@stigmer/mcp-server 3.11.1-dev.20260812192248 → 3.12.1

package/src/domains/agents/apply.ts

@@ -6,7 +6,10 @@
 import { AgentSchema } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/api_pb";
 import { AgentCommandController } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/command_pb";
 
+import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+
 import { agentInputToProto, type AgentInput } from "../../gen/agent.js";
+import { applyDeclaredVisibility } from "../apply-visibility.js";
 import { withClient } from "../client.js";
 import { toProtoJson } from "../marshal.js";
 import { rpcError } from "../rpcerr.js";
@@ -21,7 +24,13 @@ export async function applyAgent(
   const desc = `agent "${agent.metadata?.slug ?? ""}" in org "${agent.metadata?.org ?? ""}"`;
   return withClient(AgentCommandController, serverAddress, token, async (client, callOptions) => {
     try {
-      const result = await client.apply(agent, callOptions);
+      const applied = await client.apply(agent, callOptions);
+      const result = await applyDeclaredVisibility(
+        client,
+        callOptions,
+        applied,
+        agent.metadata?.visibility ?? ApiResourceVisibility.api_resource_visibility_unspecified,
+      );
       return toProtoJson(AgentSchema, result);
     } catch (err) {
       throw rpcError(err, desc);

package/src/domains/apply-visibility.ts

@@ -0,0 +1,47 @@
+// Declared-visibility follow-up for the apply tools (oss#573).
+//
+// Plain updates preserve the stored visibility on both editions — the
+// updateVisibility RPC is the only door for visibility changes, where the
+// server-side guards live (per-kind level support, default-instance
+// rejection). So when an apply tool's input declares a visibility and the
+// applied resource comes back with a different level (i.e. the resource
+// already existed), we follow up with one UpdateVisibility RPC on the same
+// controller. The CLI's skill-push and manifest-apply flows do the same.
+//
+// No-ops are skipped (input omitted visibility, create honored it, or the
+// stored level already matches), so an unchanged apply costs nothing extra.
+// Guard rejections propagate to the caller's rpcError wrapper — the model
+// sees the real FAILED_PRECONDITION / INVALID_ARGUMENT, not a silent lie.
+
+import { create } from "@bufbuild/protobuf";
+import type { CallOptions } from "@connectrpc/connect";
+import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+import { UpdateVisibilityInputSchema, type UpdateVisibilityInput } from "@stigmer/protos/ai/stigmer/commons/apiresource/io_pb";
+import type { ApiResourceMetadata } from "@stigmer/protos/ai/stigmer/commons/apiresource/metadata_pb";
+
+interface HasResourceMetadata {
+  metadata?: ApiResourceMetadata;
+}
+
+interface UpdateVisibilityClient<T> {
+  updateVisibility(input: UpdateVisibilityInput, options?: CallOptions): Promise<T>;
+}
+
+/**
+ * Land the input-declared visibility through the guarded door when the
+ * applied resource's stored level differs. Returns the resource carrying the
+ * final visibility (the follow-up's response, or `applied` unchanged when no
+ * follow-up was needed).
+ */
+export async function applyDeclaredVisibility<T extends HasResourceMetadata>(
+  client: UpdateVisibilityClient<T>,
+  callOptions: CallOptions,
+  applied: T,
+  declared: ApiResourceVisibility,
+): Promise<T> {
+  if (declared === ApiResourceVisibility.api_resource_visibility_unspecified) return applied;
+  const resourceId = applied.metadata?.id ?? "";
+  if (resourceId === "") return applied;
+  if (applied.metadata?.visibility === declared) return applied;
+  return client.updateVisibility(create(UpdateVisibilityInputSchema, { resourceId, visibility: declared }), callOptions);
+}

package/src/domains/apply.integration.test.ts

@@ -1,12 +1,13 @@
 // In-process integration test for the apply tools. Drives apply_agent,
-// apply_mcp_server, apply_workflow, apply_environment, and apply_datastore
-// through the full MCP boundary and asserts the codegen projection (src/gen/*)
+// apply_mcp_server, apply_workflow, and apply_environment through the
+// full MCP boundary and asserts the codegen projection (src/gen/*)
 // reconstitutes the proto correctly: metadata hoist + slug generation,
-// enum-string conversion (including repeated enums — datastore grant verbs),
+// enum-string conversion,
 // ApiResourceReference kind injection, the stdio/http oneof, the environment
 // data map with secret flags, and the recursive workflow task_config expansion
 // (http_call leaf, fork/for_each nesting).
 
+import { clone } from "@bufbuild/protobuf";
 import type { ConnectRouter } from "@connectrpc/connect";
 import { connectNodeAdapter } from "@connectrpc/connect-node";
 import {
@@ -18,11 +19,8 @@ import type { AddressInfo } from "node:net";
 
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
-import type { Agent } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/api_pb";
+import { type Agent, AgentSchema } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/api_pb";
 import { AgentCommandController } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/command_pb";
-import type { Datastore } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/api_pb";
-import { DatastoreCommandController } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/command_pb";
-import { DatastoreVerb, FieldType } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/spec_pb";
 import type { Environment } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/api_pb";
 import { EnvironmentCommandController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/command_pb";
 import type { McpServer as McpServerProto } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/api_pb";
@@ -32,6 +30,7 @@ import { WorkflowCommandController } from "@stigmer/protos/ai/stigmer/agentic/wo
 import { WorkflowTaskKind } from "@stigmer/protos/ai/stigmer/agentic/workflow/v1/enum_pb";
 import { ApiResourceKind } from "@stigmer/protos/ai/stigmer/commons/apiresource/apiresourcekind/api_resource_kind_pb";
 import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+import type { UpdateVisibilityInput } from "@stigmer/protos/ai/stigmer/commons/apiresource/io_pb";
 import { afterAll, beforeAll, describe, expect, it } from "vitest";
 
 import { configureLogger } from "../logger";
@@ -45,7 +44,13 @@ let appliedAgent: Agent | undefined;
 let appliedMcpServer: McpServerProto | undefined;
 let appliedWorkflow: Workflow | undefined;
 let appliedEnvironment: Environment | undefined;
-let appliedDatastore: Datastore | undefined;
+const visibilityUpdates: UpdateVisibilityInput[] = [];
+
+// The single-door contract (oss#573): a plain update preserves the STORED
+// visibility, so the apply response can disagree with the request. This slug
+// makes the mock backend simulate that — apply echoes back a pre-existing
+// resource whose stored level is org, regardless of the requested one.
+const STORED_ORG_SLUG = "stored-org-agent";
 const openSessions = new Set<ServerHttp2Session>();
 
 interface ToolResult {
@@ -62,8 +67,21 @@ beforeAll(async () => {
     router.service(AgentCommandController, {
       apply: (req) => {
         appliedAgent = req;
+        if (req.metadata?.slug === STORED_ORG_SLUG) {
+          const stored = clone(AgentSchema, req);
+          stored.metadata!.id = "agent-stored-1";
+          stored.metadata!.visibility = ApiResourceVisibility.visibility_org;
+          return stored;
+        }
         return req;
       },
+      updateVisibility: (input) => {
+        visibilityUpdates.push(input);
+        const updated = clone(AgentSchema, appliedAgent!);
+        updated.metadata!.id = input.resourceId;
+        updated.metadata!.visibility = input.visibility;
+        return updated;
+      },
     });
     router.service(McpServerCommandController, {
       apply: (req) => {
@@ -83,12 +101,6 @@ beforeAll(async () => {
         return req;
       },
     });
-    router.service(DatastoreCommandController, {
-      apply: (req) => {
-        appliedDatastore = req;
-        return req;
-      },
-    });
   };
   backend = createHttp2Server(connectNodeAdapter({ routes }));
   backend.on("session", (session) => {
@@ -119,7 +131,6 @@ describe("apply tools integration", () => {
         "apply_mcp_server",
         "apply_workflow",
         "apply_environment",
-        "apply_datastore",
       ]),
     );
   });
@@ -245,6 +256,38 @@ describe("apply tools integration", () => {
     expect(forCfg.do).toHaveLength(1);
   });
 
+  it("apply_agent lands a declared visibility the update preserved away via UpdateVisibility (oss#573)", async () => {
+    const result = await callTool("apply_agent", {
+      name: "Stored Org Agent",
+      org: "acme",
+      visibility: "PUBLIC",
+      instructions: "i",
+    });
+    expect(result.isError).toBeFalsy();
+
+    // Server "preserved" stored org; the tool must follow up once through
+    // the guarded door and return the landed level, not the stale one.
+    expect(visibilityUpdates).toHaveLength(1);
+    expect(visibilityUpdates[0].resourceId).toBe("agent-stored-1");
+    expect(visibilityUpdates[0].visibility).toBe(ApiResourceVisibility.visibility_public);
+    const text = result.content.find((c) => c.type === "text")?.text ?? "";
+    expect(JSON.parse(text).metadata.visibility).toBe("visibility_public");
+  });
+
+  it("apply_agent skips the follow-up when the server already matches", async () => {
+    visibilityUpdates.length = 0;
+    const result = await callTool("apply_agent", {
+      name: "Plain Agent",
+      org: "acme",
+      visibility: "PUBLIC",
+      instructions: "i",
+    });
+    expect(result.isError).toBeFalsy();
+    // The echo backend returns the requested level (and no id) — no diff,
+    // no follow-up.
+    expect(visibilityUpdates).toHaveLength(0);
+  });
+
   it("apply_environment rebuilds the data map with secret flags", async () => {
     const result = await callTool("apply_environment", {
       name: "GitHub Creds",
@@ -267,30 +310,4 @@ describe("apply tools integration", () => {
     });
     expect(env?.spec?.data?.REGION?.isSecret).toBe(false);
   });
-
-  it("apply_datastore maps field types and repeated grant verbs to enums", async () => {
-    const result = await callTool("apply_datastore", {
-      name: "Bookings",
-      org: "acme",
-      collections: [
-        {
-          name: "appointments",
-          fields: [{ name: "patient", type: "string", required: true }],
-          grants: [{ role: "assistant", verbs: ["read", "insert"], scope: "own" }],
-        },
-      ],
-    });
-    expect(result.isError).toBeFalsy();
-
-    const ds = appliedDatastore;
-    expect(ds?.kind).toBe("Datastore");
-    expect(ds?.metadata?.slug).toBe("bookings");
-
-    const collection = ds?.spec?.collections?.[0];
-    expect(collection?.fields?.[0]?.type).toBe(FieldType.string);
-
-    // Repeated enum: verb strings map to DatastoreVerb values, not raw strings.
-    const grant = collection?.grants?.[0];
-    expect(grant?.verbs).toEqual([DatastoreVerb.read, DatastoreVerb.insert]);
-  });
 });

package/src/domains/deletes.integration.test.ts

@@ -1,8 +1,7 @@
 // In-process integration test for the delete tools. Verifies the two-step
 // resolve→delete flow forwards the resolved id into the correct per-domain
 // delete-input shape: typed {value} for agent/skill/workflow, and
-// ApiResourceDeleteInput {resource_id} for mcp_server, environment, and
-// datastore.
+// ApiResourceDeleteInput {resource_id} for mcp_server and environment.
 
 import { create, toJson } from "@bufbuild/protobuf";
 import type { ConnectRouter } from "@connectrpc/connect";
@@ -19,9 +18,6 @@ import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
 import { AgentSchema } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/api_pb";
 import { AgentCommandController } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/command_pb";
 import { AgentQueryController } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/query_pb";
-import { DatastoreSchema } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/api_pb";
-import { DatastoreCommandController } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/command_pb";
-import { DatastoreQueryController } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/query_pb";
 import { EnvironmentSchema } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/api_pb";
 import { EnvironmentCommandController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/command_pb";
 import { EnvironmentQueryController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/query_pb";
@@ -50,18 +46,12 @@ const resolvedEnvironment = create(EnvironmentSchema, {
   kind: "environment",
   metadata: { name: "GitHub Creds", slug: "github-creds", org: "acme", id: "env-789" },
 });
-const resolvedDatastore = create(DatastoreSchema, {
-  apiVersion: "v1",
-  kind: "datastore",
-  metadata: { name: "Bookings", slug: "bookings", org: "acme", id: "dst-012" },
-});
 
 let backend: Http2Server;
 let client: Client;
 let deletedAgentId: string | undefined;
 let deletedMcpResourceId: string | undefined;
 let deletedEnvironmentResourceId: string | undefined;
-let deletedDatastoreResourceId: string | undefined;
 const openSessions = new Set<ServerHttp2Session>();
 
 interface ToolResult {
@@ -96,13 +86,6 @@ beforeAll(async () => {
         return resolvedEnvironment;
       },
     });
-    router.service(DatastoreQueryController, { getByReference: () => resolvedDatastore });
-    router.service(DatastoreCommandController, {
-      delete: (req) => {
-        deletedDatastoreResourceId = req.resourceId;
-        return resolvedDatastore;
-      },
-    });
   };
   backend = createHttp2Server(connectNodeAdapter({ routes }));
   backend.on("session", (session) => {
@@ -134,7 +117,6 @@ describe("delete tools integration", () => {
         "delete_workflow",
         "delete_mcp_server",
         "delete_environment",
-        "delete_datastore",
       ]),
     );
   });
@@ -162,10 +144,4 @@ describe("delete tools integration", () => {
     expect(result.isError).toBeFalsy();
     expect(deletedEnvironmentResourceId).toBe("env-789");
   });
-
-  it("delete_datastore resolves the id then deletes via ApiResourceDeleteInput", async () => {
-    const result = await callTool("delete_datastore", { org: "acme", slug: "bookings" });
-    expect(result.isError).toBeFalsy();
-    expect(deletedDatastoreResourceId).toBe("dst-012");
-  });
 });

package/src/domains/environments/apply.ts

@@ -11,7 +11,10 @@
 import { EnvironmentSchema } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/api_pb";
 import { EnvironmentCommandController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/command_pb";
 
+import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+
 import { environmentInputToProto, type EnvironmentInput } from "../../gen/environment.js";
+import { applyDeclaredVisibility } from "../apply-visibility.js";
 import { withClient } from "../client.js";
 import { toProtoJson } from "../marshal.js";
 import { rpcError } from "../rpcerr.js";
@@ -30,7 +33,13 @@ export async function applyEnvironment(
     token,
     async (client, callOptions) => {
       try {
-        const result = await client.apply(environment, callOptions);
+        const applied = await client.apply(environment, callOptions);
+        const result = await applyDeclaredVisibility(
+          client,
+          callOptions,
+          applied,
+          environment.metadata?.visibility ?? ApiResourceVisibility.api_resource_visibility_unspecified,
+        );
         return toProtoJson(EnvironmentSchema, result);
       } catch (err) {
         throw rpcError(err, desc);

package/src/domains/mcpservers/apply.ts

@@ -7,7 +7,10 @@
 import { McpServerSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/api_pb";
 import { McpServerCommandController } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/command_pb";
 
+import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+
 import { mcpServerInputToProto, type McpServerInput } from "../../gen/mcpserver.js";
+import { applyDeclaredVisibility } from "../apply-visibility.js";
 import { withClient } from "../client.js";
 import { toProtoJson } from "../marshal.js";
 import { rpcError } from "../rpcerr.js";
@@ -26,7 +29,13 @@ export async function applyMcpServer(
     token,
     async (client, callOptions) => {
       try {
-        const result = await client.apply(server, callOptions);
+        const applied = await client.apply(server, callOptions);
+        const result = await applyDeclaredVisibility(
+          client,
+          callOptions,
+          applied,
+          server.metadata?.visibility ?? ApiResourceVisibility.api_resource_visibility_unspecified,
+        );
         return toProtoJson(McpServerSchema, result);
       } catch (err) {
         throw rpcError(err, desc);

package/src/domains/reads.integration.test.ts

@@ -1,5 +1,5 @@
 // In-process integration test for the read tools (get_mcp_server, get_skill,
-// get_workflow, get_environment, get_datastore). Stands up a real Connect
+// get_workflow, get_environment). Stands up a real Connect
 // backend serving the query controllers, drives the MCP server through an
 // in-memory client, and asserts each tool returns the backend's protojson
 // verbatim (the parity contract) and that get_skill forwards its optional
@@ -17,8 +17,6 @@ import type { AddressInfo } from "node:net";
 
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
-import { DatastoreSchema } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/api_pb";
-import { DatastoreQueryController } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/query_pb";
 import { EnvironmentSchema } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/api_pb";
 import { EnvironmentQueryController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/query_pb";
 import { McpServerSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/api_pb";
@@ -61,11 +59,6 @@ const knownEnvironment = create(EnvironmentSchema, {
   spec: { data: { API_KEY: { value: "***REDACTED***", isSecret: true } } },
 });
 
-const knownDatastore = create(DatastoreSchema, {
-  apiVersion: "v1",
-  kind: "datastore",
-  metadata: { name: "Bookings", slug: "bookings", org: "acme", id: "dst-1" },
-});
 
 let backend: Http2Server;
 let client: Client;
@@ -92,7 +85,6 @@ beforeAll(async () => {
     });
     router.service(WorkflowQueryController, { getByReference: () => knownWorkflow });
     router.service(EnvironmentQueryController, { getByReference: () => knownEnvironment });
-    router.service(DatastoreQueryController, { getByReference: () => knownDatastore });
   };
   backend = createHttp2Server(connectNodeAdapter({ routes }));
   // Force keep-alive sessions closed on teardown, else backend.close() blocks.
@@ -125,7 +117,6 @@ describe("read tools integration", () => {
         "get_skill",
         "get_workflow",
         "get_environment",
-        "get_datastore",
       ]),
     );
   });
@@ -169,12 +160,4 @@ describe("read tools integration", () => {
     const data = (body.spec as { data: Record<string, { value: string }> }).data;
     expect(data.API_KEY?.value).toBe("***REDACTED***");
   });
-
-  it("get_datastore returns the backend protojson", async () => {
-    const result = await callTool("get_datastore", { org: "acme", slug: "bookings" });
-    expect(result.isError).toBeFalsy();
-    expect(JSON.parse(result.content[0]?.text ?? "{}")).toEqual(
-      toJson(DatastoreSchema, knownDatastore, { useProtoFieldName: true }),
-    );
-  });
 });

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

@@ -17,8 +17,6 @@ import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { InMemoryTransport } from "@modelcontextprotocol/sdk/inMemory.js";
 import { AgentSchema } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/api_pb";
 import { AgentQueryController } from "@stigmer/protos/ai/stigmer/agentic/agent/v1/query_pb";
-import { DatastoreSchema } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/api_pb";
-import { DatastoreQueryController } from "@stigmer/protos/ai/stigmer/agentic/datastore/v1/query_pb";
 import { EnvironmentSchema } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/api_pb";
 import { EnvironmentQueryController } from "@stigmer/protos/ai/stigmer/agentic/environment/v1/query_pb";
 import { McpServerSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/api_pb";
@@ -51,11 +49,6 @@ const environment = create(EnvironmentSchema, {
   kind: "environment",
   metadata: { slug: "e", org: "acme" },
 });
-const datastore = create(DatastoreSchema, {
-  apiVersion: "v1",
-  kind: "datastore",
-  metadata: { slug: "d", org: "acme" },
-});
 
 let backend: Http2Server;
 let client: Client;
@@ -78,7 +71,6 @@ beforeAll(async () => {
     });
     router.service(WorkflowQueryController, { getByReference: () => workflow });
     router.service(EnvironmentQueryController, { getByReference: () => environment });
-    router.service(DatastoreQueryController, { getByReference: () => datastore });
   };
   backend = createHttp2Server(connectNodeAdapter({ routes }));
   backend.on("session", (session) => {
@@ -111,7 +103,6 @@ describe("resource templates integration", () => {
         "stigmer_skill_version",
         "stigmer_workflow",
         "stigmer_environment",
-        "stigmer_datastore",
       ]),
     );
   });
@@ -163,13 +154,4 @@ describe("resource templates integration", () => {
       toJson(EnvironmentSchema, environment, { useProtoFieldName: true }),
     );
   });
-
-  it("reads a datastore resource", async () => {
-    const result = (await client.readResource({
-      uri: "stigmer://datastores/acme/d",
-    })) as ResourceResult;
-    expect(JSON.parse(result.contents[0]?.text ?? "{}")).toEqual(
-      toJson(DatastoreSchema, datastore, { useProtoFieldName: true }),
-    );
-  });
 });

package/src/domains/resourceuri.test.ts

@@ -76,7 +76,6 @@ describe("buildResourceURI", () => {
     expect(buildResourceURI("skill", "acme", "s")).toBe("stigmer://skills/acme/s");
     expect(buildResourceURI("workflow", "acme", "w")).toBe("stigmer://workflows/acme/w");
     expect(buildResourceURI("environment", "acme", "e")).toBe("stigmer://environments/acme/e");
-    expect(buildResourceURI("datastore", "acme", "d")).toBe("stigmer://datastores/acme/d");
   });
 
   it("round-trips with parseResourceURI", () => {
@@ -96,7 +95,6 @@ describe("buildResourceURI", () => {
   it("covers exactly the templated kinds", () => {
     expect(Object.keys(kindToAuthority).sort()).toEqual([
       "agent",
-      "datastore",
       "environment",
       "mcp_server",
       "skill",

package/src/domains/resourceuri.ts

@@ -81,7 +81,6 @@ export function parseVersionedResourceURI(uri: string): VersionedResourceRef {
  */
 export const kindToAuthority: Readonly<Record<string, string>> = {
   agent: "agents",
-  datastore: "datastores",
   environment: "environments",
   mcp_server: "mcp-servers",
   skill: "skills",

package/src/domains/search/search.integration.test.ts

@@ -40,7 +40,6 @@ const allKindsResponse = create(SearchResponseSchema, {
       org: "acme",
       slug: "github-creds",
     }),
-    create(SearchResultSchema, { kind: ApiResourceKind.datastore, org: "acme", slug: "bookings" }),
   ],
 });
 const emptyResponse = create(SearchResponseSchema, { entries: [] });
@@ -103,7 +102,6 @@ describe("search tool integration", () => {
       "stigmer://mcp-servers/acme/github",
       "stigmer://workflows/acme/release",
       "stigmer://environments/acme/github-creds",
-      "stigmer://datastores/acme/bookings",
     ]);
   });
 
@@ -121,13 +119,13 @@ describe("search tool integration", () => {
     expect(result.isError).toBe(true);
     expect(result.content[0]?.text).toContain('unknown resource kind "bogus"');
     expect(result.content[0]?.text).toContain(
-      "valid kinds: agent, skill, mcp_server, workflow, environment, datastore",
+      "valid kinds: agent, skill, mcp_server, workflow, environment",
     );
   });
 
-  it("accepts the environment and datastore kinds", async () => {
+  it("accepts the environment kind", async () => {
     nextResponse = emptyResponse;
-    const result = await callSearch({ kinds: ["environment", "datastore"] });
+    const result = await callSearch({ kinds: ["environment"] });
     expect(result.isError).toBeFalsy();
   });
 

package/src/domains/search/tools.ts

@@ -31,7 +31,6 @@ import { textOrError } from "../toolresult.js";
  */
 const knownKinds: Readonly<Record<string, ApiResourceKind>> = {
   agent: ApiResourceKind.agent,
-  datastore: ApiResourceKind.datastore,
   environment: ApiResourceKind.environment,
   skill: ApiResourceKind.skill,
   mcp_server: ApiResourceKind.mcp_server,
@@ -53,15 +52,15 @@ export function registerSearchTools(server: McpServer, target: BackendTarget): s
     "search",
     {
       description:
-        "Search and list Stigmer resources (agents, skills, MCP servers, workflows, environments, " +
-        "datastores). Set 'kinds' to filter by resource type. Set 'query' for full-text search. " +
+        "Search and list Stigmer resources (agents, skills, MCP servers, workflows, " +
+        "environments). Set 'kinds' to filter by resource type. Set 'query' for full-text search. " +
         "Set 'org' to scope to an organization. Omit 'query' to list all accessible resources.",
       inputSchema: {
         kinds: z
           .array(z.string())
           .optional()
           .describe(
-            "Resource kinds to search. Valid: agent, skill, mcp_server, workflow, environment, datastore. Empty searches all.",
+            "Resource kinds to search. Valid: agent, skill, mcp_server, workflow, environment. Empty searches all.",
           ),
         query: z
           .string()
@@ -130,7 +129,7 @@ function parseKinds(raw: string[] | undefined): ApiResourceKind[] {
     const kind = knownKinds[s];
     if (kind === undefined) {
       throw new Error(
-        `unknown resource kind "${s}"; valid kinds: agent, skill, mcp_server, workflow, environment, datastore`,
+        `unknown resource kind "${s}"; valid kinds: agent, skill, mcp_server, workflow, environment`,
       );
     }
     return kind;

package/src/domains/workflows/apply.ts

@@ -11,7 +11,10 @@
 import { WorkflowSchema } from "@stigmer/protos/ai/stigmer/agentic/workflow/v1/api_pb";
 import { WorkflowCommandController } from "@stigmer/protos/ai/stigmer/agentic/workflow/v1/command_pb";
 
+import { ApiResourceVisibility } from "@stigmer/protos/ai/stigmer/commons/apiresource/enum_pb";
+
 import { workflowInputToProto, type WorkflowInput } from "../../gen/workflow.js";
+import { applyDeclaredVisibility } from "../apply-visibility.js";
 import { withClient } from "../client.js";
 import { toProtoJson } from "../marshal.js";
 import { rpcError } from "../rpcerr.js";
@@ -30,7 +33,13 @@ export async function applyWorkflow(
     token,
     async (client, callOptions) => {
       try {
-        const result = await client.apply(workflow, callOptions);
+        const applied = await client.apply(workflow, callOptions);
+        const result = await applyDeclaredVisibility(
+          client,
+          callOptions,
+          applied,
+          workflow.metadata?.visibility ?? ApiResourceVisibility.api_resource_visibility_unspecified,
+        );
         return toProtoJson(WorkflowSchema, result);
       } catch (err) {
         throw rpcError(err, desc);