diff --git a/docs/client-configuration.md b/docs/client-configuration.md
index 66e7a381b2..5d7f48321c 100644
--- a/docs/client-configuration.md
+++ b/docs/client-configuration.md
@@ -318,6 +318,9 @@ For FreeBuff, setup writes `mcpServers.rea` into the user-scope
 `~/.agents/skills`, so setup installs its skill copy there. Because the same
 file doubles as ZCode's user-scope fallback (see above), a `freebuff`
 registration also loads in ZCode until ZCode defines its own native server.
+Setup and doctor detect FreeBuff from its own profile directory
+(`~/.config/freebuff-desktop`), not from the shared `.agents` folder that
+REA's skill installs create for every client.
 
 FreeBuff is main-only and is not part of npm 6.4.0; `rea setup --client
 freebuff` against `@latest` reports an unsupported client until a release
diff --git a/src/application/SupportedClients.ts b/src/application/SupportedClients.ts
index c552ade926..828c007c32 100644
--- a/src/application/SupportedClients.ts
+++ b/src/application/SupportedClients.ts
@@ -481,9 +481,14 @@ const devinDirectory = ({ home, platform, env }: ClientPathContext): string =>
     ? join(env.APPDATA ?? join(home, "AppData", "Roaming"), "devin")
     : join(env.XDG_CONFIG_HOME || join(home, ".config"), "devin");
 
-/** FreeBuff loads MCP servers and skills from the shared user agents directory. */
-const freebuffDirectory = ({ home }: ClientPathContext): string =>
-  join(home, ".agents");
+/**
+ * FreeBuff's own profile directory (its `state.json` root, fixed under
+ * `.config` on every platform). The shared `~/.agents` folder is not
+ * FreeBuff-specific: REA's own skill installs create it, so it cannot
+ * prove FreeBuff is installed.
+ */
+const freebuffProfileDirectory = ({ home }: ClientPathContext): string =>
+  join(home, ".config", "freebuff-desktop");
 
 /** Stable product metadata used to derive setup discovery and documentation. */
 export const SUPPORTED_CLIENT_DEFINITIONS = [
@@ -702,11 +707,12 @@ export const SUPPORTED_CLIENT_DEFINITIONS = [
   {
     name: "freebuff",
     displayName: "FreeBuff",
-    skillPath: (context: ClientPathContext) =>
-      join(freebuffDirectory(context), "skills"),
-    configPath: (context: ClientPathContext) =>
-      join(freebuffDirectory(context), "mcp.json"),
-    markerPath: freebuffDirectory,
+    // FreeBuff discovers personal skills in the shared user agents directory.
+    skillPath: ({ home }: ClientPathContext) => join(home, ".agents", "skills"),
+    // FreeBuff loads MCP servers from the shared user agents directory.
+    configPath: ({ home }: ClientPathContext) =>
+      join(home, ".agents", "mcp.json"),
+    markerPath: freebuffProfileDirectory,
     format: "json",
   },
   {
diff --git a/tests/boundary/filesystem/freebuffClientConfiguration.test.ts b/tests/boundary/filesystem/freebuffClientConfiguration.test.ts
index c27244c272..92a94dfc7d 100644
--- a/tests/boundary/filesystem/freebuffClientConfiguration.test.ts
+++ b/tests/boundary/filesystem/freebuffClientConfiguration.test.ts
@@ -1,11 +1,12 @@
 import { mkdir, readFile, writeFile } from "node:fs/promises";
-import { join } from "node:path";
+import { dirname, join } from "node:path";
 
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 
 import { readClientRegistrationStatuses } from "../../../src/application/ClientRegistrationStatus.js";
 import { npxRegistrationCommand } from "../../../src/application/ClientRegistrationIdentity.js";
 import { configureClientConfiguration } from "../../../src/application/SetupClientConfiguration.js";
+import { detectClients } from "../../../src/application/SetupHost.js";
 import { skillDestinations } from "../../../src/application/SetupSkill.js";
 import { supportedClients } from "../../../src/application/SupportedClients.js";
 import { systemUninstallHost } from "../../../src/application/Uninstall.js";
@@ -29,19 +30,35 @@ const freebuffPath = (
   supportedClients(home, platform, env).find(({ name }) => name === "freebuff");
 
 describe("FreeBuff configuration paths", () => {
-  it("resolves the shared user agents file and marker directory", () => {
+  it("resolves the shared user agents file and the profile marker directory", () => {
     expect(freebuffPath("/home/a")).toEqual({
       name: "freebuff",
       displayName: "FreeBuff",
       configPath: join("/home/a", ".agents", "mcp.json"),
-      markerPath: join("/home/a", ".agents"),
+      markerPath: join("/home/a", ".config", "freebuff-desktop"),
       format: "json",
     });
-    expect(freebuffPath("/Users/a", "darwin")?.configPath).toBe(
-      join("/Users/a", ".agents", "mcp.json"),
+    expect(freebuffPath("/Users/a", "darwin")?.markerPath).toBe(
+      join("/Users/a", ".config", "freebuff-desktop"),
     );
-    expect(freebuffPath("C:\\Users\\a", "win32")?.configPath).toBe(
-      join("C:\\Users\\a", ".agents", "mcp.json"),
+    expect(freebuffPath("C:\\Users\\a", "win32")?.markerPath).toBe(
+      join("C:\\Users\\a", ".config", "freebuff-desktop"),
+    );
+  });
+
+  it("stays undetected when only the shared agents skill directory exists", async () => {
+    const home = await createTestTempDirectory("rea-freebuff-shared-");
+    // REA's own skill installs create this directory for every client.
+    await mkdir(join(home, ".agents", "skills"), { recursive: true });
+    expect((await detectClients(home)).map(({ name }) => name)).not.toContain(
+      "freebuff",
+    );
+
+    await mkdir(join(home, ".config", "freebuff-desktop"), {
+      recursive: true,
+    });
+    expect((await detectClients(home)).map(({ name }) => name)).toContain(
+      "freebuff",
     );
   });
 
@@ -66,9 +83,8 @@ describe("FreeBuff JSON registration", () => {
   const freebuffClient = async () => {
     const home = await createTestTempDirectory("rea-freebuff-");
     const client = freebuffPath(home, process.platform);
-    if (client?.markerPath === undefined)
-      throw new Error("missing FreeBuff client");
-    await mkdir(client.markerPath, { recursive: true });
+    if (client === undefined) throw new Error("missing FreeBuff client");
+    await mkdir(dirname(client.configPath), { recursive: true });
     return { home, client };
   };