fix(cases): clone into the chosen folder itself, not a subfolder of it

The custom folder was treated as a parent, so the repository landed in <folder>/<case name>. The chosen folder is now the clone destination: an empty existing folder is cloned into directly (CloneOptions.intoEmptyDir, no temporary sibling, never removed on failure), a new folder is created, and a folder with files is refused.

CLAUDE.md

@@ -244,7 +244,7 @@ The terminal provider scans `terminalLinkLine()`, which extends `terminalPathLin
 
 **Ultracode / workflow-run visualization** (opt-in, default OFF): the Workflow tool writes a completion artifact only at run *end*, so live in-flight runs exist solely as transcript dirs. `workflow-run-watcher.ts` therefore synthesizes ACTIVE runs from transcripts until the completion artifact appears and supersedes them. It is **STANDALONE** and deliberately never imports or touches `subagent-watcher.ts`, despite reading the same tree. Two independent toggles: `showUltracodeAgents` (docked panel) and `ultracodeFloatingWindows` (floating windows); the watcher starts if **either** is on. → [architecture-invariants#ultracode-and-workflow-run-visualization](docs/architecture-invariants.md#ultracode-and-workflow-run-visualization)
 
-**Clone a repository as a case** (issue #236, Add Case → **Clone Repo**): `POST /api/cases/clone` clones synchronously into the caller's case space (bounded by `GIT_CLONE_TIMEOUT_MS`, no job store); `POST /api/cases/clone-preflight` checks anonymous cloneability and lists refs. Core in `src/git-clone.ts`. ⚠️ **The URL is a code-execution surface**: refuse every `::` form and a leading `-`, spawn only argv arrays with `--` before operands. ⚠️ Stay non-interactive (`gitNonInteractiveEnv()`) or the open request hangs; never collect credentials, refuse `user:password@` URLs. ⚠️ Timeout kills the process GROUP, remove the destination only if this attempt created it, and repo contents win over scaffolding (existing `CLAUDE.md` kept, hooks merged, repo `.claude/settings*` warned about). ⚠️ A `path` clones into a custom folder and registers a linked case: admin-only in multi-user mode, judged by `prepareNewCasePath()`, and an existing target (even empty) is refused. → [architecture-invariants#clone-a-repository-as-a-case](docs/architecture-invariants.md#clone-a-repository-as-a-case)
+**Clone a repository as a case** (issue #236, Add Case → **Clone Repo**): `POST /api/cases/clone` clones synchronously into the caller's case space (bounded by `GIT_CLONE_TIMEOUT_MS`, no job store); `POST /api/cases/clone-preflight` checks anonymous cloneability and lists refs. Core in `src/git-clone.ts`. ⚠️ **The URL is a code-execution surface**: refuse every `::` form and a leading `-`, spawn only argv arrays with `--` before operands. ⚠️ Stay non-interactive (`gitNonInteractiveEnv()`) or the open request hangs; never collect credentials, refuse `user:password@` URLs. ⚠️ Timeout kills the process GROUP, remove the destination only if this attempt created it, and repo contents win over scaffolding (existing `CLAUDE.md` kept, hooks merged, repo `.claude/settings*` warned about). ⚠️ A `path` is the folder cloned INTO (no case-name subfolder) and registers a linked case: admin-only in multi-user mode, judged by `prepareNewCasePath()`, empty or new only (`intoEmptyDir` clones straight into an empty one and never removes it). → [architecture-invariants#clone-a-repository-as-a-case](docs/architecture-invariants.md#clone-a-repository-as-a-case)
 
 **Git worktrees of a case** (case picker → **Git worktrees…**; `src/git-worktrees.ts`, `routes/worktree-routes.ts`): a local repository case keeps worktrees at `<repo>/.claude/worktrees/<name>` on `worktree-<name>`, Claude Code's own `--worktree` layout. ⚠️ Only that managed path is ever created or removed, every component `lstat`ed and realpath-checked (a symlinked `.claude` is refused). ⚠️ git never runs for a Docker or remote case, nor at or inside a Docker workspace (`worktree add` runs hooks and filters on the host). ⚠️ Remove is `git worktree remove` WITHOUT `--force`, refused while a live session is inside; branch delete is `-d`, never `-D`. ⚠️ Sessions start through the existing create paths (quick-start `worktree`, or `POST /api/sessions` `workingDir`), never a new spawn path. → [architecture-invariants#git-worktrees-of-a-case](docs/architecture-invariants.md#git-worktrees-of-a-case)
 

docs/architecture-invariants.md

@@ -468,7 +468,7 @@ Tests: `test/file-preview-markdown.test.ts` (jsdom-in-vm, pins every rule above)
 
 ### Clone a repository as a case
 
-**Clone Repo tab** (issue #236, proposed by @DodgyBadger): `POST /api/cases/clone` clones a public repository into the caller's case space and registers it as a normal local case; `POST /api/cases/clone-preflight` answers "can this be cloned anonymously, and what refs does it have?" while the user is still typing. Core in `src/git-clone.ts`, split into a PURE half (URL parse, argv/env, `ls-remote` parse, stderr classification) and a thin IO half (`probeGitRemote`, `cloneRepository`). An optional `path` (the **Clone into a custom folder** checkbox, parent folder plus case name) clones into that exact folder instead and registers it as a LINKED case, the same way `POST /api/cases` with a `path` does: it is judged by `prepareNewCasePath()` (`web/case-path.ts`: blocked trees, symlinks, parent must exist), is admin-only in multi-user mode (it writes an absolute path into the shared linked-cases registry), and refuses a folder that already exists, empty or not, because `cloneRepository` needs a fresh destination. Deleting such a case unlinks it and never removes the files. If the registry write fails after git finished, the folder is kept and the error says where it is.
+**Clone Repo tab** (issue #236, proposed by @DodgyBadger): `POST /api/cases/clone` clones a public repository into the caller's case space and registers it as a normal local case; `POST /api/cases/clone-preflight` answers "can this be cloned anonymously, and what refs does it have?" while the user is still typing. Core in `src/git-clone.ts`, split into a PURE half (URL parse, argv/env, `ls-remote` parse, stderr classification) and a thin IO half (`probeGitRemote`, `cloneRepository`). An optional `path` (the **Clone into a custom folder** checkbox) is the folder the repository is cloned INTO, exactly as given (the case name adds no subfolder), and it registers a LINKED case, the same way `POST /api/cases` with a `path` does: it is judged by `prepareNewCasePath()` (`web/case-path.ts`: blocked trees, symlinks, parent must exist), is admin-only in multi-user mode (it writes an absolute path into the shared linked-cases registry), and must be empty or not exist yet. An existing empty folder is cloned into directly (`CloneOptions.intoEmptyDir`: no temporary sibling and no rename, so a mount point works; a failed attempt empties it again but never removes it); a folder with anything in it is refused. Deleting such a case unlinks it and never removes the files. If the registry write fails after git finished, the folder is kept and the error says where it is.
 
 - ⚠️ **The URL is a code-execution surface, which is why it is parsed rather than forwarded.** `ext::sh -c <cmd>` makes git run an arbitrary command as its transport, and ANY `<name>::<payload>` dispatches to a `git-remote-<name>` helper, so every `::` form is refused outright. A repository starting with `-` is read by git as a flag; that is rejected AND every spawn puts `--` before the operands, because either defence alone is one edit away from being a hole. Spawns are argv arrays, never a shell (unlike `remote-hosts.ts`, which does build a shell line and must `shellescape`). The Zod schema deliberately only length-bounds `repository` — a weaker regex duplicate of `parseGitRepositoryUrl` would be the copy that drifts.
 - ⚠️ **Non-interactive or it hangs the request.** The clone is synchronous by design (no job store, no polling, no cancellation surface), so an invisible credential prompt would pin an open HTTP request until the timeout. `gitNonInteractiveEnv()` closes all four prompt paths at once: `GIT_TERMINAL_PROMPT=0`, empty `GIT_ASKPASS`/`SSH_ASKPASS` + `SSH_ASKPASS_REQUIRE=never` + empty `DISPLAY`, `GCM_INTERACTIVE=never`, and `ssh -oBatchMode=yes`. `HOME`/`PATH` are inherited on purpose — a user whose own agent or credential helper already works keeps working (so a private repo may well clone; Codeman just never collects or stores credentials, and refuses a `user:password@` URL). ⚠️ In multi-user mode a NON-ADMIN's clone and preflight run with `git -c credential.helper=` (`cloneWithoutCredentialHelpers`), because the helpers belong to the one server account every user shares; admins and single-user mode keep them. The Docker server image relies on exactly this: when built with the opt-in `CODEMAN_INSTALL_GH`/`CODEMAN_INSTALL_AZ` args it configures `gh` (github.com) and an `az`-backed helper (`docker/git-credential-azure-cli`, Azure DevOps) in its SYSTEM gitconfig, both silent until the user signs the CLI in, so a private clone there still fails fast rather than prompting.

docs/wiki/Core-Concepts.md

@@ -25,7 +25,7 @@ Three ways to get one, all under **New or link a case…** at the bottom of the
 | How               | Result                                                                                                                                                                                                              |
 | ----------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | **Create New**    | A fresh `~/codeman-cases/<name>` with a scaffolded `CLAUDE.md`, or with **Create in a custom folder**, a new folder inside a parent you choose, scaffolded the same way and registered in place like a linked case. |
-| **Clone Repo**    | A repo cloned into `~/codeman-cases/<name>` (or into a folder you choose) and registered as a case. Private repos need this machine's own git credentials (see below).                                              |
+| **Clone Repo**    | A repo cloned into `~/codeman-cases/<name>` (or straight into an empty folder you choose) and registered as a case. Private repos need this machine's own git credentials (see below).                              |
 | **Link Existing** | An existing folder anywhere on disk, registered in place. Nothing is copied or moved.                                                                                                                               |
 
 Linked cases keep living where they are. Deleting a case in Codeman removes the

src/git-clone.ts

@@ -50,7 +50,7 @@
 import { spawn, execFileSync } from 'node:child_process';
 import { randomBytes } from 'node:crypto';
 import { existsSync } from 'node:fs';
-import { rename, rm } from 'node:fs/promises';
+import { lstat, readdir, rename, rm } from 'node:fs/promises';
 import { basename, dirname, join } from 'node:path';
 import { EXEC_TIMEOUT_MS } from './config/exec-timeout.js';
 
@@ -188,8 +188,13 @@ export interface GitFailure {
 export interface CloneOptions {
   /** Pre-validated operand from `parseGitRepositoryUrl`. */
   repository: string;
-  /** Absolute destination directory. Must NOT exist; created by git. */
+  /** Absolute destination directory. Must NOT exist (created by git), unless `intoEmptyDir` is set. */
   destination: string;
+  /**
+   * Clone straight into `destination` when it already exists as an EMPTY directory (the folder a user
+   * picked), instead of refusing it. A folder with anything in it, or a symlink, is still refused.
+   */
+  intoEmptyDir?: boolean;
   /** Optional branch or tag (`--branch <ref> --single-branch`). */
   ref?: string;
   /** `--depth 1`: history-less but much faster on large repos. */
@@ -847,6 +852,25 @@ export async function probeGitRemote(
   };
 }
 
+/** True for a real (not symlinked) directory with nothing in it. Any read error counts as not empty. */
+async function isEmptyDirectory(path: string): Promise<boolean> {
+  try {
+    const st = await lstat(path);
+    return st.isDirectory() && (await readdir(path)).length === 0;
+  } catch {
+    return false;
+  }
+}
+
+/** Remove everything inside `path`, keeping `path` itself. Best effort. */
+async function emptyDirectory(path: string): Promise<void> {
+  try {
+    for (const entry of await readdir(path)) await rm(join(path, entry), { recursive: true, force: true });
+  } catch {
+    /* nothing to clean, or it vanished */
+  }
+}
+
 /**
  * Clone `repository` into `destination`.
  *
@@ -872,10 +896,19 @@ export async function cloneRepository(opts: CloneOptions): Promise<CloneResult>
     };
   }
   if (existsSync(opts.destination)) {
-    return {
-      ok: false,
-      failure: { code: 'DESTINATION_EXISTS', message: 'The destination directory already exists.', stderr: '' },
-    };
+    if (!opts.intoEmptyDir || !(await isEmptyDirectory(opts.destination))) {
+      return {
+        ok: false,
+        failure: { code: 'DESTINATION_EXISTS', message: 'The destination directory already exists.', stderr: '' },
+      };
+    }
+    // The folder is the user's own, so there is no temporary sibling to rename into place: git fills it.
+    const direct = await runGit(buildCloneArgs(opts), opts.timeoutMs ?? GIT_CLONE_TIMEOUT_MS, MAX_STDERR_BYTES);
+    if (direct.code === 0 && !direct.spawnError) return { ok: true, stderr: sanitizeGitOutput(direct.stderr) };
+    // It was empty when the clone began, so whatever is in it now is this attempt's partial tree. The
+    // folder itself stays.
+    await emptyDirectory(opts.destination);
+    return { ok: false, failure: classifyGitFailure(direct.stderr, direct.timedOut, direct.spawnError) };
   }
 
   // Sibling of the destination (same filesystem), so the rename is atomic.

src/web/public/index.html

@@ -3658,15 +3658,15 @@
             </div>
             <div class="form-row" id="cloneCustomPathToggleRow">
               <label class="checkbox-row"><input type="checkbox" id="cloneCustomPathToggle" onchange="app.toggleCloneCustomPath()"> 📁 Clone into a custom folder</label>
-              <span class="form-hint">By default the clone goes under ~/codeman-cases. Choose another folder and it is cloned there instead; it is listed like any other case, and deleting the case only unlinks it (your files stay).</span>
+              <span class="form-hint">By default the clone goes under ~/codeman-cases. Choose a folder and the repository is cloned into that folder itself (it must be empty); it is listed like any other case, and deleting the case only unlinks it (your files stay).</span>
             </div>
             <div class="form-row" id="cloneCustomPathRow" style="display:none">
-              <label>Parent Folder</label>
+              <label>Folder</label>
               <div class="path-input-group">
                 <input type="text" id="cloneCasePath" placeholder="~/projects" autocomplete="off" autocapitalize="off" autocorrect="off" spellcheck="false" oninput="app.updateCloneCasePathPreview()">
                 <button type="button" class="btn path-input-browse" onclick="app.openCloneCasePathPicker()">Browse&hellip;</button>
               </div>
-              <span class="form-hint" id="cloneCasePathPreview">Pick the folder the clone should be created inside.</span>
+              <span class="form-hint" id="cloneCasePathPreview">Pick the empty folder to clone into.</span>
             </div>
             <div class="form-row">
               <label>Branch or Tag (optional)</label>

src/web/public/session-ui.js

@@ -4142,26 +4142,24 @@ Object.assign(CodemanApp.prototype, {
     const hint = document.getElementById('cloneCaseNameHint');
     if (hint) {
       hint.textContent = custom.checked
-        ? 'Filled in from the URL. Cloned into a folder of this name inside the parent folder below.'
+        ? 'Filled in from the URL. Names the case only: the repository is cloned into the folder chosen below.'
         : 'Filled in from the URL. Cloned into ~/codeman-cases/<name>, so deleting the case deletes this working tree.';
     }
     this.updateCloneCasePathPreview();
   },
 
-  /** The folder the clone would be created in: the parent field plus the case name. */
+  /** The folder the repository is cloned into: exactly what the field holds (no case name is added). */
   _cloneTargetPath() {
-    const rawParent = (document.getElementById('cloneCasePath')?.value || '').trim();
-    const name = (document.getElementById('cloneCaseName')?.value || '').trim();
-    if (!rawParent || !name) return '';
+    const raw = (document.getElementById('cloneCasePath')?.value || '').trim();
     // Trailing slashes off, but `/` stays the root rather than becoming an empty path.
-    return `${rawParent.replace(/\/+$/, '')}/${name}`;
+    return raw.length > 1 ? raw.replace(/\/+$/, '') || '/' : raw;
   },
 
   updateCloneCasePathPreview() {
     const hint = document.getElementById('cloneCasePathPreview');
     if (!hint) return;
     const target = this._cloneTargetPath();
-    hint.textContent = target ? `Will clone into: ${target}` : 'Pick the folder the clone should be created inside.';
+    hint.textContent = target ? `Will clone into: ${target}` : 'Pick the empty folder to clone into.';
   },
 
   openCloneCasePathPicker() {
@@ -4214,14 +4212,12 @@ Object.assign(CodemanApp.prototype, {
   onCloneNameEdited() {
     // Once the user types a name, autofill stops fighting them.
     this._cloneNameEdited = !!document.getElementById('cloneCaseName')?.value.trim();
-    this.updateCloneCasePathPreview();
   },
 
   onCloneUrlInput() {
     const url = document.getElementById('cloneRepoUrl')?.value.trim() || '';
     const nameInput = document.getElementById('cloneCaseName');
     if (nameInput && !this._cloneNameEdited) nameInput.value = this._repoNameFromUrl(url);
-    this.updateCloneCasePathPreview();
     clearTimeout(this._clonePreflightTimer);
     this._clonePreflightAbort?.abort();
     this._clonePreflightAbort = null;
@@ -4277,7 +4273,6 @@ Object.assign(CodemanApp.prototype, {
     // the case name is validated against), but never over a name the user typed.
     const nameInput = document.getElementById('cloneCaseName');
     if (nameInput && !this._cloneNameEdited && parse.suggestedName) nameInput.value = parse.suggestedName;
-    this.updateCloneCasePathPreview();
 
     const where = parse.owner ? `${parse.provider} ${parse.owner}/${parse.repo}` : `${parse.provider} ${parse.repo}`;
     if (data.gitAvailable === false) {

src/web/routes/case-routes.ts

@@ -714,6 +714,7 @@ export function registerCaseRoutes(
 
       const casesDir = resolveCasesDir(user);
       let casePath: string | null;
+      let intoEmptyDir = false;
       if (customPath !== undefined) {
         const prepared = await prepareNewCasePath(customPath, {
           home: homedir(),
@@ -738,18 +739,12 @@ export function registerCaseRoutes(
                 : prepared.code === 'EXISTS'
                   ? ApiErrorCode.ALREADY_EXISTS
                   : ApiErrorCode.INVALID_INPUT,
-            prepared.reason
-          );
-        }
-        // git clones into a fresh folder it creates itself; an empty existing one is refused rather than
-        // removed and re-made (the removal could race another writer).
-        if (prepared.existedEmpty) {
-          reply.code(409);
-          return createErrorResponse(
-            ApiErrorCode.ALREADY_EXISTS,
-            `${prepared.path} already exists. Pick a parent folder where the case folder does not exist yet.`
+            prepared.code === 'EXISTS'
+              ? `${customPath} already has files in it. Pick an empty folder, or a folder that does not exist yet.`
+              : prepared.reason
           );
         }
+        intoEmptyDir = prepared.existedEmpty;
         casePath = prepared.path;
         // The same folder listed as a local case in the cases dir would make deleting it remove files.
         if (existsSync(join(casesDir, name))) {
@@ -776,7 +771,8 @@ export function registerCaseRoutes(
         return createErrorResponse(ApiErrorCode.ALREADY_EXISTS, `That folder is already the case "${linkedAs}"`);
       }
       if (
-        existsSync(casePath) ||
+        // A custom folder was judged by prepareNewCasePath (an existing empty one is fine).
+        (customPath === undefined && existsSync(casePath)) ||
         linkedCases[name] ||
         dockerCases.some((item) => item.name === name) ||
         remoteCases.some((item) => item.name === name)
@@ -797,6 +793,7 @@ export function registerCaseRoutes(
       const clone = await cloneRepository({
         repository: parsed.repository,
         destination: casePath,
+        ...(intoEmptyDir ? { intoEmptyDir: true } : {}),
         withoutCredentialHelpers: cloneWithoutCredentialHelpers(req),
         ...(ref ? { ref } : {}),
         ...(shallow ? { shallow: true } : {}),

test/routes/case-clone-custom-folder.test.ts

@@ -1,14 +1,24 @@
 /**
- * @fileoverview POST /api/cases/clone with a `path`: clone into a custom folder and register it as a
- * linked case. Real filesystem under test/setup.ts's temp HOME and a REAL `git` cloning a local bare
- * repo (the path policy itself is in test/case-path.test.ts). Port: N/A (app.inject()).
+ * @fileoverview POST /api/cases/clone with a `path`: clone INTO that folder (an empty or not yet existing one,
+ * with no subfolder added) and register it as a linked case. Real filesystem under test/setup.ts's temp
+ * HOME and a REAL `git` cloning a local bare repo (the path policy itself is in test/case-path.test.ts).
+ * Port: N/A (app.inject()).
  *
  * Like case-custom-path-routes.test.ts this suite rewrites the linked-cases registry, so it refuses to
  * start outside the sandboxed HOME (a raw `npx vitest` would reach the real ~/.codeman).
  */
 import { afterAll, afterEach, beforeAll, beforeEach, describe, expect, it } from 'vitest';
 import { execFileSync } from 'node:child_process';
-import { existsSync, mkdirSync, mkdtempSync, readFileSync, realpathSync, rmSync, writeFileSync } from 'node:fs';
+import {
+  existsSync,
+  mkdirSync,
+  mkdtempSync,
+  readdirSync,
+  readFileSync,
+  realpathSync,
+  rmSync,
+  writeFileSync,
+} from 'node:fs';
 import { homedir, tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { createRouteTestHarness } from './_route-test-utils.js';
@@ -103,18 +113,33 @@ describe.skipIf(!isGitAvailable())('POST /api/cases/clone with a custom folder',
     writeFileSync(join(target, 'mine.txt'), 'keep me');
     const res = await clone(app, { name: 'busy', repository: origin, path: target });
     expect(res.statusCode).toBe(409);
+    expect(res.json().error).toMatch(/already has files/);
     expect(readFileSync(join(target, 'mine.txt'), 'utf8')).toBe('keep me');
     expect(linked()).toEqual({});
   });
 
-  it('refuses an existing EMPTY folder rather than removing and re-making it', async () => {
+  it('clones straight INTO the chosen empty folder, with no subfolder named after the case', async () => {
     const { app } = await createRouteTestHarness(registerCaseRoutes);
-    const target = join(workDir, 'empty');
+    const target = join(workDir, 'picked');
     mkdirSync(target);
-    const res = await clone(app, { name: 'empty', repository: origin, path: target });
-    expect(res.statusCode).toBe(409);
-    expect(res.json().error).toMatch(/already exists/);
-    expect(existsSync(join(target, '.git'))).toBe(false);
+    const res = await clone(app, { name: 'a-different-name', repository: origin, path: target });
+    expect(res.statusCode).toBe(200);
+    expect(res.json().data.case).toEqual({ name: 'a-different-name', path: target });
+    expect(existsSync(join(target, 'README.md'))).toBe(true);
+    expect(existsSync(join(target, '.git'))).toBe(true);
+    expect(existsSync(join(target, 'a-different-name'))).toBe(false);
+    expect(linked()).toEqual({ 'a-different-name': target });
+  });
+
+  it('leaves the empty folder in place, and empty, when the clone fails', async () => {
+    const { app } = await createRouteTestHarness(registerCaseRoutes);
+    const target = join(workDir, 'stays');
+    mkdirSync(target);
+    const res = await clone(app, { name: 'stays', repository: join(root, 'no-such-repo.git'), path: target });
+    expect(res.json().success).toBe(false);
+    expect(existsSync(target)).toBe(true);
+    expect(readdirSync(target)).toEqual([]);
+    expect(linked()).toEqual({});
   });
 
   it('refuses a blocked tree such as ~/.ssh', async () => {