unpaginated branches (organization, api_key) shipped silently ignoring it.
 
-import { create } from "@bufbuild/protobuf";
+import { create, type DescMessage, type Message } from "@bufbuild/protobuf";
 import { AgentChannelSchema } from "@stigmer/protos/ai/stigmer/agentic/agentchannel/v1/api_pb";
 import { ListAgentChannelsRequestSchema } from "@stigmer/protos/ai/stigmer/agentic/agentchannel/v1/io_pb";
 import { AgentInstanceSchema } from "@stigmer/protos/ai/stigmer/agentic/agentinstance/v1/api_pb";
@@ -43,7 +49,19 @@ export const SEARCH_KINDS: ReadonlySet<ApiResourceKind> = new Set<ApiResourceKin
   ApiResourceKind.environment,
 ]);
 
-type ListFn = (client: Stigmer, org: string, limit: number, format: OutputFormat) => Promise<string>;
+// One fetched page of a listing: what to render (entries + schema) and how
+// (table). Rendering and --limit truncation happen centrally in
+// listResources — a handler cannot opt out of either.
+interface ListPage {
+  readonly schema: DescMessage;
+  readonly entries: readonly Message[];
+  readonly table: TableShape;
+}
+
+// Where the RPC paginates, the handler still forwards `limit` as the page
+// size so the server does the bounding; the dispatcher's slice is then a
+// no-op. Where it doesn't, the slice IS the bound.
+type ListFn = (client: Stigmer, org: string, limit: number) => Promise<ListPage>;
 
 // Dedicated-RPC list handlers for the non-search-indexed kinds. Every kind
 // declaring List in the verb matrix must appear here or in SEARCH_KINDS —
@@ -51,49 +69,53 @@ type ListFn = (client: Stigmer, org: string, limit: number, format: OutputFormat
 export const LIST_HANDLERS: ReadonlyMap<ApiResourceKind, ListFn> = new Map<ApiResourceKind, ListFn>([
   [
     ApiResourceKind.organization,
-    async (client, _org, _limit, format) => {
+    async (client) => {
+      // findMyOrganizations is caller-scoped and unpaginated (Empty request;
+      // a caller's org set is small by nature). The paginated `find` RPC is
+      // platform-admin-only — the wrong surface for `list organization`.
       const result = await client.organization.findMyOrganizations();
-      return renderCollection(OrganizationSchema, result.entries, format, ORG_TABLE);
+      return { schema: OrganizationSchema, entries: result.entries, table: ORG_TABLE };
     },
   ],
   [
     ApiResourceKind.api_key,
-    async (client, _org, _limit, format) => {
+    async (client) => {
+      // findAll is caller-scoped and unpaginated (Empty request).
       const result = await client.apiKey.findAll();
-      return renderCollection(ApiKeySchema, result.entries, format, APIKEY_TABLE);
+      return { schema: ApiKeySchema, entries: result.entries, table: APIKEY_TABLE };
     },
   ],
   [
     ApiResourceKind.agent_instance,
-    async (client, org, limit, format) => {
+    async (client, org, limit) => {
       const result = await client.agentInstance.list(
         create(ListAgentInstancesRequestSchema, { org, pageInfo: create(PageInfoSchema, { num: 1, size: limit }) }),
       );
-      return renderCollection(AgentInstanceSchema, result.items, format, INSTANCE_TABLE);
+      return { schema: AgentInstanceSchema, entries: result.items, table: INSTANCE_TABLE };
     },
   ],
   [
     ApiResourceKind.agent_channel,
-    async (client, org, limit, format) => {
+    async (client, org, limit) => {
       const result = await client.agentChannel.list(
         create(ListAgentChannelsRequestSchema, { org, pageInfo: create(PageInfoSchema, { num: 1, size: limit }) }),
       );
-      return renderCollection(AgentChannelSchema, result.items, format, AGENT_CHANNEL_TABLE);
+      return { schema: AgentChannelSchema, entries: result.items, table: AGENT_CHANNEL_TABLE };
     },
   ],
   [
     ApiResourceKind.channel_app,
-    async (client, org, limit, format) => {
+    async (client, org) => {
       // listByOrg has no pagination on its contract (the per-org set is small
-      // by design); the limit is applied client-side so --limit stays honest.
+      // by design); the dispatcher's slice bounds the output.
       // `channelapp` (not `channelApp`) is a recorded SDK codegen naming quirk.
       const result = await client.channelapp.listByOrg(create(ListChannelAppsByOrgInputSchema, { org }));
-      return renderCollection(ChannelAppSchema, result.entries.slice(0, limit), format, CHANNEL_APP_TABLE);
+      return { schema: ChannelAppSchema, entries: result.entries, table: CHANNEL_APP_TABLE };
     },
   ],
   [
     ApiResourceKind.schedule,
-    async (client, org, limit, format) => {
+    async (client, org, limit) => {
       // ListSchedulesRequest requires an org (min_len 1), but an unset cloud
       // context resolves to "" — refuse with actionable copy instead of
       // relaying the server's raw validation error.
@@ -105,7 +127,7 @@ export const LIST_HANDLERS: ReadonlyMap<ApiResourceKind, ListFn> = new Map<ApiRe
       const result = await client.schedule.list(
         create(ListSchedulesRequestSchema, { org, pageInfo: create(PageInfoSchema, { num: 1, size: limit }) }),
       );
-      return renderCollection(ScheduleSchema, result.items, format, SCHEDULE_TABLE);
+      return { schema: ScheduleSchema, entries: result.items, table: SCHEDULE_TABLE };
     },
   ],
 ]);
@@ -117,15 +139,31 @@ export async function listResources(
   limit: number,
   format: OutputFormat,
 ): Promise<string> {
+  const page = await fetchListPage(client, kind, org, limit);
+  // The single point where --limit binds the output. For paginated RPCs the
+  // handler already asked the server for at most `limit` entries and this is
+  // a no-op; for unpaginated RPCs it is the truncation itself. Slicing here
+  // rather than per-handler is what keeps the flag honest for every kind —
+  // organization and api_key shipped ignoring it when handlers owned this
+  // (stigmer/stigmer#312).
+  return renderCollection(page.schema, page.entries.slice(0, limit), format, page.table);
+}
+
+async function fetchListPage(
+  client: Stigmer,
+  kind: ApiResourceKind,
+  org: string,
+  limit: number,
+): Promise<ListPage> {
   const dedicated = LIST_HANDLERS.get(kind);
   if (dedicated !== undefined) {
-    return dedicated(client, org, limit, format);
+    return dedicated(client, org, limit);
   }
   if (!SEARCH_KINDS.has(kind)) {
     throw new UsageError("list is not implemented for this resource type");
   }
   const result = await client.search.query({ kinds: [kind], org, page: { num: 1, size: limit } });
-  return renderCollection(SearchResultSchema, result.entries, format, SEARCH_TABLE);
+  return { schema: SearchResultSchema, entries: result.entries, table: SEARCH_TABLE };
 }
 
 // Shared with `search` — both render SearchService results identically.

package/src/resources/read-verbs.integration.test.ts

@@ -67,6 +67,23 @@ const knownApiKey = create(ApiKeySchema, {
   spec: { fingerprint: "abcd", neverExpires: true },
 });
 
+// Second org/API-key entries so the list tests can pin the
+// dispatcher-applied --limit slice — both RPCs are unpaginated (Empty
+// request), the exact shape that shipped ignoring the flag when handlers
+// owned rendering (stigmer/stigmer#312).
+const secondOrg = create(OrganizationSchema, {
+  apiVersion: "tenancy.stigmer.ai/v1",
+  kind: "Organization",
+  metadata: { name: "Beta Clinic", slug: "beta-clinic", org: "beta-clinic", id: "beta-clinic" },
+});
+
+const secondApiKey = create(ApiKeySchema, {
+  apiVersion: "iam.stigmer.ai/v1",
+  kind: "ApiKey",
+  metadata: { name: "local-dev", org: "acme", id: "key_2" },
+  spec: { fingerprint: "ef01", neverExpires: true },
+});
+
 const knownSearchResult = create(SearchResultSchema, {
   kind: ApiResourceKind.agent,
   id: "agt_1",
@@ -223,10 +240,10 @@ beforeAll(async () => {
       },
     });
     router.service(OrganizationQueryController, {
-      findMyOrganizations: () => ({ entries: [knownOrg] }),
+      findMyOrganizations: () => ({ entries: [knownOrg, secondOrg] }),
     });
     router.service(ApiKeyQueryController, {
-      findAll: () => ({ entries: [knownApiKey] }),
+      findAll: () => ({ entries: [knownApiKey, secondApiKey] }),
     });
     router.service(EnvironmentQueryController, {
       get: (req) => {
@@ -441,11 +458,27 @@ describe("list integration", () => {
 
   it("lists organizations via findMyOrganizations as JSON", async () => {
     const out = await listResources(client, ApiResourceKind.organization, "acme", 50, "json");
+    expect(JSON.parse(out)).toEqual([
+      toJson(OrganizationSchema, knownOrg, { useProtoFieldName: true }),
+      toJson(OrganizationSchema, secondOrg, { useProtoFieldName: true }),
+    ]);
+  });
+
+  it("applies --limit to organizations (findMyOrganizations has no pagination)", async () => {
+    const out = await listResources(client, ApiResourceKind.organization, "acme", 1, "json");
     expect(JSON.parse(out)).toEqual([toJson(OrganizationSchema, knownOrg, { useProtoFieldName: true })]);
   });
 
   it("lists API keys via findAll as JSON", async () => {
     const out = await listResources(client, ApiResourceKind.api_key, "acme", 50, "json");
+    expect(JSON.parse(out)).toEqual([
+      toJson(ApiKeySchema, knownApiKey, { useProtoFieldName: true }),
+      toJson(ApiKeySchema, secondApiKey, { useProtoFieldName: true }),
+    ]);
+  });
+
+  it("applies --limit to API keys (findAll has no pagination)", async () => {
+    const out = await listResources(client, ApiResourceKind.api_key, "acme", 1, "json");
     expect(JSON.parse(out)).toEqual([toJson(ApiKeySchema, knownApiKey, { useProtoFieldName: true })]);
   });
 

package/src/resources/run/attachments.test.ts

@@ -110,4 +110,26 @@ describe("directory zipping", () => {
     writeFileSync(join(empty, ".hidden"), "x"); // only hidden -> nothing attachable
     await expect(processAttachments(uploader, [empty], [])).rejects.toThrow(/no attachable files/);
   });
+
+  it("uniquifies duplicate directory basenames so mount paths never contradict (issue #364)", async () => {
+    // Two dirs named `data` from different parents would otherwise derive the
+    // SAME explicit mount path, which the runner rejects as a contradiction.
+    const dirA = join(dir, "a", "data");
+    const dirB = join(dir, "b", "data");
+    mkdirSync(dirA, { recursive: true });
+    mkdirSync(dirB, { recursive: true });
+    writeFileSync(join(dirA, "one.txt"), "1");
+    writeFileSync(join(dirB, "two.txt"), "2");
+
+    const progress: string[] = [];
+    const result = await processAttachments(uploader, [dirA, dirB], [], (l) => progress.push(l));
+
+    expect(result.attachments).toHaveLength(2);
+    expect(result.attachments[0].filename).toBe("data.zip");
+    expect(result.attachments[0].mountPath).toBe("inputs/data/");
+    expect(result.attachments[1].filename).toBe("data-2.zip");
+    expect(result.attachments[1].mountPath).toBe("inputs/data-2/");
+    // The rename is disclosed to the user on the progress sink.
+    expect(progress.some((l) => l.includes("'data/'") && l.includes("'data-2/'"))).toBe(true);
+  });
 });