diff --git a/packages/cli/src/commands/install.spec.ts b/packages/cli/src/commands/install.spec.ts
index db4abda..4c6f25e 100644
--- a/packages/cli/src/commands/install.spec.ts
+++ b/packages/cli/src/commands/install.spec.ts
@@ -49,7 +49,8 @@ vi.mock("@codemcp/ade-harnesses", () => ({
       "kiro",
       "opencode"
     ]),
-  installSkills: vi.fn().mockResolvedValue(undefined)
+  installSkills: vi.fn().mockResolvedValue(undefined),
+  writeInlineSkills: vi.fn().mockResolvedValue([])
 }));
 
 import * as clack from "@clack/prompts";
diff --git a/packages/cli/src/commands/install.ts b/packages/cli/src/commands/install.ts
index 460d646..5d0831d 100644
--- a/packages/cli/src/commands/install.ts
+++ b/packages/cli/src/commands/install.ts
@@ -3,7 +3,8 @@ import { readLockFile } from "@codemcp/ade-core";
 import {
   getHarnessWriter,
   getHarnessIds,
-  installSkills
+  installSkills,
+  writeInlineSkills
 } from "@codemcp/ade-harnesses";
 
 export async function runInstall(
@@ -41,6 +42,15 @@ export async function runInstall(
     }
   }
 
+  const modifiedSkills = await writeInlineSkills(logicalConfig, projectRoot);
+  if (modifiedSkills.length > 0) {
+    clack.log.warn(
+      `The following skills have been locally modified and will NOT be updated:\n` +
+        modifiedSkills.map((s) => `  - ${s}`).join("\n") +
+        `\n\nTo use the latest defaults, remove .ade/skills/ and re-run install.`
+    );
+  }
+
   await installSkills(logicalConfig.skills, projectRoot);
 
   if (logicalConfig.knowledge_sources.length > 0) {
diff --git a/packages/cli/src/commands/setup.spec.ts b/packages/cli/src/commands/setup.spec.ts
index 5e43589..97d0cae 100644
--- a/packages/cli/src/commands/setup.spec.ts
+++ b/packages/cli/src/commands/setup.spec.ts
@@ -51,7 +51,8 @@ vi.mock("@codemcp/ade-harnesses", () => ({
     install: vi.fn().mockResolvedValue(undefined)
   }),
   getHarnessIds: vi.fn().mockReturnValue(["claude-code"]),
-  installSkills: vi.fn().mockResolvedValue(undefined)
+  installSkills: vi.fn().mockResolvedValue(undefined),
+  writeInlineSkills: vi.fn().mockResolvedValue([])
 }));
 
 import * as clack from "@clack/prompts";
diff --git a/packages/cli/src/commands/setup.ts b/packages/cli/src/commands/setup.ts
index 493a210..95930d2 100644
--- a/packages/cli/src/commands/setup.ts
+++ b/packages/cli/src/commands/setup.ts
@@ -18,7 +18,8 @@ import {
 import {
   allHarnessWriters,
   getHarnessWriter,
-  installSkills
+  installSkills,
+  writeInlineSkills
 } from "@codemcp/ade-harnesses";
 
 export async function runSetup(
@@ -162,6 +163,15 @@ export async function runSetup(
     }
   }
 
+  const modifiedSkills = await writeInlineSkills(logicalConfig, projectRoot);
+  if (modifiedSkills.length > 0) {
+    clack.log.warn(
+      `The following skills have been locally modified and will NOT be updated:\n` +
+        modifiedSkills.map((s) => `  - ${s}`).join("\n") +
+        `\n\nTo use the latest defaults, remove .ade/skills/ and re-run setup.`
+    );
+  }
+
   await installSkills(logicalConfig.skills, projectRoot);
 
   if (logicalConfig.knowledge_sources.length > 0) {
diff --git a/packages/harnesses/src/index.ts b/packages/harnesses/src/index.ts
index 9087d1e..f2d3643 100644
--- a/packages/harnesses/src/index.ts
+++ b/packages/harnesses/src/index.ts
@@ -1,5 +1,6 @@
 export type { HarnessWriter } from "./types.js";
 export { installSkills } from "./skills-installer.js";
+export { writeInlineSkills } from "./util.js";
 
 export { universalWriter } from "./writers/universal.js";
 export { claudeCodeWriter } from "./writers/claude-code.js";
diff --git a/packages/harnesses/src/util.ts b/packages/harnesses/src/util.ts
index d5e3642..45b8a32 100644
--- a/packages/harnesses/src/util.ts
+++ b/packages/harnesses/src/util.ts
@@ -185,12 +185,14 @@ export async function writeGitHooks(
 export async function writeInlineSkills(
   config: LogicalConfig,
   projectRoot: string
-): Promise<void> {
+): Promise<string[]> {
+  const modified: string[] = [];
+
   for (const skill of config.skills) {
     if (!("body" in skill)) continue;
 
     const skillDir = join(projectRoot, ".ade", "skills", skill.name);
-    await mkdir(skillDir, { recursive: true });
+    const skillPath = join(skillDir, "SKILL.md");
 
     const frontmatter = [
       "---",
@@ -199,10 +201,21 @@ export async function writeInlineSkills(
       "---"
     ].join("\n");
 
-    await writeFile(
-      join(skillDir, "SKILL.md"),
-      `${frontmatter}\n\n${skill.body}\n`,
-      "utf-8"
-    );
+    const expected = `${frontmatter}\n\n${skill.body}\n`;
+
+    try {
+      const existing = await readFile(skillPath, "utf-8");
+      if (existing !== expected) {
+        modified.push(skill.name);
+        continue;
+      }
+    } catch {
+      // File doesn't exist yet — fall through to write
+    }
+
+    await mkdir(skillDir, { recursive: true });
+    await writeFile(skillPath, expected, "utf-8");
   }
+
+  return modified;
 }
diff --git a/packages/harnesses/src/writers/claude-code.spec.ts b/packages/harnesses/src/writers/claude-code.spec.ts
index fc1efc2..656b17c 100644
--- a/packages/harnesses/src/writers/claude-code.spec.ts
+++ b/packages/harnesses/src/writers/claude-code.spec.ts
@@ -8,6 +8,7 @@ import type {
   PermissionPolicy
 } from "@codemcp/ade-core";
 import { claudeCodeWriter } from "./claude-code.js";
+import { writeInlineSkills } from "../util.js";
 
 function autonomyPolicy(profile: AutonomyProfile): PermissionPolicy {
   switch (profile) {
@@ -290,7 +291,7 @@ describe("claudeCodeWriter", () => {
     });
   });
 
-  it("writes inline SKILL.md files", async () => {
+  it("writes inline SKILL.md files via writeInlineSkills", async () => {
     const config: LogicalConfig = {
       mcp_servers: [],
       instructions: [],
@@ -307,7 +308,7 @@ describe("claudeCodeWriter", () => {
       setup_notes: []
     };
 
-    await claudeCodeWriter.install(config, dir);
+    await writeInlineSkills(config, dir);
 
     const skillMd = await readFile(
       join(dir, ".ade", "skills", "tanstack-architecture", "SKILL.md"),
diff --git a/packages/harnesses/src/writers/claude-code.ts b/packages/harnesses/src/writers/claude-code.ts
index e0b6609..9f584a7 100644
--- a/packages/harnesses/src/writers/claude-code.ts
+++ b/packages/harnesses/src/writers/claude-code.ts
@@ -6,7 +6,6 @@ import {
   writeJson,
   writeMcpServers,
   writeAgentMd,
-  writeInlineSkills,
   writeGitHooks
 } from "../util.js";
 import { allowsCapability, keepsWebOnAsk } from "../permission-policy.js";
@@ -27,7 +26,6 @@ export const claudeCodeWriter: HarnessWriter = {
     });
 
     await writeClaudeSettings(config, projectRoot);
-    await writeInlineSkills(config, projectRoot);
     await writeGitHooks(config.git_hooks, projectRoot);
   }
 };