diff --git a/design/repo.md b/design/repo.md
index f0087d8b..e09fe9e5 100644
--- a/design/repo.md
+++ b/design/repo.md
@@ -51,6 +51,24 @@ The compiled swamp binary should include everything it needs to initialize a
 repository, including the skill files, so that they can be written out by the
 cli.
 
+## Superseded Skill Detection
+
+When the CLI binary is upgraded but `swamp repo upgrade` is not run, the
+repo retains old skill directories that have been consolidated in the new
+version. The `SUPERSEDED_SKILLS` constant in `repo_service.ts` lists these
+directory names.
+
+On every CLI startup (for repo-scoped commands), the CLI checks all enrolled
+tools' skill directories for superseded subdirectories. If any are found, a
+warning is emitted via the deferred-warning system:
+
+```
+WRN 2 superseded skill(s) found: swamp-data-query, swamp-extension-model. Run 'swamp repo upgrade' to update skills.
+```
+
+This check is non-fatal — it never blocks startup. `swamp repo upgrade`
+removes the superseded directories via `removeSupersededSkills()`.
+
 ## Repository Layout
 
 Source-of-truth files live in top-level directories tracked in git:
diff --git a/src/cli/mod.ts b/src/cli/mod.ts
index fb2ee3f7..f8df615e 100644
--- a/src/cli/mod.ts
+++ b/src/cli/mod.ts
@@ -87,6 +87,9 @@ import {
   RepoMarkerRepository,
 } from "../infrastructure/persistence/repo_marker_repository.ts";
 import { RepoPath } from "../domain/repo/repo_path.ts";
+import { detectSupersededSkills } from "../domain/repo/repo_service.ts";
+import { resolvePrimaryTool } from "../domain/repo/primary_tool.ts";
+import { SKILL_DIRS } from "../domain/repo/skill_dirs.ts";
 import { ExtensionAutoResolver } from "../domain/extensions/extension_auto_resolver.ts";
 import { ExtensionApiClient } from "../infrastructure/http/extension_api_client.ts";
 import { DEFAULT_SWAMP_CLUB_URL } from "../domain/auth/auth_credentials.ts";
@@ -358,6 +361,7 @@ export async function configureExtensionLoaders(
   );
 
   await checkForMissingPulledExtensions(repoDir, marker, deferredWarnings);
+  await checkForSupersededSkills(repoDir, marker, deferredWarnings);
 }
 
 /**
@@ -424,7 +428,14 @@ export function commandNeedsLoaderSetup(args: string[]): boolean {
 
 /** A deferred warning message to emit after logging is initialized. */
 export interface DeferredWarning {
-  kind: "model" | "vault" | "driver" | "datastore" | "report" | "extensions";
+  kind:
+    | "model"
+    | "vault"
+    | "driver"
+    | "datastore"
+    | "report"
+    | "extensions"
+    | "skills";
   file: string;
   error: string;
 }
@@ -843,6 +854,37 @@ async function checkForMissingPulledExtensions(
   }
 }
 
+async function checkForSupersededSkills(
+  repoDir: string,
+  marker: RepoMarkerData | null,
+  deferredWarnings: DeferredWarning[],
+): Promise<void> {
+  try {
+    const tools = marker?.tools?.length
+      ? marker.tools
+      : [resolvePrimaryTool(marker)];
+    const allStale = new Set<string>();
+    for (const tool of tools) {
+      const dir = SKILL_DIRS[tool];
+      if (!dir) continue;
+      const stale = await detectSupersededSkills(join(repoDir, dir));
+      for (const name of stale) allStale.add(name);
+    }
+    if (allStale.size > 0) {
+      const names = [...allStale].sort();
+      deferredWarnings.push({
+        kind: "skills",
+        file: repoDir,
+        error: `${names.length} superseded skill(s) found: ${
+          names.join(", ")
+        }. Run 'swamp repo upgrade' to update skills.`,
+      });
+    }
+  } catch {
+    // Non-fatal — don't block startup for skill dir read errors
+  }
+}
+
 /** Default telemetry endpoint */
 const DEFAULT_TELEMETRY_ENDPOINT = "https://telemetry.swamp-club.com";
 
@@ -1111,7 +1153,7 @@ export async function runCli(args: string[]): Promise<void> {
 
       // Emit deferred warnings now that logging is initialized
       for (const warning of deferredWarnings) {
-        if (warning.kind === "extensions") {
+        if (warning.kind === "extensions" || warning.kind === "skills") {
           logger.warn`${warning.error}`;
         } else {
           logger
diff --git a/src/domain/repo/repo_service.ts b/src/domain/repo/repo_service.ts
index 290c1398..df74be0f 100644
--- a/src/domain/repo/repo_service.ts
+++ b/src/domain/repo/repo_service.ts
@@ -104,7 +104,7 @@ function formatToolsList(tools: AiTool[]): string {
   return tools.length === 0 ? "none" : tools.join(", ");
 }
 
-const SUPERSEDED_SKILLS = [
+export const SUPERSEDED_SKILLS: readonly string[] = [
   "swamp-extension-model",
   "swamp-extension-vault",
   "swamp-extension-driver",
@@ -125,6 +125,21 @@ async function removeSupersededSkills(skillsDir: string): Promise<void> {
   }
 }
 
+export async function detectSupersededSkills(
+  skillsDir: string,
+): Promise<string[]> {
+  const found: string[] = [];
+  for (const name of SUPERSEDED_SKILLS) {
+    try {
+      await Deno.stat(join(skillsDir, name));
+      found.push(name);
+    } catch {
+      // Not found — not stale
+    }
+  }
+  return found;
+}
+
 /**
  * Pulled extensions present for one of the previously-enrolled tools that
  * were NOT copied into a newly-added tool's skills directory. Surfaced so
diff --git a/src/domain/repo/repo_service_test.ts b/src/domain/repo/repo_service_test.ts
index 64ec76eb..9e5ce9e0 100644
--- a/src/domain/repo/repo_service_test.ts
+++ b/src/domain/repo/repo_service_test.ts
@@ -19,7 +19,7 @@
 
 import { assertEquals, assertRejects, assertStringIncludes } from "@std/assert";
 import { join } from "@std/path";
-import { RepoService } from "./repo_service.ts";
+import { detectSupersededSkills, RepoService } from "./repo_service.ts";
 import { RepoPath } from "./repo_path.ts";
 import {
   type AiTool,
@@ -2484,3 +2484,27 @@ Deno.test("RepoService.upgrade adding a tool with no pulled extensions emits no
     assertEquals(result.extensionsToReinstall, []);
   });
 });
+
+Deno.test("detectSupersededSkills: returns empty when no superseded dirs exist", async () => {
+  await withTempDir(async (tempDir) => {
+    const result = await detectSupersededSkills(tempDir);
+    assertEquals(result, []);
+  });
+});
+
+Deno.test("detectSupersededSkills: detects superseded skill directories", async () => {
+  await withTempDir(async (tempDir) => {
+    await Deno.mkdir(join(tempDir, "swamp-extension-model"));
+    await Deno.mkdir(join(tempDir, "swamp-data-query"));
+    // Non-superseded dir should be ignored
+    await Deno.mkdir(join(tempDir, "swamp-model"));
+
+    const result = await detectSupersededSkills(tempDir);
+    assertEquals(result.sort(), ["swamp-data-query", "swamp-extension-model"]);
+  });
+});
+
+Deno.test("detectSupersededSkills: returns empty for nonexistent directory", async () => {
+  const result = await detectSupersededSkills("/tmp/nonexistent-dir-326");
+  assertEquals(result, []);
+});