diff --git a/packages/app/src/desktop/components/integrations-section.tsx b/packages/app/src/desktop/components/integrations-section.tsx
index 4fcddef99..2b66f357b 100644
--- a/packages/app/src/desktop/components/integrations-section.tsx
+++ b/packages/app/src/desktop/components/integrations-section.tsx
@@ -8,11 +8,7 @@ import { SettingsSection } from "@/screens/settings/settings-section";
 import { Button } from "@/components/ui/button";
 import { openExternalUrl } from "@/utils/open-external-url";
 import { confirmDialog } from "@/utils/confirm-dialog";
-import {
-  shouldUseDesktopDaemon,
-  type SkillOp,
-  type SkillsStatus,
-} from "@/desktop/daemon/desktop-daemon";
+import { shouldUseDesktopDaemon, type SkillsStatus } from "@/desktop/daemon/desktop-daemon";
 import { useCliInstall, useSkillsStatus } from "@/desktop/hooks/use-install-status";
 
 const CLI_DOCS_URL = "https://paseo.sh/docs/cli";
@@ -21,21 +17,6 @@ const ROW_WITH_BORDER_STYLE = [settingsStyles.row, settingsStyles.rowBorder];
 const UNINSTALL_MESSAGE =
   "Removes all Paseo orchestration skills from ~/.agents, ~/.claude, ~/.codex.";
 
-const OP_KIND_ORDER: Record<SkillOp["kind"], number> = { add: 0, update: 1, delete: 2 };
-const OP_KIND_LABEL: Record<SkillOp["kind"], string> = {
-  add: "Add skill",
-  update: "Update skill",
-  delete: "Delete skill",
-};
-
-function formatUpdateMessage(ops: readonly SkillOp[]): string {
-  const sorted = [...ops].sort((a, b) => {
-    const kindOrder = OP_KIND_ORDER[a.kind] - OP_KIND_ORDER[b.kind];
-    return kindOrder !== 0 ? kindOrder : a.name.localeCompare(b.name);
-  });
-  return sorted.map((op) => `${OP_KIND_LABEL[op.kind]} ${op.name}`).join("\n");
-}
-
 export function IntegrationsSection() {
   const { theme } = useUnistyles();
   const showSection = shouldUseDesktopDaemon();
@@ -75,15 +56,8 @@ export function IntegrationsSection() {
 
   const handleUpdateSkills = useCallback(async () => {
     if (isSkillsWorking) return;
-    const ops = skillsStatus?.ops ?? [];
-    const confirmed = await confirmDialog({
-      title: "Update Paseo skills?",
-      message: ops.length > 0 ? formatUpdateMessage(ops) : "Sync bundled skills to your machine.",
-      confirmLabel: "Update",
-    });
-    if (!confirmed) return;
     await updateSkills();
-  }, [isSkillsWorking, skillsStatus, updateSkills]);
+  }, [isSkillsWorking, updateSkills]);
 
   const handleUninstallSkills = useCallback(async () => {
     if (isSkillsWorking) return;
diff --git a/packages/desktop/src/desktop-startup.test.ts b/packages/desktop/src/desktop-startup.test.ts
index c766a22a7..c447c216d 100644
--- a/packages/desktop/src/desktop-startup.test.ts
+++ b/packages/desktop/src/desktop-startup.test.ts
@@ -36,6 +36,24 @@ describe("desktop startup", () => {
     expect(calls).toEqual(["cli", "env", "gui"]);
   });
 
+  it("starts skills auto-update after GUI startup", async () => {
+    const calls: string[] = [];
+    await runDesktopStartup({
+      hasPendingOpenProjectPath: false,
+      runCliPassthroughIfRequested: vi.fn(async () => {
+        calls.push("cli");
+        return false;
+      }),
+      inheritLoginShellEnv: vi.fn(() => calls.push("env")),
+      bootstrapGui: vi.fn(async () => {
+        calls.push("gui");
+      }),
+      autoUpdateInstalledSkills: vi.fn(() => calls.push("skills")),
+    });
+
+    expect(calls).toEqual(["cli", "env", "gui", "skills"]);
+  });
+
   it("does not route open-project launches through CLI passthrough", async () => {
     const runCliPassthroughIfRequested = vi.fn(async () => true);
     const calls: string[] = [];
diff --git a/packages/desktop/src/desktop-startup.ts b/packages/desktop/src/desktop-startup.ts
index 6ee8a0f0f..25943e342 100644
--- a/packages/desktop/src/desktop-startup.ts
+++ b/packages/desktop/src/desktop-startup.ts
@@ -3,6 +3,7 @@ export interface DesktopStartupDependencies {
   runCliPassthroughIfRequested: () => Promise<boolean>;
   inheritLoginShellEnv: () => void;
   bootstrapGui: () => Promise<void>;
+  autoUpdateInstalledSkills?: () => void;
 }
 
 export async function runDesktopStartup(deps: DesktopStartupDependencies): Promise<void> {
@@ -12,4 +13,5 @@ export async function runDesktopStartup(deps: DesktopStartupDependencies): Promi
 
   deps.inheritLoginShellEnv();
   await deps.bootstrapGui();
+  deps.autoUpdateInstalledSkills?.();
 }
diff --git a/packages/desktop/src/integrations/skills/index.ts b/packages/desktop/src/integrations/skills/index.ts
index 5020b97f0..d568e7436 100644
--- a/packages/desktop/src/integrations/skills/index.ts
+++ b/packages/desktop/src/integrations/skills/index.ts
@@ -1,4 +1,5 @@
 export {
+  autoUpdateInstalledSkills,
   getSkillsStatus,
   installSkills,
   uninstallSkills,
diff --git a/packages/desktop/src/integrations/skills/operations.test.ts b/packages/desktop/src/integrations/skills/operations.test.ts
index ee8617492..a31a24266 100644
--- a/packages/desktop/src/integrations/skills/operations.test.ts
+++ b/packages/desktop/src/integrations/skills/operations.test.ts
@@ -11,6 +11,7 @@ vi.mock("electron", () => ({
 }));
 
 import {
+  autoUpdateInstalledSkills,
   getSkillsStatus,
   installSkills,
   PASEO_SKILL_NAMES,
@@ -60,6 +61,18 @@ async function writeOnDiskSkill(
   await writeFiles(path.join(agentsDir, name), files);
 }
 
+async function writeOnDiskSkillToAllTargets(
+  targets: SkillTargets,
+  name: string,
+  files: Record<string, string>,
+): Promise<void> {
+  await Promise.all([
+    writeOnDiskSkill(targets.agentsDir, name, files),
+    writeOnDiskSkill(targets.claudeDir, name, files),
+    writeOnDiskSkill(targets.codexDir, name, files),
+  ]);
+}
+
 async function writeCurrentBundle(sourceDir: string): Promise<void> {
   await writeBundleSkill(sourceDir, "paseo", { "SKILL.md": "paseo-v1" });
   await writeBundleSkill(sourceDir, "paseo-loop", { "SKILL.md": "loop-v1" });
@@ -112,8 +125,22 @@ describe("getSkillsStatus", () => {
 
   it("returns up-to-date when every bundled skill matches on disk", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
-    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "paseo-v1" });
-    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo-loop", { "SKILL.md": "loop-v1" });
+
+    const status = await getSkillsStatus(sandbox.targets);
+
+    expect(status).toEqual({ state: "up-to-date", ops: [] });
+  });
+
+  it("ignores user-added files inside current managed skill dirs", async () => {
+    await writeCurrentBundle(sandbox.targets.sourceDir);
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", {
+      "SKILL.md": "paseo-v1",
+      "my-context.md": "user context",
+    });
 
     const status = await getSkillsStatus(sandbox.targets);
 
@@ -123,7 +150,24 @@ describe("getSkillsStatus", () => {
   it("returns drift with a single update op when one bundled file diverges", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
     await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "stale" });
+    await writeOnDiskSkill(sandbox.targets.claudeDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo-loop", { "SKILL.md": "loop-v1" });
+
+    const status = await getSkillsStatus(sandbox.targets);
+
+    expect(status.state).toBe("drift");
+    expect(status.ops).toEqual([{ kind: "update", name: "paseo" }]);
+  });
+
+  it("returns drift when a secondary agent target is stale", async () => {
+    await writeCurrentBundle(sandbox.targets.sourceDir);
+    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "paseo-v1" });
     await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkill(sandbox.targets.claudeDir, "paseo", { "SKILL.md": "stale" });
+    await writeOnDiskSkill(sandbox.targets.claudeDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo-loop", { "SKILL.md": "loop-v1" });
 
     const status = await getSkillsStatus(sandbox.targets);
 
@@ -133,7 +177,7 @@ describe("getSkillsStatus", () => {
 
   it("returns drift with add ops for the bundled skills missing from disk", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
-    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo", { "SKILL.md": "paseo-v1" });
 
     const status = await getSkillsStatus(sandbox.targets);
 
@@ -143,8 +187,8 @@ describe("getSkillsStatus", () => {
 
   it("returns drift with a delete op for a legacy skill name still on disk", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
-    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "paseo-v1" });
-    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkillToAllTargets(sandbox.targets, "paseo-loop", { "SKILL.md": "loop-v1" });
     await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-chat", { "SKILL.md": "chat-old" });
 
     const status = await getSkillsStatus(sandbox.targets);
@@ -156,6 +200,8 @@ describe("getSkillsStatus", () => {
   it("emits add + update + delete ops sorted by name when state is mixed", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
     await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "stale" });
+    await writeOnDiskSkill(sandbox.targets.claudeDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo", { "SKILL.md": "paseo-v1" });
     await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-chat", { "SKILL.md": "chat-old" });
 
     const status = await getSkillsStatus(sandbox.targets);
@@ -226,6 +272,51 @@ describe("installSkills / updateSkills", () => {
     }
   });
 
+  it("repairs secondary agent targets even when agents skills are current", async () => {
+    await writeCurrentBundle(sandbox.targets.sourceDir);
+    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+    await writeOnDiskSkill(sandbox.targets.claudeDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo", { "SKILL.md": "paseo-v1" });
+    await writeOnDiskSkill(sandbox.targets.codexDir, "paseo-loop", { "SKILL.md": "loop-v1" });
+
+    const status = await updateSkills(sandbox.targets);
+
+    expect(status).toEqual({ state: "up-to-date", ops: [] });
+    expect(
+      await fs.readFile(path.join(sandbox.targets.claudeDir, "paseo-loop", "SKILL.md"), "utf-8"),
+    ).toBe("loop-v1");
+  });
+
+  it("auto-updates drifted installed skills", async () => {
+    await writeCurrentBundle(sandbox.targets.sourceDir);
+    await writeOnDiskSkill(sandbox.targets.agentsDir, "paseo", { "SKILL.md": "stale" });
+
+    const status = await autoUpdateInstalledSkills(sandbox.targets);
+
+    expect(status).toEqual({ state: "up-to-date", ops: [] });
+    expect(
+      await fs.readFile(path.join(sandbox.targets.agentsDir, "paseo", "SKILL.md"), "utf-8"),
+    ).toBe("paseo-v1");
+  });
+
+  it("does not auto-install skills on a clean machine", async () => {
+    await writeCurrentBundle(sandbox.targets.sourceDir);
+
+    const status = await autoUpdateInstalledSkills(sandbox.targets);
+
+    expect(status).toEqual({
+      state: "not-installed",
+      ops: [
+        { kind: "add", name: "paseo" },
+        { kind: "add", name: "paseo-loop" },
+      ],
+    });
+    expect(await pathExists(path.join(sandbox.targets.agentsDir, "paseo"))).toBe(false);
+    expect(await pathExists(path.join(sandbox.targets.claudeDir, "paseo"))).toBe(false);
+    expect(await pathExists(path.join(sandbox.targets.codexDir, "paseo"))).toBe(false);
+  });
+
   it("is idempotent — running install twice keeps state at up-to-date", async () => {
     await writeCurrentBundle(sandbox.targets.sourceDir);
 
diff --git a/packages/desktop/src/integrations/skills/operations.ts b/packages/desktop/src/integrations/skills/operations.ts
index 8acaa17b7..35fd6f060 100644
--- a/packages/desktop/src/integrations/skills/operations.ts
+++ b/packages/desktop/src/integrations/skills/operations.ts
@@ -41,6 +41,7 @@ export const PASEO_SKILL_NAMES = [
 ] as const;
 
 type SkillFiles = Map<string, string>;
+type TargetSkills = Map<string, SkillFiles>;
 
 function resolveSkillTargets(): SkillTargets {
   return {
@@ -74,23 +75,34 @@ async function hashSkills(rootDir: string): Promise<Map<string, SkillFiles>> {
   return out;
 }
 
-function diff(bundle: Map<string, SkillFiles>, disk: Map<string, SkillFiles>): SkillOp[] {
+function diff(bundle: TargetSkills, disks: readonly TargetSkills[]): SkillOp[] {
   const ops: SkillOp[] = [];
   for (const name of PASEO_SKILL_NAMES) {
     const b = bundle.get(name);
-    const d = disk.get(name);
-    if (b && !d) ops.push({ kind: "add", name });
-    else if (b && d && !filesEqual(b, d)) ops.push({ kind: "update", name });
-    else if (!b && d) ops.push({ kind: "delete", name });
+    const targetFiles = disks.map((disk) => disk.get(name));
+    const installedTargets = targetFiles.filter(
+      (files): files is SkillFiles => files !== undefined,
+    );
+    if (b) {
+      const missingTargets = installedTargets.length < disks.length;
+      const changedTargets = installedTargets.some((files) => !bundleFilesMatch(b, files));
+      if (missingTargets) ops.push({ kind: "add", name });
+      else if (changedTargets) ops.push({ kind: "update", name });
+    } else if (installedTargets.length > 0) {
+      ops.push({ kind: "delete", name });
+    }
   }
   ops.sort((a, b) => compareStrings(a.name, b.name));
   return ops;
 }
 
-function filesEqual(a: SkillFiles, b: SkillFiles): boolean {
-  if (a.size !== b.size) return false;
-  for (const [rel, sha] of a) {
-    if (b.get(rel) !== sha) return false;
+function hasInstalledPaseoSkill(disks: readonly TargetSkills[]): boolean {
+  return disks.some((disk) => disk.size > 0);
+}
+
+function bundleFilesMatch(bundle: SkillFiles, disk: SkillFiles): boolean {
+  for (const [rel, sha] of bundle) {
+    if (disk.get(rel) !== sha) return false;
   }
   return true;
 }
@@ -107,16 +119,25 @@ function compareStrings(a: string, b: string): number {
 
 export async function getSkillsStatus(targets?: SkillTargets): Promise<SkillsStatus> {
   const t = targets ?? resolveSkillTargets();
-  const [bundle, disk] = await Promise.all([hashSkills(t.sourceDir), hashSkills(t.agentsDir)]);
-  const ops = diff(bundle, disk);
+  const [bundle, agentsDisk, claudeDisk, codexDisk] = await Promise.all([
+    hashSkills(t.sourceDir),
+    hashSkills(t.agentsDir),
+    hashSkills(t.claudeDir),
+    hashSkills(t.codexDir),
+  ]);
+  const disks = [agentsDisk, claudeDisk, codexDisk];
+  const ops = diff(bundle, disks);
 
-  if (disk.size === 0) return { state: "not-installed", ops };
+  if (!hasInstalledPaseoSkill(disks)) return { state: "not-installed", ops };
   if (ops.length === 0) return { state: "up-to-date", ops };
   return { state: "drift", ops };
 }
 
-async function applySkills(targets: SkillTargets): Promise<SkillsStatus> {
-  const status = await getSkillsStatus(targets);
+async function applySkills(
+  targets: SkillTargets,
+  initialStatus?: SkillsStatus,
+): Promise<SkillsStatus> {
+  const status = initialStatus ?? (await getSkillsStatus(targets));
 
   const writes = status.ops
     .filter((op) => op.kind === "add" || op.kind === "update")
@@ -151,6 +172,13 @@ export async function updateSkills(targets?: SkillTargets): Promise<SkillsStatus
   return applySkills(targets ?? resolveSkillTargets());
 }
 
+export async function autoUpdateInstalledSkills(targets?: SkillTargets): Promise<SkillsStatus> {
+  const t = targets ?? resolveSkillTargets();
+  const status = await getSkillsStatus(t);
+  if (status.state !== "drift") return status;
+  return applySkills(t, status);
+}
+
 export async function uninstallSkills(targets?: SkillTargets): Promise<SkillsStatus> {
   const t = targets ?? resolveSkillTargets();
   for (const name of PASEO_SKILL_NAMES) {
diff --git a/packages/desktop/src/integrations/skills/sync.test.ts b/packages/desktop/src/integrations/skills/sync.test.ts
index 52c7bbbcc..0bd7e4915 100644
--- a/packages/desktop/src/integrations/skills/sync.test.ts
+++ b/packages/desktop/src/integrations/skills/sync.test.ts
@@ -137,12 +137,23 @@ describe("syncSkills", () => {
     expect(await fs.readFile(path.join(customSkill, "SKILL.md"), "utf-8")).toBe("user content");
   });
 
-  it("does not delete files on disk that are no longer in the bundle", async () => {
-    await writeBundleSkill(sandbox.sourceDir, "paseo", { "SKILL.md": "new" });
+  it("removes stale files previously written to managed skill dirs", async () => {
+    await writeBundleSkill(sandbox.sourceDir, "paseo", {
+      "SKILL.md": "old",
+      "references/stale.md": "stale",
+    });
     const onDiskSkill = path.join(sandbox.agentsDir, "paseo");
-    await fs.mkdir(path.join(onDiskSkill, "references"), { recursive: true });
-    await fs.writeFile(path.join(onDiskSkill, "SKILL.md"), "old");
-    await fs.writeFile(path.join(onDiskSkill, "references", "stale.md"), "stale");
+
+    await syncSkills({
+      sourceDir: sandbox.sourceDir,
+      agentsDir: sandbox.agentsDir,
+      claudeDir: sandbox.claudeDir,
+      codexDir: sandbox.codexDir,
+      skillNames: ["paseo"],
+    });
+
+    await fs.rm(path.join(sandbox.sourceDir, "paseo"), { recursive: true, force: true });
+    await writeBundleSkill(sandbox.sourceDir, "paseo", { "SKILL.md": "new" });
 
     await syncSkills({
       sourceDir: sandbox.sourceDir,
@@ -153,8 +164,32 @@ describe("syncSkills", () => {
     });
 
     expect(await fs.readFile(path.join(onDiskSkill, "SKILL.md"), "utf-8")).toBe("new");
-    expect(await fs.readFile(path.join(onDiskSkill, "references", "stale.md"), "utf-8")).toBe(
-      "stale",
+    await expect(fs.access(path.join(onDiskSkill, "references", "stale.md"))).rejects.toThrow();
+    await expect(fs.access(path.join(onDiskSkill, "references"))).rejects.toThrow();
+  });
+
+  it("preserves user-added files in managed skill dirs", async () => {
+    await writeBundleSkill(sandbox.sourceDir, "paseo", { "SKILL.md": "new" });
+    const onDiskSkill = path.join(sandbox.agentsDir, "paseo");
+    await fs.mkdir(path.join(onDiskSkill, "references"), { recursive: true });
+    await fs.writeFile(path.join(onDiskSkill, "SKILL.md"), "old");
+    await fs.writeFile(path.join(onDiskSkill, "my-context.md"), "user context");
+    await fs.writeFile(path.join(onDiskSkill, "references", "notes.md"), "user notes");
+
+    await syncSkills({
+      sourceDir: sandbox.sourceDir,
+      agentsDir: sandbox.agentsDir,
+      claudeDir: sandbox.claudeDir,
+      codexDir: sandbox.codexDir,
+      skillNames: ["paseo"],
+    });
+
+    expect(await fs.readFile(path.join(onDiskSkill, "SKILL.md"), "utf-8")).toBe("new");
+    expect(await fs.readFile(path.join(onDiskSkill, "my-context.md"), "utf-8")).toBe(
+      "user context",
+    );
+    expect(await fs.readFile(path.join(onDiskSkill, "references", "notes.md"), "utf-8")).toBe(
+      "user notes",
     );
   });
 
diff --git a/packages/desktop/src/integrations/skills/sync.ts b/packages/desktop/src/integrations/skills/sync.ts
index 8004b3a79..4741101ed 100644
--- a/packages/desktop/src/integrations/skills/sync.ts
+++ b/packages/desktop/src/integrations/skills/sync.ts
@@ -1,3 +1,4 @@
+import { createHash } from "node:crypto";
 import { promises as fs } from "node:fs";
 import path from "node:path";
 
@@ -15,6 +16,13 @@ export interface SkillSyncResult {
   processedSkills: number;
 }
 
+const MANAGED_FILES_MANIFEST = ".paseo-managed-files.json";
+
+interface ManagedFilesManifest {
+  version: 1;
+  files: Record<string, string>;
+}
+
 async function writeFileIfChanged(srcPath: string, dstPath: string): Promise<boolean> {
   const src = await fs.readFile(srcPath);
   const dst = await fs.readFile(dstPath).catch(() => null);
@@ -30,10 +38,12 @@ export async function listFilesRecursive(rootDir: string): Promise<string[]> {
     const entries = await fs.readdir(dir, { withFileTypes: true });
     for (const entry of entries) {
       const full = path.join(dir, entry.name);
+      const rel = path.relative(rootDir, full);
+      if (rel === MANAGED_FILES_MANIFEST) continue;
       if (entry.isDirectory()) {
         await walk(full);
       } else if (entry.isFile()) {
-        out.push(path.relative(rootDir, full));
+        out.push(rel);
       }
     }
   }
@@ -41,14 +51,89 @@ export async function listFilesRecursive(rootDir: string): Promise<string[]> {
   return out;
 }
 
+async function readManagedFilesManifest(dstDir: string): Promise<ManagedFilesManifest | null> {
+  const raw = await fs
+    .readFile(path.join(dstDir, MANAGED_FILES_MANIFEST), "utf-8")
+    .catch(() => null);
+  if (!raw) return null;
+  const parsed = safeParseJson(raw) as Partial<ManagedFilesManifest> | null;
+  if (!parsed) return null;
+  if (parsed.version !== 1 || typeof parsed.files !== "object" || parsed.files === null)
+    return null;
+  return { version: 1, files: parsed.files as Record<string, string> };
+}
+
+function safeParseJson(raw: string): unknown {
+  try {
+    return JSON.parse(raw);
+  } catch {
+    return null;
+  }
+}
+
+async function hashFile(filePath: string): Promise<string> {
+  const buf = await fs.readFile(filePath);
+  return createHash("sha256").update(buf).digest("hex");
+}
+
+async function writeManifestIfChanged(
+  dstDir: string,
+  files: Record<string, string>,
+): Promise<boolean> {
+  const manifest: ManagedFilesManifest = { version: 1, files };
+  const next = `${JSON.stringify(manifest, null, 2)}\n`;
+  const manifestPath = path.join(dstDir, MANAGED_FILES_MANIFEST);
+  const current = await fs.readFile(manifestPath, "utf-8").catch(() => null);
+  if (current === next) return false;
+  await fs.mkdir(dstDir, { recursive: true });
+  await fs.writeFile(manifestPath, next);
+  return true;
+}
+
+async function pruneEmptyParentDirs(rootDir: string, rels: readonly string[]): Promise<void> {
+  const dirs = new Set<string>();
+  for (const rel of rels) {
+    let dir = path.dirname(rel);
+    while (dir !== ".") {
+      dirs.add(dir);
+      dir = path.dirname(dir);
+    }
+  }
+  const deepestFirst = [...dirs].sort(
+    (a, b) => b.split(path.sep).length - a.split(path.sep).length,
+  );
+  for (const rel of deepestFirst) {
+    await fs.rmdir(path.join(rootDir, rel)).catch(() => {});
+  }
+}
+
 async function syncDirectoryFiles(srcDir: string, dstDir: string): Promise<number> {
   const files = await listFilesRecursive(srcDir);
+  const srcFileSet = new Set(files);
+  const srcHashes: Record<string, string> = {};
+  for (const rel of files) {
+    srcHashes[rel] = await hashFile(path.join(srcDir, rel));
+  }
+  const previousManifest = await readManagedFilesManifest(dstDir);
   let changed = 0;
   for (const rel of files) {
     if (await writeFileIfChanged(path.join(srcDir, rel), path.join(dstDir, rel))) {
       changed++;
     }
   }
+
+  const deletedRels: string[] = [];
+  for (const [rel, previousHash] of Object.entries(previousManifest?.files ?? {})) {
+    if (srcFileSet.has(rel)) continue;
+    const dstPath = path.join(dstDir, rel);
+    const currentHash = await hashFile(dstPath).catch(() => null);
+    if (currentHash !== previousHash) continue;
+    await fs.rm(dstPath, { force: true });
+    deletedRels.push(rel);
+    changed++;
+  }
+  await pruneEmptyParentDirs(dstDir, deletedRels);
+  if (await writeManifestIfChanged(dstDir, srcHashes)) changed++;
   return changed;
 }
 
diff --git a/packages/desktop/src/main.ts b/packages/desktop/src/main.ts
index 42324bf03..01e4883da 100644
--- a/packages/desktop/src/main.ts
+++ b/packages/desktop/src/main.ts
@@ -64,6 +64,7 @@ import {
   stopDesktopManagedDaemonOnQuitIfNeeded,
 } from "./daemon/quit-lifecycle.js";
 import { runDesktopStartup } from "./desktop-startup.js";
+import { autoUpdateInstalledSkills } from "./integrations/skills/index.js";
 
 const DEV_SERVER_URL = process.env.EXPO_DEV_URL ?? "http://localhost:8081";
 const APP_SCHEME = "paseo";
@@ -714,6 +715,11 @@ void runDesktopStartup({
   runCliPassthroughIfRequested,
   inheritLoginShellEnv,
   bootstrapGui: bootstrap,
+  autoUpdateInstalledSkills: () => {
+    void autoUpdateInstalledSkills().catch((error) => {
+      log.error("[skills] auto-update failed", error);
+    });
+  },
 }).catch((error) => {
   const message = error instanceof Error ? (error.stack ?? error.message) : String(error);
   process.stderr.write(`${message}\n`);
diff --git a/public-docs/skills.md b/public-docs/skills.md
index 99518d6d7..f1b5a0755 100644
--- a/public-docs/skills.md
+++ b/public-docs/skills.md
@@ -16,6 +16,8 @@ Two ways to install:
 - **Desktop app:** Settings → Integrations → Install
 - **Manual:** `npx skills add getpaseo/paseo`, this installs to `~/.agents/skills/` and sets up symlinks for each agent.
 
+When the desktop app finds installed Paseo skills, it keeps the bundled skills up to date on startup. If automatic update fails, use Settings → Integrations → Update or the manual command above.
+
 ## `/paseo`, Paseo Reference
 
 The foundational skill. Paseo reference for managing agents and worktrees. Load it when an agent needs to create agents, send them prompts, or manage worktrees.