diff --git a/packages/coding-agent/CHANGELOG.md b/packages/coding-agent/CHANGELOG.md
index 114c7b3ef..467263d15 100644
--- a/packages/coding-agent/CHANGELOG.md
+++ b/packages/coding-agent/CHANGELOG.md
@@ -1871,6 +1871,7 @@
 ### Fixed
 
 - Fixed `@`-mention auto-read injecting an unrelated, same-named file when a mention did not point at a real path — e.g. an npm scope like `@scope/`, a partial path, or a bare token. `generateFileMentionMessages` resolution previously fell back to prefix and repo-wide fuzzy matching (globbing the whole project on every such mention) and auto-read the single "best" guess. Resolution is now exact-only: a mention is auto-read only when it resolves to an existing file or directory; otherwise it is left as prose. The TUI `@`-selector already inserts the real, complete path before send, so post-send guessing was both unnecessary and the source of the wrong-file reads. Directories still resolve and are listed. Removes the per-mention `**/*` project scan.
+- Fixed Git-mutating automation silently mis-handling pure Jujutsu workspaces (`.jj/repo/` present, no colocated `.git/`). `task/worktree.ts#getRepoRoot` previously threw a generic "Git repository not found" for isolated subagent setup, and `autoresearch/git.ts#ensureAutoresearchBranch` returned a soft "Not in a git repository" warning that let `/autoresearch` proceed with no branch isolation or auto-commits. Both paths now detect a pure jj workspace via the new `jj.isPureJjRepo` helper and surface an actionable Jujutsu-specific error pointing at `jj git init --colocate`. Colocated jj-git (both `.jj/` and `.git/` at the same root) and plain Git checkouts behave exactly as before ([#1935](https://github.com/can1357/oh-my-pi/issues/1935)).
 
 ## [15.9.2] - 2026-06-05
 
diff --git a/packages/coding-agent/src/autoresearch/git.ts b/packages/coding-agent/src/autoresearch/git.ts
index 95c54700a..43cb0e886 100644
--- a/packages/coding-agent/src/autoresearch/git.ts
+++ b/packages/coding-agent/src/autoresearch/git.ts
@@ -1,5 +1,6 @@
 import type { ExtensionAPI } from "../extensibility/extensions";
 import * as git from "../utils/git";
+import * as jj from "../utils/jj";
 import { normalizePathSpec } from "./helpers";
 
 const AUTORESEARCH_BRANCH_PREFIX = "autoresearch/";
@@ -37,6 +38,17 @@ export async function ensureAutoresearchBranch(
 	workDir: string,
 	goal: string | null,
 ): Promise<EnsureAutoresearchBranchResult> {
+	// Pure-jj check runs first so a jj workspace nested under an unrelated
+	// outer Git checkout is rejected at its own root rather than silently
+	// creating `autoresearch/*` branches and commits in the surrounding Git
+	// tree behind jj's back.
+	if (await jj.isPureJjRepo(workDir)) {
+		return {
+			ok: false,
+			error: "Autoresearch needs a Git checkout for branch isolation and baseline commits, but this workspace is pure Jujutsu (`.jj/` without a colocated `.git/`). Run `jj git init --colocate` to add a Git checkout before starting autoresearch.",
+		};
+	}
+
 	const repoRoot = await git.repo.root(workDir);
 	if (!repoRoot) {
 		return {
diff --git a/packages/coding-agent/src/task/worktree.ts b/packages/coding-agent/src/task/worktree.ts
index a10220e41..f80b37ee7 100644
--- a/packages/coding-agent/src/task/worktree.ts
+++ b/packages/coding-agent/src/task/worktree.ts
@@ -6,6 +6,7 @@ import * as natives from "@oh-my-pi/pi-natives";
 import { getWorktreeDir, hashPath, logger, Snowflake } from "@oh-my-pi/pi-utils";
 import * as git from "../utils/git";
 import { mapWithConcurrencyLimit } from "./parallel";
+import * as jj from "../utils/jj";
 
 const { IsoBackendKind } = natives;
 type IsoBackendKind = natives.IsoBackendKind;
@@ -28,12 +29,19 @@ export interface WorktreeBaseline {
 }
 
 export async function getRepoRoot(cwd: string): Promise<string> {
-	const repoRoot = await git.repo.root(cwd);
-	if (!repoRoot) {
-		throw new Error("Git repository not found for isolated task execution.");
+	// Pure-jj check runs first so a jj workspace nested under an unrelated
+	// outer Git checkout is rejected at its own root rather than silently
+	// mutating the surrounding Git tree behind jj's back.
+	if (await jj.isPureJjRepo(cwd)) {
+		throw new Error(
+			"Isolated task execution requires a Git checkout, but this workspace is pure Jujutsu (`.jj/` without a colocated `.git/`). Run `jj git init --colocate` to add a Git checkout, or set `task.isolation.mode: none` to disable task isolation.",
+		);
 	}
 
-	return repoRoot;
+	const repoRoot = await git.repo.root(cwd);
+	if (repoRoot) return repoRoot;
+
+	throw new Error("Git repository not found for isolated task execution.");
 }
 
 const GIT_NO_INDEX_NULL_PATH = process.platform === "win32" ? "NUL" : "/dev/null";
diff --git a/packages/coding-agent/src/utils/jj.ts b/packages/coding-agent/src/utils/jj.ts
index 228325bff..655decf97 100644
--- a/packages/coding-agent/src/utils/jj.ts
+++ b/packages/coding-agent/src/utils/jj.ts
@@ -2,6 +2,7 @@ import * as fs from "node:fs/promises";
 import * as path from "node:path";
 import { $which } from "@oh-my-pi/pi-utils";
 import { LRUCache } from "lru-cache/raw";
+import * as git from "./git";
 
 // ════════════════════════════════════════════════════════════════════════════
 // Types
@@ -246,3 +247,49 @@ export const repo = {
 		return (await repo.root(cwd)) !== null;
 	},
 };
+
+/**
+ * Detect a "pure" Jujutsu workspace — one where Git-mutating automation has
+ * no safe Git target. Invoking `git checkout -b`, `git worktree add`, or
+ * `git apply` against a pure jj workspace either fails outright (no `.git/`
+ * present) or mutates state that jj itself cannot reconcile.
+ *
+ * `cwd` is "pure jj" iff its nearest jj workspace ancestor is **closer than**
+ * its nearest Git checkout ancestor (or no Git checkout is present at all).
+ * Both lookups walk upward from `cwd`, so the deeper ancestor is the one the
+ * user is actually working inside.
+ *
+ * Returns:
+ * - `false` for plain Git checkouts (no jj metadata anywhere up the tree).
+ * - `false` for colocated jj-git workspaces — `jj git init --colocate` keeps
+ *   `.jj/` and `.git/` at the same root.
+ * - `false` when a nested Git checkout (e.g. a vendored repo or fixture)
+ *   lives **under** an outer jj workspace; Git automation targets the inner
+ *   repo and never touches the surrounding jj tree.
+ * - `true` when jj is the deeper ancestor — either a standalone pure jj
+ *   workspace, or a jj workspace nested under an unrelated outer Git
+ *   checkout, where Git automation against the outer root would silently
+ *   bypass jj.
+ * - `false` for directories backed by neither tool.
+ */
+export async function isPureJjRepo(cwd: string): Promise<boolean> {
+	const jjRoot = await repo.root(cwd);
+	if (jjRoot === null) return false;
+	const gitRoot = await git.repo.root(cwd);
+	if (gitRoot === null) return true;
+	return isStrictDescendant(path.resolve(jjRoot), path.resolve(gitRoot));
+}
+
+/**
+ * Return `true` when `child` is a strict descendant of `ancestor` (same path
+ * counts as `false`). Both arguments must already be resolved absolute paths.
+ */
+function isStrictDescendant(child: string, ancestor: string): boolean {
+	const rel = path.relative(ancestor, child);
+	if (rel === "" || rel === ".") return false;
+	if (rel.startsWith("..")) return false;
+	// `path.relative` returns an absolute path only when the two arguments
+	// live on different filesystem roots (Windows drives, UNC shares); not a
+	// real ancestor relationship.
+	return !path.isAbsolute(rel);
+}
diff --git a/packages/coding-agent/test/autoresearch-git.test.ts b/packages/coding-agent/test/autoresearch-git.test.ts
new file mode 100644
index 000000000..503c2926e
--- /dev/null
+++ b/packages/coding-agent/test/autoresearch-git.test.ts
@@ -0,0 +1,132 @@
+import { afterEach, describe, expect, it } from "bun:test";
+import * as fs from "node:fs/promises";
+import * as os from "node:os";
+import * as path from "node:path";
+import { ensureAutoresearchBranch } from "../src/autoresearch/git";
+import type { ExtensionAPI } from "../src/extensibility/extensions";
+import * as jj from "../src/utils/jj";
+
+const tempDirs: string[] = [];
+
+async function mkTempDir(prefix: string): Promise<string> {
+	const dir = await fs.mkdtemp(path.join(os.tmpdir(), prefix));
+	tempDirs.push(dir);
+	return dir;
+}
+
+async function runGit(cwd: string, args: string[]): Promise<void> {
+	const env = { ...process.env, HOME: cwd, GIT_CONFIG_GLOBAL: "/dev/null", GIT_CONFIG_SYSTEM: "/dev/null" };
+	const proc = Bun.spawn(["git", "-C", cwd, ...args], { env, stdout: "ignore", stderr: "pipe" });
+	const code = await proc.exited;
+	if (code !== 0) {
+		const stderr = await new Response(proc.stderr).text();
+		throw new Error(`git ${args.join(" ")} failed (${code}): ${stderr}`);
+	}
+}
+
+async function initGitWithCommit(dir: string): Promise<void> {
+	await runGit(dir, ["init", "-q", "-b", "main"]);
+	await runGit(dir, ["config", "user.email", "test@example.com"]);
+	await runGit(dir, ["config", "user.name", "Test"]);
+	await fs.writeFile(path.join(dir, "README"), "seed\n");
+	await runGit(dir, ["add", "."]);
+	await runGit(dir, ["commit", "-q", "-m", "init"]);
+}
+
+// `ensureAutoresearchBranch` never invokes the `api` it receives — its two
+// internal helpers (`readGitWorkDirPrefix`, `branchExists`) immediately
+// `void api`. The stub keeps the signature honest without spinning up the
+// real extension runtime.
+const stubApi = {} as unknown as ExtensionAPI;
+
+afterEach(async () => {
+	jj.repo.clearRootCache();
+	await Promise.all(tempDirs.splice(0).map(dir => fs.rm(dir, { recursive: true, force: true })));
+});
+
+describe("ensureAutoresearchBranch jj guardrails", () => {
+	it("rejects pure jj workspaces before touching git state", async () => {
+		const dir = await mkTempDir("omp-ar-purejj-");
+		await fs.mkdir(path.join(dir, ".jj", "repo", "store"), { recursive: true });
+
+		const result = await ensureAutoresearchBranch(stubApi, dir, "demo");
+
+		expect(result.ok).toBe(false);
+		if (result.ok) throw new Error("unreachable");
+		expect(result.error).toMatch(/pure Jujutsu/);
+		expect(result.error).toMatch(/jj git init --colocate/);
+	});
+
+	it("creates an autoresearch branch in a colocated jj-git workspace", async () => {
+		const dir = await mkTempDir("omp-ar-colocated-");
+		await initGitWithCommit(dir);
+		await fs.mkdir(path.join(dir, ".jj", "repo", "store"), { recursive: true });
+
+		const result = await ensureAutoresearchBranch(stubApi, dir, "demo goal");
+
+		expect(result.ok).toBe(true);
+		if (!result.ok) throw new Error("unreachable");
+		expect(result.created).toBe(true);
+		expect(result.branchName).toMatch(/^autoresearch\/demo-goal-\d{8}$/);
+	});
+
+	it("creates an autoresearch branch in a plain git repo (unchanged behavior)", async () => {
+		const dir = await mkTempDir("omp-ar-plaingit-");
+		await initGitWithCommit(dir);
+
+		const result = await ensureAutoresearchBranch(stubApi, dir, "demo");
+
+		expect(result.ok).toBe(true);
+		if (!result.ok) throw new Error("unreachable");
+		expect(result.created).toBe(true);
+		expect(result.branchName).toMatch(/^autoresearch\/demo-\d{8}$/);
+	});
+
+	it("returns the soft no-git warning for directories backed by neither tool", async () => {
+		const dir = await mkTempDir("omp-ar-empty-");
+
+		const result = await ensureAutoresearchBranch(stubApi, dir, "demo");
+
+		expect(result.ok).toBe(true);
+		if (!result.ok) throw new Error("unreachable");
+		expect(result.branchName).toBeNull();
+		expect(result.warning).toMatch(/Not in a git repository/);
+	});
+
+	it("rejects a pure jj workspace nested inside an unrelated outer git checkout", async () => {
+		// `git.repo.root(inner)` walks up and finds the outer .git — without
+		// the pure-jj check running first, autoresearch would create
+		// `autoresearch/*` branches and commits in the surrounding git tree
+		// behind jj's back.
+		const outer = await mkTempDir("omp-ar-nested-outer-");
+		await initGitWithCommit(outer);
+		const inner = path.join(outer, "nested-jj");
+		await fs.mkdir(path.join(inner, ".jj", "repo", "store"), { recursive: true });
+
+		const result = await ensureAutoresearchBranch(stubApi, inner, "demo");
+
+		expect(result.ok).toBe(false);
+		if (result.ok) throw new Error("unreachable");
+		expect(result.error).toMatch(/pure Jujutsu/);
+		expect(result.error).toMatch(/jj git init --colocate/);
+	});
+
+	it("creates an autoresearch branch in a nested git checkout under an outer jj workspace", async () => {
+		// Mirror image of the case above: `jj.repo.root(inner)` finds the outer
+		// .jj, but `git.repo.root(inner)` finds the inner .git, so autoresearch
+		// safely targets the nested checkout and never touches the surrounding
+		// jj tree.
+		const outer = await mkTempDir("omp-ar-outerjj-");
+		await fs.mkdir(path.join(outer, ".jj", "repo", "store"), { recursive: true });
+		const inner = path.join(outer, "vendor");
+		await fs.mkdir(inner, { recursive: true });
+		await initGitWithCommit(inner);
+
+		const result = await ensureAutoresearchBranch(stubApi, inner, "demo");
+
+		expect(result.ok).toBe(true);
+		if (!result.ok) throw new Error("unreachable");
+		expect(result.created).toBe(true);
+		expect(result.branchName).toMatch(/^autoresearch\/demo-\d{8}$/);
+	});
+});
diff --git a/packages/coding-agent/test/task/worktree.test.ts b/packages/coding-agent/test/task/worktree.test.ts
index 958f20555..a5cad7d2d 100644
--- a/packages/coding-agent/test/task/worktree.test.ts
+++ b/packages/coding-agent/test/task/worktree.test.ts
@@ -7,10 +7,14 @@ import {
 	captureDeltaPatch,
 	ensureIsolation,
 	getGitNoIndexNullPath,
+	getRepoRoot,
 	mergeTaskBranches,
 	parseIsolationMode,
 } from "@oh-my-pi/pi-coding-agent/task/worktree";
 import * as natives from "@oh-my-pi/pi-natives";
+import * as jj from "@oh-my-pi/pi-coding-agent/utils/jj";
+
+const tempDirs: string[] = [];
 
 async function runGit(repo: string, args: string[]): Promise<string> {
 	const proc = Bun.spawn(["git", ...args], {
@@ -30,6 +34,27 @@ async function runGit(repo: string, args: string[]): Promise<string> {
 	return stdout.trim();
 }
 
+async function createGitRepo(): Promise<{ baseBranch: string; repo: string }> {
+	const repo = await fs.mkdtemp(path.join(os.tmpdir(), "omp-worktree-"));
+	tempDirs.push(repo);
+	await runGit(repo, ["init"]);
+	await runGit(repo, ["config", "user.email", "test@example.com"]);
+	await runGit(repo, ["config", "user.name", "Test User"]);
+	await fs.writeFile(path.join(repo, "merged.txt"), "base version\n");
+	await fs.writeFile(path.join(repo, "staged.txt"), "base staged\n");
+	await runGit(repo, ["add", "."]);
+	await runGit(repo, ["commit", "-m", "initial"]);
+	return {
+		baseBranch: await runGit(repo, ["branch", "--show-current"]),
+		repo,
+	};
+}
+
+afterEach(async () => {
+	vi.restoreAllMocks();
+	jj.repo.clearRootCache();
+	await Promise.all(tempDirs.splice(0).map(dir => fs.rm(dir, { recursive: true, force: true })));
+});
 describe("worktree isolation helpers", () => {
 	it("returns platform-specific null path for git --no-index diffs", () => {
 		const expected = process.platform === "win32" ? "NUL" : "/dev/null";
@@ -198,3 +223,59 @@ describe("worktree isolation helpers", () => {
 		});
 	});
 });
+
+describe("getRepoRoot", () => {
+	it("returns the git root for a plain git checkout", async () => {
+		const { repo } = await createGitRepo();
+		expect(await getRepoRoot(repo)).toBe(repo);
+	});
+
+	it("returns the git root for a colocated jj-git workspace", async () => {
+		const { repo } = await createGitRepo();
+		await fs.mkdir(path.join(repo, ".jj", "repo", "store"), { recursive: true });
+		expect(await getRepoRoot(repo)).toBe(repo);
+	});
+
+	it("rejects pure jj workspaces with an actionable Jujutsu message", async () => {
+		const dir = await fs.mkdtemp(path.join(os.tmpdir(), "omp-purejj-"));
+		tempDirs.push(dir);
+		await fs.mkdir(path.join(dir, ".jj", "repo", "store"), { recursive: true });
+		await expect(getRepoRoot(dir)).rejects.toThrow(/pure Jujutsu/);
+		await expect(getRepoRoot(dir)).rejects.toThrow(/jj git init --colocate/);
+	});
+
+	it("preserves the generic git-not-found error for directories without any repo", async () => {
+		const dir = await fs.mkdtemp(path.join(os.tmpdir(), "omp-norepo-"));
+		tempDirs.push(dir);
+		await expect(getRepoRoot(dir)).rejects.toThrow("Git repository not found for isolated task execution.");
+	});
+
+	it("rejects a pure jj workspace nested inside an unrelated outer git checkout", async () => {
+		// `git.repo.root(inner)` walks up and finds the outer .git — without
+		// the pure-jj check running first, isolation would silently target the
+		// surrounding git tree behind jj's back.
+		const { repo: outer } = await createGitRepo();
+		const inner = path.join(outer, "nested-jj");
+		await fs.mkdir(path.join(inner, ".jj", "repo", "store"), { recursive: true });
+
+		await expect(getRepoRoot(inner)).rejects.toThrow(/pure Jujutsu/);
+		await expect(getRepoRoot(inner)).rejects.toThrow(/jj git init --colocate/);
+	});
+
+	it("returns the nested git root when a git checkout lives under an outer jj workspace", async () => {
+		// Mirror image of the case above: `jj.repo.root(inner)` finds the outer
+		// .jj, but `git.repo.root(inner)` finds the inner .git, so Git
+		// automation targets the nested checkout safely. Isolation must keep
+		// working here exactly as it did before the pure-jj guard landed.
+		const outer = await fs.mkdtemp(path.join(os.tmpdir(), "omp-outerjj-"));
+		tempDirs.push(outer);
+		await fs.mkdir(path.join(outer, ".jj", "repo", "store"), { recursive: true });
+		const inner = path.join(outer, "vendor");
+		await fs.mkdir(inner, { recursive: true });
+		await runGit(inner, ["init", "-q", "-b", "main"]);
+		await runGit(inner, ["config", "user.email", "test@example.com"]);
+		await runGit(inner, ["config", "user.name", "Test"]);
+
+		expect(await getRepoRoot(inner)).toBe(inner);
+	});
+});
diff --git a/packages/coding-agent/test/utils/jj.test.ts b/packages/coding-agent/test/utils/jj.test.ts
index 9f5050120..1b0ff868a 100644
--- a/packages/coding-agent/test/utils/jj.test.ts
+++ b/packages/coding-agent/test/utils/jj.test.ts
@@ -77,3 +77,79 @@ describe("jj workspace detection", () => {
 		expect(resolved?.storeDir).toBe(path.join(dir, ".jj", "repo", "store"));
 	});
 });
+
+describe("isPureJjRepo", () => {
+	const tempDirs: string[] = [];
+
+	afterEach(async () => {
+		jj.repo.clearRootCache();
+		await Promise.all(tempDirs.splice(0).map(dir => fs.rm(dir, { recursive: true, force: true })));
+	});
+
+	async function createTempDir(prefix: string): Promise<string> {
+		const dir = await fs.mkdtemp(path.join(os.tmpdir(), prefix));
+		tempDirs.push(dir);
+		return dir;
+	}
+
+	async function initGit(dir: string): Promise<void> {
+		const env = { ...process.env, HOME: dir, GIT_CONFIG_GLOBAL: "/dev/null", GIT_CONFIG_SYSTEM: "/dev/null" };
+		const exit = async (args: string[]) => {
+			const proc = Bun.spawn(["git", "-C", dir, ...args], { env, stdout: "ignore", stderr: "pipe" });
+			const code = await proc.exited;
+			if (code !== 0) {
+				const stderr = await new Response(proc.stderr).text();
+				throw new Error(`git ${args.join(" ")} failed (${code}): ${stderr}`);
+			}
+		};
+		await exit(["init", "-q", "-b", "main"]);
+		await exit(["config", "user.email", "test@example.com"]);
+		await exit(["config", "user.name", "Test"]);
+	}
+
+	it("flags a pure jj workspace (no colocated git)", async () => {
+		const dir = await createTempDir("omp-jj-pure-");
+		await fs.mkdir(path.join(dir, ".jj", "repo", "store"), { recursive: true });
+		expect(await jj.isPureJjRepo(dir)).toBe(true);
+	});
+
+	it("treats a colocated jj-git workspace as non-pure", async () => {
+		const dir = await createTempDir("omp-jj-colocated-");
+		await fs.mkdir(path.join(dir, ".jj", "repo", "store"), { recursive: true });
+		await initGit(dir);
+		expect(await jj.isPureJjRepo(dir)).toBe(false);
+	});
+
+	it("returns false for a plain git checkout (no jj metadata)", async () => {
+		const dir = await createTempDir("omp-jj-plaingit-");
+		await initGit(dir);
+		expect(await jj.isPureJjRepo(dir)).toBe(false);
+	});
+
+	it("returns false when neither jj nor git metadata is present", async () => {
+		const dir = await createTempDir("omp-jj-empty-");
+		expect(await jj.isPureJjRepo(dir)).toBe(false);
+	});
+
+	it("flags a jj workspace nested inside an unrelated git checkout as pure", async () => {
+		const outer = await createTempDir("omp-jj-nested-outer-");
+		await initGit(outer);
+		const inner = path.join(outer, "nested");
+		await fs.mkdir(path.join(inner, ".jj", "repo", "store"), { recursive: true });
+		// The inner directory is its own jj workspace; the surrounding git
+		// checkout would mutate state outside jj's model.
+		expect(await jj.isPureJjRepo(inner)).toBe(true);
+	});
+
+	it("treats a nested git checkout under an outer jj workspace as non-pure", async () => {
+		// `git.repo.root(inner)` returns the inner .git, so Git automation
+		// targets the nested checkout safely and never touches the surrounding
+		// jj tree — the inner git wins.
+		const outer = await createTempDir("omp-jj-nested-jj-outer-");
+		await fs.mkdir(path.join(outer, ".jj", "repo", "store"), { recursive: true });
+		const inner = path.join(outer, "vendor");
+		await fs.mkdir(inner, { recursive: true });
+		await initGit(inner);
+		expect(await jj.isPureJjRepo(inner)).toBe(false);
+	});
+});