diff --git a/src/cli/commands/extension_fmt.ts b/src/cli/commands/extension_fmt.ts
index b8c5101a..e26249d4 100644
--- a/src/cli/commands/extension_fmt.ts
+++ b/src/cli/commands/extension_fmt.ts
@@ -31,7 +31,10 @@ import {
   resolveRepoDir,
 } from "../context.ts";
 import { requireInitializedRepo } from "../repo_context.ts";
-import { resolveExtensionFiles } from "../resolve_extension_files.ts";
+import {
+  isPulledExtensionManifest,
+  resolveExtensionFiles,
+} from "../resolve_extension_files.ts";
 import { UserError } from "../../domain/errors.ts";
 
 interface ExtensionFmtOptions extends GlobalOptions {
@@ -60,14 +63,19 @@ export const extensionFmtCommand = new Command()
     const cliCtx = createContext(options, ["extension", "fmt"]);
     cliCtx.logger.debug`Starting extension fmt`;
 
-    // 1. Validate repo
     const repoDir = resolveRepoDir(options.repoDir);
+    if (isPulledExtensionManifest(repoDir, manifestPath)) {
+      throw new UserError(
+        "Cannot run fmt on a pulled extension. Pulled extensions are read-only " +
+          "copies from the registry. To format a local extension, point at its manifest " +
+          "under your extensions/ directory instead.",
+      );
+    }
+
     const { repoContext } = await requireInitializedRepo({
       repoDir,
       outputMode: cliCtx.outputMode,
     });
-
-    // 2. Resolve extension files (manifest, models, workflows, additional files)
     const {
       allModelFiles,
       allVaultFiles,
diff --git a/src/cli/commands/extension_quality.ts b/src/cli/commands/extension_quality.ts
index dfbcc867..efccb5cd 100644
--- a/src/cli/commands/extension_quality.ts
+++ b/src/cli/commands/extension_quality.ts
@@ -35,7 +35,10 @@ import {
   resolveRepoDir,
 } from "../context.ts";
 import { requireInitializedRepo } from "../repo_context.ts";
-import { resolveExtensionFiles } from "../resolve_extension_files.ts";
+import {
+  isPulledExtensionManifest,
+  resolveExtensionFiles,
+} from "../resolve_extension_files.ts";
 import { UserError } from "../../domain/errors.ts";
 
 interface ExtensionQualityOptions extends GlobalOptions {
@@ -94,6 +97,14 @@ export const extensionQualityCommand = new Command()
       cliCtx.logger.debug`Starting extension quality`;
 
       const repoDir = resolveRepoDir(options.repoDir);
+      if (isPulledExtensionManifest(repoDir, manifestPath)) {
+        throw new UserError(
+          "Cannot run quality on a pulled extension. Pulled extensions are read-only " +
+            "copies from the registry. To score a local extension, point at its manifest " +
+            "under your extensions/ directory instead.",
+        );
+      }
+
       const { repoContext } = await requireInitializedRepo({
         repoDir,
         outputMode: cliCtx.outputMode,
diff --git a/src/cli/resolve_extension_files.ts b/src/cli/resolve_extension_files.ts
index f94b79e2..2fe2b949 100644
--- a/src/cli/resolve_extension_files.ts
+++ b/src/cli/resolve_extension_files.ts
@@ -99,6 +99,18 @@ function normalizeAdditionalFileEntry(entry: string): string {
   return segments.join("/").toLowerCase();
 }
 
+export function isPulledExtensionManifest(
+  repoDir: string,
+  manifestPath: string,
+): boolean {
+  const absolute = isAbsolute(manifestPath)
+    ? manifestPath
+    : resolve(repoDir, manifestPath);
+  const pulledRoot = join(resolve(repoDir), ".swamp", "pulled-extensions");
+  return resolve(absolute).startsWith(pulledRoot + "/") ||
+    resolve(absolute).startsWith(pulledRoot + "\\");
+}
+
 export async function resolveExtensionFiles(
   ctx: ResolveExtensionFilesContext,
 ): Promise<ResolvedExtensionFiles> {
diff --git a/src/cli/resolve_extension_files_test.ts b/src/cli/resolve_extension_files_test.ts
index 968340c8..cdde4d1b 100644
--- a/src/cli/resolve_extension_files_test.ts
+++ b/src/cli/resolve_extension_files_test.ts
@@ -21,7 +21,10 @@ import { assertEquals, assertRejects } from "@std/assert";
 import { join } from "@std/path";
 import { stringify as stringifyYaml } from "@std/yaml";
 import { getLogger } from "@logtape/logtape";
-import { resolveExtensionFiles } from "./resolve_extension_files.ts";
+import {
+  isPulledExtensionManifest,
+  resolveExtensionFiles,
+} from "./resolve_extension_files.ts";
 import { UserError } from "../domain/errors.ts";
 import type { RepositoryContext } from "../infrastructure/persistence/repository_factory.ts";
 
@@ -858,3 +861,36 @@ Deno.test("resolveExtensionFiles default paths.base preserves swamp-extensions p
     assertEquals(result.modelEntryPoints, [join(modelsDir, "backups.ts")]);
   });
 });
+
+// ── isPulledExtensionManifest ──────────────────────────────────────────
+
+Deno.test("isPulledExtensionManifest: returns true for absolute path under .swamp/pulled-extensions", () => {
+  const repoDir = "/repo";
+  const manifestPath =
+    "/repo/.swamp/pulled-extensions/@bixu/wheelshop/manifest.yaml";
+  assertEquals(isPulledExtensionManifest(repoDir, manifestPath), true);
+});
+
+Deno.test("isPulledExtensionManifest: returns true for relative path under .swamp/pulled-extensions", () => {
+  const repoDir = "/repo";
+  const manifestPath = ".swamp/pulled-extensions/@bixu/wheelshop/manifest.yaml";
+  assertEquals(isPulledExtensionManifest(repoDir, manifestPath), true);
+});
+
+Deno.test("isPulledExtensionManifest: returns false for local extension manifest", () => {
+  const repoDir = "/repo";
+  const manifestPath = "extensions/models/my-model/manifest.yaml";
+  assertEquals(isPulledExtensionManifest(repoDir, manifestPath), false);
+});
+
+Deno.test("isPulledExtensionManifest: returns false for absolute local extension manifest", () => {
+  const repoDir = "/repo";
+  const manifestPath = "/repo/extensions/models/my-model/manifest.yaml";
+  assertEquals(isPulledExtensionManifest(repoDir, manifestPath), false);
+});
+
+Deno.test("isPulledExtensionManifest: returns false for path containing pulled-extensions outside .swamp", () => {
+  const repoDir = "/repo";
+  const manifestPath = "/repo/pulled-extensions/manifest.yaml";
+  assertEquals(isPulledExtensionManifest(repoDir, manifestPath), false);
+});