@stigmer/cli 3.1.5 → 3.1.6

package/commands/apply.js

@@ -127,7 +127,7 @@ async function runFileApply(path, orgOverride, dryRun, format) {
         if (outcome.appliedMcpServer !== undefined)
             appliedMcpServers.push(outcome.appliedMcpServer);
     }
-    await discoverAppliedMcpServers(client.stigmer, appliedMcpServers, (line) => process.stderr.write(`${line}\n`));
+    await discoverAppliedMcpServers(client.stigmer, appliedMcpServers, org, (line) => process.stderr.write(`${line}\n`));
 }
 function buildAtomicGuidance() {
     const result = CommandResult.warning("No stigmer.yaml found in current directory or parents");

package/commands/apply.js.map

@@ -1 +1 @@
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package/commands/connect.js

@@ -30,6 +30,17 @@ async function runConnect(reference, options, command) {
     const client = connectBackend();
     ensureAuthenticated(client.config);
     const org = resolveOrganization(client.config, globalOrg(command));
+    // Connecting pushes to the backend, which requires an org for credential
+    // resolution. Fail with actionable guidance instead of the backend's cryptic
+    // "org value length must be at least 1" validation error. Dry-run discovers
+    // locally (no backend push) and needs no org for an id reference, so it is
+    // exempt — mirrors the org guard in run/draft/resume.
+    if (options.dryRun !== true && org === "") {
+        throw new UsageError("organization not set\n\n" +
+            "Set it with:\n" +
+            "  stigmer config context set --org <org>\n" +
+            "  stigmer connect mcp-server <server> --org <org>");
+    }
     const result = await connectMcpServer(client.stigmer, {
         reference,
         org,

package/commands/connect.js.map

@@ -1 +1 @@
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+{"version":3,"file":"connect.js","sourceRoot":"","sources":["../../src/commands/connect.ts"],"names":[],"mappings":"AAAA,iFAAiF;AACjF,4EAA4E;AAC5E,4DAA4D;AAC5D,EAAE;AACF,+EAA+E;AAC/E,8EAA8E;AAC9E,iBAAiB;AAGjB,OAAO,EAAE,mBAAmB,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AAC9E,OAAO,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAQxC,MAAM,uBAAuB,GAAG,EAAE,CAAC;AAEnC,MAAM,UAAU,eAAe,CAAC,OAAgB;IAC9C,MAAM,OAAO,GAAG,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,WAAW,CAAC,wDAAwD,CAAC,CAAC;IAEjH,OAAO;SACJ,OAAO,CAAC,yBAAyB,CAAC;SAClC,WAAW,CAAC,iDAAiD,CAAC;SAC9D,MAAM,CAAC,qBAAqB,EAAE,sCAAsC,EAAE,MAAM,CAAC,uBAAuB,CAAC,CAAC;SACtG,MAAM,CAAC,WAAW,EAAE,6DAA6D,CAAC;SAClF,MAAM,CACL,mBAAmB,EACnB,sDAAsD,EACtD,CAAC,KAAa,EAAE,QAAkB,EAAE,EAAE,CAAC,CAAC,GAAG,QAAQ,EAAE,KAAK,CAAC,EAC3D,EAAE,CACH;SACA,MAAM,CAAC,CAAC,SAAiB,EAAE,OAAqB,EAAE,OAAgB,EAAE,EAAE,CAAC,UAAU,CAAC,SAAS,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC;AACrH,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,SAAiB,EAAE,OAAqB,EAAE,OAAgB;IAClF,MAAM,SAAS,GAAG,YAAY,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;IAChD,MAAM,CAAC,EAAE,cAAc,EAAE,EAAE,EAAE,gBAAgB,EAAE,EAAE,EAAE,mBAAmB,EAAE,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;QAC5F,MAAM,CAAC,eAAe,CAAC;QACvB,MAAM,CAAC,iCAAiC,CAAC;QACzC,MAAM,CAAC,iCAAiC,CAAC;KAC1C,CAAC,CAAC;IAEH,MAAM,MAAM,GAAG,cAAc,EAAE,CAAC;IAChC,mBAAmB,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;IACnC,MAAM,GAAG,GAAG,mBAAmB,CAAC,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC;IAEnE,yEAAyE;IACzE,6EAA6E;IAC7E,4EAA4E;IAC5E,2EAA2E;IAC3E,sDAAsD;IACtD,IAAI,OAAO,CAAC,MAAM,KAAK,IAAI,IAAI,GAAG,KAAK,EAAE,EAAE,CAAC;QAC1C,MAAM,IAAI,UAAU,CAClB,0BAA0B;YACxB,gBAAgB;YAChB,4CAA4C;YAC5C,mDAAmD,CACtD,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,MAAM,CAAC,OAAO,EAAE;QACpD,SAAS;QACT,GAAG;QACH,SAAS;QACT,MAAM,EAAE,OAAO,CAAC,MAAM,KAAK,IAAI;QAC/B,YAAY,EAAE,OAAO,CAAC,GAAG;QACzB,WAAW,EAAE,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI;QACvC,WAAW,EAAE,OAAO,CAAC,MAAM,CAAC,KAAK,KAAK,IAAI;KAC3C,CAAC,CAAC;IAEH,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;IAChD,mBAAmB,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,IAAI,IAAI,CAAC,EAAE,QAAQ,CAAC,CAAC;AACrF,CAAC;AAED,8EAA8E;AAC9E,mEAAmE;AACnE,SAAS,YAAY,CAAC,GAAuB;IAC3C,IAAI,GAAG,KAAK,SAAS,IAAI,GAAG,KAAK,EAAE;QAAE,OAAO,uBAAuB,GAAG,IAAI,CAAC;IAC3E,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC;IAC5B,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,IAAI,OAAO,GAAG,CAAC,EAAE,CAAC;QAC7C,MAAM,IAAI,UAAU,CAAC,sBAAsB,GAAG,iCAAiC,CAAC,CAAC;IACnF,CAAC;IACD,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,GAAG,IAAI,CAAC,CAAC;AACpC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@stigmer/cli",
-  "version": "3.1.5",
+  "version": "3.1.6",
   "description": "Stigmer command-line interface — manage agents, workflows, MCP servers, skills, and executions from the terminal",
   "license": "Apache-2.0",
   "type": "module",
@@ -35,10 +35,10 @@
     "@connectrpc/connect": "^2.0.0",
     "@connectrpc/connect-node": "^2.1.1",
     "@modelcontextprotocol/sdk": "^1.26.0",
-    "@stigmer/ink": "3.1.5",
-    "@stigmer/mcp-server": "3.1.5",
-    "@stigmer/protos": "3.1.5",
-    "@stigmer/sdk": "3.1.5",
+    "@stigmer/ink": "3.1.6",
+    "@stigmer/mcp-server": "3.1.6",
+    "@stigmer/protos": "3.1.6",
+    "@stigmer/sdk": "3.1.6",
     "commander": "^12.1.0",
     "fflate": "^0.8.3",
     "ink": "^7.0.0",

package/resources/apply/declarative.js

@@ -229,7 +229,7 @@ export async function reconcileProjectMembers(project, resources, skillSources,
                 members.push(reference(deps.org, res.handler.kind, slug));
         }
     }
-    await discoverAppliedMcpServers(deps.stigmer, appliedMcpServers, deps.info);
+    await discoverAppliedMcpServers(deps.stigmer, appliedMcpServers, deps.org, deps.info);
     injectOrg(project, deps.org);
     if (project.spec === undefined)
         project.spec = create(ProjectSpecSchema, {});

package/resources/apply/declarative.js.map

@@ -1 +1 @@
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package/resources/apply/discovery.d.ts

@@ -2,6 +2,13 @@ import type { McpServer } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/
 import type { Stigmer } from "@stigmer/sdk";
 /** A sink for human progress/warning lines (discovery output is not parity). */
 export type DiscoverySink = (line: string) => void;
-/** Connect each applied stdio MCP server to trigger capability discovery. */
-export declare function discoverAppliedMcpServers(client: Stigmer, servers: readonly McpServer[], sink?: DiscoverySink): Promise<void>;
+/**
+ * Connect each applied stdio MCP server to trigger capability discovery.
+ *
+ * `org` is the resolved apply organization. The backend requires it on every
+ * ConnectInput, and it is guaranteed non-empty here: `applyMessage` injects org
+ * into each resource and the backend rejects an org-less MCP server apply, so
+ * any server that reached `servers` was applied under this org.
+ */
+export declare function discoverAppliedMcpServers(client: Stigmer, servers: readonly McpServer[], org: string, sink?: DiscoverySink): Promise<void>;
 //# sourceMappingURL=discovery.d.ts.map

package/resources/apply/discovery.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"discovery.d.ts","sourceRoot":"","sources":["../../../src/resources/apply/discovery.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wDAAwD,CAAC;AAExF,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAG5C,gFAAgF;AAChF,MAAM,MAAM,aAAa,GAAG,CAAC,IAAI,EAAE,MAAM,KAAK,IAAI,CAAC;AAEnD,6EAA6E;AAC7E,wBAAsB,yBAAyB,CAC7C,MAAM,EAAE,OAAO,EACf,OAAO,EAAE,SAAS,SAAS,EAAE,EAC7B,IAAI,CAAC,EAAE,aAAa,GACnB,OAAO,CAAC,IAAI,CAAC,CA4Bf"}
+{"version":3,"file":"discovery.d.ts","sourceRoot":"","sources":["../../../src/resources/apply/discovery.ts"],"names":[],"mappings":"AASA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wDAAwD,CAAC;AAExF,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAG5C,gFAAgF;AAChF,MAAM,MAAM,aAAa,GAAG,CAAC,IAAI,EAAE,MAAM,KAAK,IAAI,CAAC;AAEnD;;;;;;;GAOG;AACH,wBAAsB,yBAAyB,CAC7C,MAAM,EAAE,OAAO,EACf,OAAO,EAAE,SAAS,SAAS,EAAE,EAC7B,GAAG,EAAE,MAAM,EACX,IAAI,CAAC,EAAE,aAAa,GACnB,OAAO,CAAC,IAAI,CAAC,CA6Bf"}

package/resources/apply/discovery.js

@@ -8,8 +8,15 @@
 import { create } from "@bufbuild/protobuf";
 import { ConnectInputSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/io_pb";
 import { buildRuntimeEnv } from "../mcp/runtime-env.js";
-/** Connect each applied stdio MCP server to trigger capability discovery. */
-export async function discoverAppliedMcpServers(client, servers, sink) {
+/**
+ * Connect each applied stdio MCP server to trigger capability discovery.
+ *
+ * `org` is the resolved apply organization. The backend requires it on every
+ * ConnectInput, and it is guaranteed non-empty here: `applyMessage` injects org
+ * into each resource and the backend rejects an org-less MCP server apply, so
+ * any server that reached `servers` was applied under this org.
+ */
+export async function discoverAppliedMcpServers(client, servers, org, sink) {
     if (servers.length === 0)
         return;
     sink?.(`Discovering capabilities for ${servers.length} applied MCP server(s)...`);
@@ -26,6 +33,7 @@ export async function discoverAppliedMcpServers(client, servers, sink) {
         try {
             await client.mcpServer.connect(create(ConnectInputSchema, {
                 mcpServerId: server.metadata?.id ?? "",
+                org,
                 runtimeEnv: buildRuntimeEnv(server),
             }));
             sink?.(`Discovered capabilities for ${name}`);

package/resources/apply/discovery.js.map

@@ -1 +1 @@
-{"version":3,"file":"discovery.js","sourceRoot":"","sources":["../../../src/resources/apply/discovery.ts"],"names":[],"mappings":"AAAA,uCAAuC;AACvC,EAAE;AACF,8EAA8E;AAC9E,+EAA+E;AAC/E,8EAA8E;AAC9E,2EAA2E;AAC3E,mFAAmF;AAEnF,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAE5C,OAAO,EAAE,kBAAkB,EAAE,MAAM,uDAAuD,CAAC;AAE3F,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAKxD,6EAA6E;AAC7E,MAAM,CAAC,KAAK,UAAU,yBAAyB,CAC7C,MAAe,EACf,OAA6B,EAC7B,IAAoB;IAEpB,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO;IACjC,IAAI,EAAE,CAAC,gCAAgC,OAAO,CAAC,MAAM,2BAA2B,CAAC,CAAC;IAElF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,WAAW,CAAC;QAElD,wEAAwE;QACxE,IAAI,MAAM,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,KAAK,OAAO;YAAE,SAAS;QAExD,MAAM,OAAO,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;QAC7C,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACvB,IAAI,EAAE,CAAC,0BAA0B,IAAI,gCAAgC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC3F,SAAS;QACX,CAAC;QAED,IAAI,CAAC;YACH,MAAM,MAAM,CAAC,SAAS,CAAC,OAAO,CAC5B,MAAM,CAAC,kBAAkB,EAAE;gBACzB,WAAW,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;gBACtC,UAAU,EAAE,eAAe,CAAC,MAAM,CAAC;aACpC,CAAC,CACH,CAAC;YACF,IAAI,EAAE,CAAC,+BAA+B,IAAI,EAAE,CAAC,CAAC;QAChD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,IAAI,EAAE,CAAC,wBAAwB,IAAI,KAAM,GAAa,CAAC,OAAO,EAAE,CAAC,CAAC;QACpE,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,oBAAoB,CAAC,MAAiB;IAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,EAAE,GAAG,IAAI,EAAE,CAAC;IACnC,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,KAAK,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QAC/C,IAAI,IAAI,CAAC,QAAQ,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YAAE,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC5E,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}
+{"version":3,"file":"discovery.js","sourceRoot":"","sources":["../../../src/resources/apply/discovery.ts"],"names":[],"mappings":"AAAA,uCAAuC;AACvC,EAAE;AACF,8EAA8E;AAC9E,+EAA+E;AAC/E,8EAA8E;AAC9E,2EAA2E;AAC3E,mFAAmF;AAEnF,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAE5C,OAAO,EAAE,kBAAkB,EAAE,MAAM,uDAAuD,CAAC;AAE3F,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAKxD;;;;;;;GAOG;AACH,MAAM,CAAC,KAAK,UAAU,yBAAyB,CAC7C,MAAe,EACf,OAA6B,EAC7B,GAAW,EACX,IAAoB;IAEpB,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO;IACjC,IAAI,EAAE,CAAC,gCAAgC,OAAO,CAAC,MAAM,2BAA2B,CAAC,CAAC;IAElF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,WAAW,CAAC;QAElD,wEAAwE;QACxE,IAAI,MAAM,CAAC,IAAI,EAAE,UAAU,EAAE,IAAI,KAAK,OAAO;YAAE,SAAS;QAExD,MAAM,OAAO,GAAG,oBAAoB,CAAC,MAAM,CAAC,CAAC;QAC7C,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACvB,IAAI,EAAE,CAAC,0BAA0B,IAAI,gCAAgC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC3F,SAAS;QACX,CAAC;QAED,IAAI,CAAC;YACH,MAAM,MAAM,CAAC,SAAS,CAAC,OAAO,CAC5B,MAAM,CAAC,kBAAkB,EAAE;gBACzB,WAAW,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;gBACtC,GAAG;gBACH,UAAU,EAAE,eAAe,CAAC,MAAM,CAAC;aACpC,CAAC,CACH,CAAC;YACF,IAAI,EAAE,CAAC,+BAA+B,IAAI,EAAE,CAAC,CAAC;QAChD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,IAAI,EAAE,CAAC,wBAAwB,IAAI,KAAM,GAAa,CAAC,OAAO,EAAE,CAAC,CAAC;QACpE,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,oBAAoB,CAAC,MAAiB;IAC7C,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,EAAE,GAAG,IAAI,EAAE,CAAC;IACnC,MAAM,OAAO,GAAa,EAAE,CAAC;IAC7B,KAAK,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QAC/C,IAAI,IAAI,CAAC,QAAQ,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YAAE,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC5E,CAAC;IACD,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/resources/connect/connect.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"connect.d.ts","sourceRoot":"","sources":["../../../src/resources/connect/connect.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wDAAwD,CAAC;AAExF,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,2DAA2D,CAAC;AAExG,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAC5C,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAO1D,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC;IACzB,QAAQ,CAAC,YAAY,EAAE,SAAS,MAAM,EAAE,CAAC;IACzC,6DAA6D;IAC7D,QAAQ,CAAC,WAAW,EAAE,WAAW,CAAC;IAClC,0EAA0E;IAC1E,QAAQ,CAAC,WAAW,EAAE,OAAO,CAAC;CAC/B;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,CAAC,MAAM,EAAE,SAAS,CAAC;IAC3B,QAAQ,CAAC,YAAY,EAAE,sBAAsB,GAAG,SAAS,CAAC;IAC1D,iFAAiF;IACjF,QAAQ,CAAC,OAAO,EAAE,SAAS,GAAG,SAAS,CAAC;CACzC;AAED,gFAAgF;AAChF,wBAAsB,gBAAgB,CAAC,MAAM,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,CAAC,CAkBpG"}
+{"version":3,"file":"connect.d.ts","sourceRoot":"","sources":["../../../src/resources/connect/connect.ts"],"names":[],"mappings":"AAYA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,wDAAwD,CAAC;AAExF,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,2DAA2D,CAAC;AAExG,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAC5C,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAO1D,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,MAAM,EAAE,OAAO,CAAC;IACzB,QAAQ,CAAC,YAAY,EAAE,SAAS,MAAM,EAAE,CAAC;IACzC,6DAA6D;IAC7D,QAAQ,CAAC,WAAW,EAAE,WAAW,CAAC;IAClC,0EAA0E;IAC1E,QAAQ,CAAC,WAAW,EAAE,OAAO,CAAC;CAC/B;AAED,MAAM,WAAW,aAAa;IAC5B,QAAQ,CAAC,MAAM,EAAE,SAAS,CAAC;IAC3B,QAAQ,CAAC,YAAY,EAAE,sBAAsB,GAAG,SAAS,CAAC;IAC1D,iFAAiF;IACjF,QAAQ,CAAC,OAAO,EAAE,SAAS,GAAG,SAAS,CAAC;CACzC;AAED,gFAAgF;AAChF,wBAAsB,gBAAgB,CAAC,MAAM,EAAE,OAAO,EAAE,IAAI,EAAE,cAAc,GAAG,OAAO,CAAC,aAAa,CAAC,CAmBpG"}

package/resources/connect/connect.js

@@ -27,6 +27,7 @@ export async function connectMcpServer(client, opts) {
     await ensureOAuthSatisfied(client, server, opts);
     const updated = await client.mcpServer.connect(create(ConnectInputSchema, {
         mcpServerId: server.metadata?.id ?? "",
+        org: opts.org,
         runtimeEnv: buildRuntimeEnv(server, opts.envOverrides),
     }));
     return { server, capabilities: updated.status?.discoveredCapabilities, updated };

package/resources/connect/connect.js.map

@@ -1 +1 @@
-{"version":3,"file":"connect.js","sourceRoot":"","sources":["../../../src/resources/connect/connect.ts"],"names":[],"mappings":"AAAA,mFAAmF;AACnF,4EAA4E;AAC5E,gFAAgF;AAChF,iEAAiE;AACjE,EAAE;AACF,+EAA+E;AAC/E,+EAA+E;AAC/E,4EAA4E;AAC5E,6EAA6E;AAC7E,8EAA8E;AAE9E,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAE5C,OAAO,EAAE,kBAAkB,EAAE,8BAA8B,EAAE,MAAM,uDAAuD,CAAC;AAK3H,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAC1D,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAqB9C,gFAAgF;AAChF,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,MAAe,EAAE,IAAoB;IAC1E,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC;IAExE,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,IAAI,MAAM,CAAC,IAAI,KAAK,SAAS;YAAE,MAAM,IAAI,UAAU,CAAC,sDAAsD,CAAC,CAAC;QAC5G,MAAM,YAAY,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;QACzF,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC;IACtD,CAAC;IAED,MAAM,oBAAoB,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IAEjD,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,OAAO,CAC5C,MAAM,CAAC,kBAAkB,EAAE;QACzB,WAAW,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;QACtC,UAAU,EAAE,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,YAAY,CAAC;KACvD,CAAC,CACH,CAAC;IACF,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,OAAO,CAAC,MAAM,EAAE,sBAAsB,EAAE,OAAO,EAAE,CAAC;AACnF,CAAC;AAED,iFAAiF;AACjF,kBAAkB;AAClB,KAAK,UAAU,gBAAgB,CAAC,MAAe,EAAE,SAAiB,EAAE,GAAW;IAC7E,MAAM,QAAQ,GAAG,eAAe,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,QAAQ,IAAI,EAAE,CAAC;IAC5E,MAAM,MAAM,GAAG,cAAc,CAAC,SAAS,EAAE,GAAG,EAAE,QAAQ,CAAC,CAAC;IACxD,IAAI,MAAM,CAAC,IAAI,KAAK,IAAI;QAAE,OAAO,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IACjE,OAAO,MAAM,CAAC,SAAS,CAAC,cAAc,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,CAAC,CAAC;AACjF,CAAC;AAED,gFAAgF;AAChF,8EAA8E;AAC9E,0EAA0E;AAC1E,4EAA4E;AAC5E,KAAK,UAAU,oBAAoB,CAAC,MAAe,EAAE,MAAiB,EAAE,IAAoB;IAC1F,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,IAAI,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO;IAEnE,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,mBAAmB,CACvD,MAAM,CAAC,8BAA8B,EAAE;QACrC,UAAU,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;QACrC,GAAG,EAAE,IAAI,CAAC,GAAG;KACd,CAAC,CACH,CAAC;IACF,IAAI,MAAM,CAAC,SAAS;QAAE,OAAO;IAE7B,IAAI,CAAC,IAAI,CAAC,WAAW;QAAE,MAAM,kBAAkB,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;IAExE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,CAAC;IACpD,MAAM,YAAY,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;AACvF,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAiB,EAAE,SAAiB;IAC9D,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,SAAS,CAAC;IACzE,OAAO,IAAI,UAAU,CACnB,eAAe,IAAI,2EAA2E;QAC5F,8BAA8B;QAC9B,wFAAwF;QACxF,gEAAgE,IAAI,kBAAkB,CACzF,CAAC;AACJ,CAAC;AAED,SAAS,aAAa,CAAC,MAAiB;IACtC,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,YAAY,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;AACxD,CAAC"}
+{"version":3,"file":"connect.js","sourceRoot":"","sources":["../../../src/resources/connect/connect.ts"],"names":[],"mappings":"AAAA,mFAAmF;AACnF,4EAA4E;AAC5E,gFAAgF;AAChF,iEAAiE;AACjE,EAAE;AACF,+EAA+E;AAC/E,+EAA+E;AAC/E,4EAA4E;AAC5E,6EAA6E;AAC7E,8EAA8E;AAE9E,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAE5C,OAAO,EAAE,kBAAkB,EAAE,8BAA8B,EAAE,MAAM,uDAAuD,CAAC;AAK3H,OAAO,EAAE,UAAU,EAAE,MAAM,uBAAuB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAC1D,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,EAAE,cAAc,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAqB9C,gFAAgF;AAChF,MAAM,CAAC,KAAK,UAAU,gBAAgB,CAAC,MAAe,EAAE,IAAoB;IAC1E,MAAM,MAAM,GAAG,MAAM,gBAAgB,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC;IAExE,IAAI,IAAI,CAAC,MAAM,EAAE,CAAC;QAChB,IAAI,MAAM,CAAC,IAAI,KAAK,SAAS;YAAE,MAAM,IAAI,UAAU,CAAC,sDAAsD,CAAC,CAAC;QAC5G,MAAM,YAAY,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;QACzF,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,SAAS,EAAE,CAAC;IACtD,CAAC;IAED,MAAM,oBAAoB,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,CAAC,CAAC;IAEjD,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,OAAO,CAC5C,MAAM,CAAC,kBAAkB,EAAE;QACzB,WAAW,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;QACtC,GAAG,EAAE,IAAI,CAAC,GAAG;QACb,UAAU,EAAE,eAAe,CAAC,MAAM,EAAE,IAAI,CAAC,YAAY,CAAC;KACvD,CAAC,CACH,CAAC;IACF,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,OAAO,CAAC,MAAM,EAAE,sBAAsB,EAAE,OAAO,EAAE,CAAC;AACnF,CAAC;AAED,iFAAiF;AACjF,kBAAkB;AAClB,KAAK,UAAU,gBAAgB,CAAC,MAAe,EAAE,SAAiB,EAAE,GAAW;IAC7E,MAAM,QAAQ,GAAG,eAAe,EAAE,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,QAAQ,IAAI,EAAE,CAAC;IAC5E,MAAM,MAAM,GAAG,cAAc,CAAC,SAAS,EAAE,GAAG,EAAE,QAAQ,CAAC,CAAC;IACxD,IAAI,MAAM,CAAC,IAAI,KAAK,IAAI;QAAE,OAAO,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;IACjE,OAAO,MAAM,CAAC,SAAS,CAAC,cAAc,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,IAAI,EAAE,MAAM,CAAC,IAAI,EAAE,CAAC,CAAC;AACjF,CAAC;AAED,gFAAgF;AAChF,8EAA8E;AAC9E,0EAA0E;AAC1E,4EAA4E;AAC5E,KAAK,UAAU,oBAAoB,CAAC,MAAe,EAAE,MAAiB,EAAE,IAAoB;IAC1F,IAAI,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,IAAI,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC;QAAE,OAAO;IAEnE,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,mBAAmB,CACvD,MAAM,CAAC,8BAA8B,EAAE;QACrC,UAAU,EAAE,MAAM,CAAC,QAAQ,EAAE,EAAE,IAAI,EAAE;QACrC,GAAG,EAAE,IAAI,CAAC,GAAG;KACd,CAAC,CACH,CAAC;IACF,IAAI,MAAM,CAAC,SAAS;QAAE,OAAO;IAE7B,IAAI,CAAC,IAAI,CAAC,WAAW;QAAE,MAAM,kBAAkB,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC;IAExE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,YAAY,CAAC,CAAC;IACpD,MAAM,YAAY,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;AACvF,CAAC;AAED,SAAS,kBAAkB,CAAC,MAAiB,EAAE,SAAiB;IAC9D,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,MAAM,CAAC,QAAQ,EAAE,IAAI,IAAI,SAAS,CAAC;IACzE,OAAO,IAAI,UAAU,CACnB,eAAe,IAAI,2EAA2E;QAC5F,8BAA8B;QAC9B,wFAAwF;QACxF,gEAAgE,IAAI,kBAAkB,CACzF,CAAC;AACJ,CAAC;AAED,SAAS,aAAa,CAAC,MAAiB;IACtC,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,EAAE,YAAY,IAAI,EAAE,CAAC,KAAK,EAAE,CAAC;AACxD,CAAC"}

package/src/commands/apply.ts

@@ -184,7 +184,7 @@ async function runFileApply(
     if (outcome.appliedMcpServer !== undefined) appliedMcpServers.push(outcome.appliedMcpServer);
   }
 
-  await discoverAppliedMcpServers(client.stigmer, appliedMcpServers, (line) => process.stderr.write(`${line}\n`));
+  await discoverAppliedMcpServers(client.stigmer, appliedMcpServers, org, (line) => process.stderr.write(`${line}\n`));
 }
 
 function buildAtomicGuidance(): CommandResult {

package/src/commands/connect.test.ts

@@ -0,0 +1,73 @@
+// Command-level contract for the `connect mcp-server` org guard (issue #140).
+//
+// Connecting pushes to the backend, which requires an org. Rather than let the
+// backend reject the request with the cryptic "org value length must be at least
+// 1" validation error, the command fails fast with actionable guidance — but
+// only when it is actually going to push. `--dry-run` discovers locally and must
+// stay usable with no org configured.
+//
+// Runs in standalone mode so `load()` returns the default (local, org-less)
+// config without reading the user's real config file. The guard runs before any
+// network call, so the non-dry-run case is fully deterministic and offline.
+
+import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
+import { classify, ExitCode } from "../errors/index.js";
+import { buildProgram } from "../program.js";
+
+interface RunOutcome {
+  readonly exitCode: number;
+  readonly message: string;
+}
+
+// Runs `connect mcp-server <ref> [flags]` in standalone mode with output
+// suppressed, returning the thrown error's classified exit code and message (or
+// a success sentinel). `--standalone` is a program-global flag, so it must
+// precede the subcommand (commander's enablePositionalOptions).
+async function runConnect(ref: string, ...flags: string[]): Promise<RunOutcome> {
+  const program = buildProgram();
+  program.exitOverride();
+  const outSpy = vi.spyOn(process.stdout, "write").mockReturnValue(true);
+  const errSpy = vi.spyOn(process.stderr, "write").mockReturnValue(true);
+  try {
+    await program.parseAsync(["node", "stigmer", "--standalone", "connect", "mcp-server", ref, ...flags]);
+    return { exitCode: ExitCode.Success, message: "" };
+  } catch (err) {
+    return { exitCode: classify(err)?.exitCode ?? -1, message: err instanceof Error ? err.message : String(err) };
+  } finally {
+    outSpy.mockRestore();
+    errSpy.mockRestore();
+  }
+}
+
+let savedOrg: string | undefined;
+let savedApiKey: string | undefined;
+
+beforeEach(() => {
+  savedOrg = process.env.STIGMER_ORG_ID;
+  savedApiKey = process.env.STIGMER_API_KEY;
+  delete process.env.STIGMER_ORG_ID;
+  delete process.env.STIGMER_API_KEY;
+});
+
+afterEach(() => {
+  if (savedOrg === undefined) delete process.env.STIGMER_ORG_ID;
+  else process.env.STIGMER_ORG_ID = savedOrg;
+  if (savedApiKey === undefined) delete process.env.STIGMER_API_KEY;
+  else process.env.STIGMER_API_KEY = savedApiKey;
+});
+
+describe("connect mcp-server org guard", () => {
+  it("fails fast with actionable guidance when no org is set (non-dry-run)", async () => {
+    const outcome = await runConnect("mcp_test");
+    expect(outcome.message).toContain("organization not set");
+    expect(outcome.exitCode).toBe(ExitCode.Usage);
+  });
+
+  it("does not apply the org guard in dry-run mode (offline dry-run stays usable)", async () => {
+    // Dry-run skips the push, so the guard must not fire even with no org. The
+    // command proceeds past the guard and fails later for an unrelated reason
+    // (no reachable backend) — never with the org guidance error.
+    const outcome = await runConnect("mcp_test", "--dry-run");
+    expect(outcome.message).not.toContain("organization not set");
+  });
+});

package/src/commands/connect.ts

@@ -49,6 +49,20 @@ async function runConnect(reference: string, options: ConnectFlags, command: Com
   ensureAuthenticated(client.config);
   const org = resolveOrganization(client.config, globalOrg(command));
 
+  // Connecting pushes to the backend, which requires an org for credential
+  // resolution. Fail with actionable guidance instead of the backend's cryptic
+  // "org value length must be at least 1" validation error. Dry-run discovers
+  // locally (no backend push) and needs no org for an id reference, so it is
+  // exempt — mirrors the org guard in run/draft/resume.
+  if (options.dryRun !== true && org === "") {
+    throw new UsageError(
+      "organization not set\n\n" +
+        "Set it with:\n" +
+        "  stigmer config context set --org <org>\n" +
+        "  stigmer connect mcp-server <server> --org <org>",
+    );
+  }
+
   const result = await connectMcpServer(client.stigmer, {
     reference,
     org,

package/src/resources/apply/declarative.ts

@@ -311,7 +311,7 @@ export async function reconcileProjectMembers(
     }
   }
 
-  await discoverAppliedMcpServers(deps.stigmer, appliedMcpServers, deps.info);
+  await discoverAppliedMcpServers(deps.stigmer, appliedMcpServers, deps.org, deps.info);
 
   injectOrg(project, deps.org);
   if (project.spec === undefined) project.spec = create(ProjectSpecSchema, {});

package/src/resources/apply/discovery.integration.test.ts

@@ -0,0 +1,99 @@
+// In-process integration test for post-apply MCP discovery.
+//
+// Stands up a Connect backend serving McpServerCommandController.connect, points
+// an SDK node client at it, and drives discoverAppliedMcpServers. The mock
+// mirrors the backend's protovalidate rule (org min_len=1) by rejecting an empty
+// org, so a regression that drops org from ConnectInput is caught here rather
+// than silently passing (issue #140: the CLI used to omit org entirely).
+
+import { create } from "@bufbuild/protobuf";
+import { Code, ConnectError, type ConnectRouter } from "@connectrpc/connect";
+import { connectNodeAdapter } from "@connectrpc/connect-node";
+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 type { ConnectInput } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/io_pb";
+import type { Stigmer } from "@stigmer/sdk";
+import { createNodeClient, normalizeEndpoint } from "@stigmer/sdk/node";
+import { createServer as createHttp2Server, type Http2Server, type ServerHttp2Session } from "node:http2";
+import type { AddressInfo } from "node:net";
+import { afterAll, beforeAll, beforeEach, describe, expect, it } from "vitest";
+import { discoverAppliedMcpServers } from "./discovery.js";
+
+let backend: Http2Server;
+let client: Stigmer;
+const openSessions = new Set<ServerHttp2Session>();
+
+let connectCalls: ConnectInput[] = [];
+
+beforeEach(() => {
+  connectCalls = [];
+});
+
+// A stdio MCP server with no env declarations, so discovery does not skip it and
+// buildRuntimeEnv stays empty (no local process needed — connect is mocked).
+function stdioServer(id: string, org: string) {
+  return create(McpServerSchema, {
+    metadata: { id, name: id, slug: id, org },
+    spec: { serverType: { case: "stdio", value: { command: "noop" } } },
+  });
+}
+
+beforeAll(async () => {
+  const routes = (router: ConnectRouter) => {
+    router.service(McpServerCommandController, {
+      connect: (req) => {
+        if (req.org === "") {
+          throw new ConnectError("org – value length must be at least 1 characters", Code.InvalidArgument);
+        }
+        connectCalls.push(req);
+        return create(McpServerSchema, { metadata: { id: req.mcpServerId } });
+      },
+    });
+  };
+
+  backend = createHttp2Server(connectNodeAdapter({ routes }));
+  backend.on("session", (session) => {
+    openSessions.add(session);
+    session.on("close", () => openSessions.delete(session));
+  });
+  await new Promise<void>((resolve) => backend.listen(0, "127.0.0.1", resolve));
+  const port = (backend.address() as AddressInfo).port;
+  client = createNodeClient({ baseUrl: normalizeEndpoint(`127.0.0.1:${port}`) });
+});
+
+afterAll(async () => {
+  for (const session of openSessions) session.destroy();
+  await new Promise<void>((resolve) => backend.close(() => resolve()));
+});
+
+describe("discoverAppliedMcpServers", () => {
+  it("forwards the resolved org on ConnectInput for each applied stdio server", async () => {
+    const lines: string[] = [];
+    await discoverAppliedMcpServers(client, [stdioServer("mcp_1", "acme")], "acme", (l) => lines.push(l));
+
+    expect(connectCalls).toHaveLength(1);
+    expect(connectCalls[0].mcpServerId).toBe("mcp_1");
+    expect(connectCalls[0].org).toBe("acme");
+    expect(lines.join("\n")).toContain("Discovered capabilities for mcp_1");
+  });
+
+  it("surfaces the backend's org validation as a per-server warning when org is empty (regression guard)", async () => {
+    const lines: string[] = [];
+    await discoverAppliedMcpServers(client, [stdioServer("mcp_1", "acme")], "", (l) => lines.push(l));
+
+    // Best-effort: an empty org must never crash the apply — it degrades to a
+    // warning. This proves the mock (and thus the backend) rejects empty org, so
+    // the happy-path org assertion above is a real guard, not a tautology.
+    expect(connectCalls).toHaveLength(0);
+    expect(lines.join("\n")).toContain("Discovery failed for mcp_1");
+  });
+
+  it("skips non-stdio servers without calling connect", async () => {
+    const httpServer = create(McpServerSchema, {
+      metadata: { id: "mcp_http", name: "http", slug: "http", org: "acme" },
+      spec: { serverType: { case: "http", value: { url: "https://example.com/mcp" } } },
+    });
+    await discoverAppliedMcpServers(client, [httpServer], "acme");
+    expect(connectCalls).toHaveLength(0);
+  });
+});

package/src/resources/apply/discovery.ts

@@ -15,10 +15,18 @@ import { buildRuntimeEnv } from "../mcp/runtime-env.js";
 /** A sink for human progress/warning lines (discovery output is not parity). */
 export type DiscoverySink = (line: string) => void;
 
-/** Connect each applied stdio MCP server to trigger capability discovery. */
+/**
+ * Connect each applied stdio MCP server to trigger capability discovery.
+ *
+ * `org` is the resolved apply organization. The backend requires it on every
+ * ConnectInput, and it is guaranteed non-empty here: `applyMessage` injects org
+ * into each resource and the backend rejects an org-less MCP server apply, so
+ * any server that reached `servers` was applied under this org.
+ */
 export async function discoverAppliedMcpServers(
   client: Stigmer,
   servers: readonly McpServer[],
+  org: string,
   sink?: DiscoverySink,
 ): Promise<void> {
   if (servers.length === 0) return;
@@ -40,6 +48,7 @@ export async function discoverAppliedMcpServers(
       await client.mcpServer.connect(
         create(ConnectInputSchema, {
           mcpServerId: server.metadata?.id ?? "",
+          org,
           runtimeEnv: buildRuntimeEnv(server),
         }),
       );

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

@@ -6,7 +6,7 @@
 // guidance gate, and the dry-run path (local discovery, no Connect RPC).
 
 import { create } from "@bufbuild/protobuf";
-import type { ConnectRouter } from "@connectrpc/connect";
+import { Code, ConnectError, type ConnectRouter } from "@connectrpc/connect";
 import { connectNodeAdapter } from "@connectrpc/connect-node";
 import { McpServerSchema } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/api_pb";
 import { McpServerCommandController } from "@stigmer/protos/ai/stigmer/agentic/mcpserver/v1/command_pb";
@@ -69,7 +69,14 @@ beforeAll(async () => {
       getOAuthGrantStatus: () => create(GetOAuthGrantStatusOutputSchema, { connected: grantConnected }),
     });
     router.service(McpServerCommandController, {
-      connect: (req) => (connectCalls.push(req), updatedServer),
+      // 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) => {
+        if (req.org === "") throw new ConnectError("org – value length must be at least 1 characters", Code.InvalidArgument);
+        connectCalls.push(req);
+        return updatedServer;
+      },
     });
   };
 
@@ -102,6 +109,9 @@ describe("connect push path", () => {
 
     expect(connectCalls).toHaveLength(1);
     expect(connectCalls[0].mcpServerId).toBe("mcp_1");
+    // The org resolved by the command must ride along on ConnectInput — the
+    // backend requires it (issue #140: the CLI used to drop it entirely).
+    expect(connectCalls[0].org).toBe("acme");
     expect(connectCalls[0].runtimeEnv.GITHUB_TOKEN.value).toBe("ghp-override");
     expect(connectCalls[0].runtimeEnv.GITHUB_TOKEN.isSecret).toBe(true);
 

package/src/resources/connect/connect.ts

@@ -56,6 +56,7 @@ export async function connectMcpServer(client: Stigmer, opts: ConnectOptions): P
   const updated = await client.mcpServer.connect(
     create(ConnectInputSchema, {
       mcpServerId: server.metadata?.id ?? "",
+      org: opts.org,
       runtimeEnv: buildRuntimeEnv(server, opts.envOverrides),
     }),
   );