diff --git a/apps/desktop/src/main/__tests__/project-management-service.test.ts b/apps/desktop/src/main/__tests__/project-management-service.test.ts
index 8b6384f5b6..e1138ed173 100644
--- a/apps/desktop/src/main/__tests__/project-management-service.test.ts
+++ b/apps/desktop/src/main/__tests__/project-management-service.test.ts
@@ -1,8 +1,12 @@
 import assert from 'node:assert/strict';
+import { execFile } from 'node:child_process';
 import { mkdir, mkdtemp, realpath, rm } from 'node:fs/promises';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 import { test } from 'node:test';
+import { promisify } from 'node:util';
+
+const execFileAsync = promisify(execFile);
 import { createProjectCatalog, type ProjectCatalog } from '@maka/storage';
 import {
   createProjectManagementService,
@@ -67,6 +71,49 @@ test('owns Project selection and reversible lifecycle actions in Desktop', async
   }
 });
 
+test('adding a nested folder selects that folder instead of the parent project', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-nested-add-'));
+  const parentPath = join(base, 'parent-project');
+  const childPath = join(parentPath, 'child-project');
+  await mkdir(childPath, { recursive: true });
+  await execFileAsync('git', ['init', '--quiet'], { cwd: parentPath });
+
+  const selected: string[] = [];
+  let nextDirectory = parentPath;
+  let nextId = 0;
+  const catalog = createProjectCatalog(join(base, 'storage'), {
+    now: () => 1_000,
+    createId: () => `project-${++nextId}`,
+  });
+  const service = createProjectManagementService({
+    capabilities: LOCAL_CAPABILITIES,
+    catalog: managementCatalog(catalog),
+    chooseDirectory: async () => nextDirectory,
+    selection: {
+      currentSelection: async () => ({ projectId: undefined, path: parentPath }),
+      setSelection: (_projectId, path) => selected.push(path),
+    },
+  });
+
+  try {
+    const parent = await service.add();
+    assert.equal(parent.ok, true);
+    if (!parent.ok) return;
+    assert.equal(parent.path, await realpath(parentPath));
+
+    nextDirectory = childPath;
+    const child = await service.add();
+    assert.equal(child.ok, true);
+    if (!child.ok) return;
+    assert.notEqual(child.project.id, parent.project.id);
+    assert.equal(child.path, await realpath(childPath));
+    assert.equal(selected.at(-1), await realpath(childPath));
+  } finally {
+    catalog.close();
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
 test('rejects malformed Project identities before catalog access', async () => {
   const service = createProjectManagementService({
     capabilities: LOCAL_CAPABILITIES,
@@ -117,9 +164,7 @@ test('does not silently replace a stale Project preference with another Project'
   const service = createProjectManagementService({
     capabilities: LOCAL_CAPABILITIES,
     catalog: {
-      list: async () => [
-        { id: 'other', name: 'Other', locations: [], available: true },
-      ],
+      list: async () => [{ id: 'other', name: 'Other', locations: [], available: true }],
       register: unexpected,
       relink: unexpected,
       rename: unexpected,
diff --git a/packages/storage/src/__tests__/project-catalog.test.ts b/packages/storage/src/__tests__/project-catalog.test.ts
index 4a11b4c154..36782d0fa7 100644
--- a/packages/storage/src/__tests__/project-catalog.test.ts
+++ b/packages/storage/src/__tests__/project-catalog.test.ts
@@ -10,6 +10,7 @@ import {
   createProjectCatalog as createProjectCatalogBase,
   type ProjectCatalog,
   ProjectUnavailableError,
+  ProjectPathMismatchError,
   type ResolvedProjectLocation,
   resolveProjectLocation,
 } from '../project-catalog.js';
@@ -116,6 +117,96 @@ test('a repository and its linked worktree resolve to one project identity', asy
   }
 });
 
+test('registering a nested folder keeps that folder instead of the enclosing repository', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-nested-folder-'));
+  try {
+    const parent = join(base, 'parent-project');
+    const child = join(parent, 'child-project');
+    await mkdir(child, { recursive: true });
+    await execFileAsync('git', ['init', '--quiet'], { cwd: parent });
+    const catalog = createProjectCatalog(join(base, 'storage'), {
+      now: () => 1_000,
+      createId: (() => {
+        let id = 0;
+        return () => `project-${++id}`;
+      })(),
+    });
+
+    const parentProject = await catalog.register(parent);
+    const childProject = await catalog.register(child);
+    const parentPath = await realpath(parent);
+    const childPath = await realpath(child);
+
+    assert.notEqual(childProject.id, parentProject.id);
+    assert.equal(parentProject.preferredPath, parentPath);
+    assert.equal(childProject.preferredPath, childPath);
+    assert.equal(childProject.name, 'child-project');
+
+    // session.create → HostWorkspaceResolver.touch(projectId, preferredPath)
+    const touched = await catalog.touch(childProject.id, childProject.preferredPath);
+    assert.equal(touched.id, childProject.id);
+    assert.equal(touched.preferredPath, childPath);
+    await assert.rejects(
+      () => catalog.touch(childProject.id, parentPath),
+      (error) => error instanceof ProjectPathMismatchError && error.projectId === childProject.id,
+    );
+  } finally {
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
+test('relink and relinkWithSessions keep a nested repository directory', async () => {
+  const base = await mkdtemp(join(tmpdir(), 'maka-project-nested-relink-'));
+  const storage = join(base, 'storage');
+  const sessions = createSessionStore(storage);
+  try {
+    const parent = join(base, 'parent-project');
+    const child = join(parent, 'child-project');
+    const childTwo = join(parent, 'child-two');
+    const elsewhere = join(base, 'elsewhere');
+    const elsewhereTwo = join(base, 'elsewhere-two');
+    await mkdir(child, { recursive: true });
+    await mkdir(childTwo, { recursive: true });
+    await mkdir(elsewhere, { recursive: true });
+    await mkdir(elsewhereTwo, { recursive: true });
+    await execFileAsync('git', ['init', '--quiet'], { cwd: parent });
+    const catalog = createProjectCatalog(storage, {
+      now: () => 1_000,
+      createId: (() => {
+        let id = 0;
+        return () => `project-${++id}`;
+      })(),
+    });
+
+    const parentProject = await catalog.register(parent);
+    const original = await catalog.register(elsewhere);
+    const originalSessions = await catalog.register(elsewhereTwo);
+    const childPath = await realpath(child);
+    const childTwoPath = await realpath(childTwo);
+    const assigned = await sessions.create(sessionInput(elsewhereTwo, originalSessions.id));
+
+    const relinked = await catalog.relink(original.id, child);
+    assert.equal(relinked.id, original.id);
+    assert.notEqual(relinked.id, parentProject.id);
+    assert.equal(relinked.preferredPath, childPath);
+
+    const { project: relinkedSessions, updatedSessionIds } = await catalog.relinkWithSessions(
+      originalSessions.id,
+      childTwo,
+    );
+    assert.equal(relinkedSessions.id, originalSessions.id);
+    assert.notEqual(relinkedSessions.id, parentProject.id);
+    assert.equal(relinkedSessions.preferredPath, childTwoPath);
+    assert.deepEqual(updatedSessionIds, [assigned.id]);
+    const header = await sessions.readHeaderSnapshot(assigned.id);
+    assert.equal(header.projectId, relinkedSessions.id);
+    assert.equal(header.cwd, childTwoPath);
+  } finally {
+    await sessions.close?.();
+    await rm(base, { recursive: true, force: true });
+  }
+});
+
 async function resolveProjectLocationWithoutGit(path: string): Promise<ResolvedProjectLocation> {
   const stdout = await runProjectCatalogWithoutGit(
     'const [moduleUrl, path] = process.argv.slice(1); const { resolveProjectLocation } = await import(moduleUrl); console.log(JSON.stringify(await resolveProjectLocation({ path })));',
diff --git a/packages/storage/src/project-catalog.ts b/packages/storage/src/project-catalog.ts
index 5fc0ae7b14..3882aad95e 100644
--- a/packages/storage/src/project-catalog.ts
+++ b/packages/storage/src/project-catalog.ts
@@ -164,7 +164,7 @@ class SqliteProjectCatalog implements ProjectCatalog {
   }
 
   async register(path: string): Promise<ProjectRecord> {
-    const resolved = await resolveProjectLocation({ path });
+    const resolved = await resolveUserSelectedProjectLocation(path);
     return this.upsertResolvedProject(resolved, this.now());
   }
 
@@ -271,27 +271,24 @@ class SqliteProjectCatalog implements ProjectCatalog {
   }
 
   async touch(projectId: string, path?: string): Promise<ProjectRecord> {
-    let resolved: Awaited<ReturnType<typeof resolveProjectLocation>> | undefined;
-    try {
-      resolved = path ? await resolveProjectLocation({ path }) : undefined;
-    } catch {
-      throw new ProjectUnavailableError(projectId);
+    let canonicalPath: string | undefined;
+    if (path) {
+      try {
+        canonicalPath = normalize(await realpath(resolve(path)));
+      } catch {
+        throw new ProjectUnavailableError(projectId);
+      }
     }
-    const resolvedPath = resolved
-      ? resolved.kind === 'git'
-        ? resolved.git!.worktreeRoot
-        : resolved.canonicalPath
-      : undefined;
     const touched = await this.mutate((file) => {
       const project = findProjectById(file.projects, projectId);
       if (!project) throw new ProjectNotFoundError(projectId);
-      const location = resolvedPath
-        ? project.locations.find((item) => item.path === resolvedPath)
+      const location = canonicalPath
+        ? project.locations.find((item) => item.path === canonicalPath)
         : [...project.locations].sort(
             (a, b) => b.lastUsedAt - a.lastUsedAt || a.path.localeCompare(b.path),
           )[0];
-      if (resolvedPath && !location) {
-        throw new ProjectPathMismatchError(projectId, resolvedPath);
+      if (canonicalPath && !location) {
+        throw new ProjectPathMismatchError(projectId, canonicalPath);
       }
       const timestamp = this.now();
       if (location) location.lastUsedAt = timestamp;
@@ -302,7 +299,7 @@ class SqliteProjectCatalog implements ProjectCatalog {
   }
 
   async relink(projectId: string, path: string): Promise<ProjectRecord> {
-    const resolved = await resolveProjectLocation({ path });
+    const resolved = await resolveUserSelectedProjectLocation(path);
     const timestamp = this.now();
     const locationPath =
       resolved.kind === 'git' ? resolved.git!.worktreeRoot : resolved.canonicalPath;
@@ -322,7 +319,7 @@ class SqliteProjectCatalog implements ProjectCatalog {
     projectId: string,
     path: string,
   ): Promise<{ project: ProjectRecord; updatedSessionIds: readonly string[] }> {
-    const resolved = await resolveProjectLocation({ path });
+    const resolved = await resolveUserSelectedProjectLocation(path);
     const timestamp = this.now();
     const locationPath =
       resolved.kind === 'git' ? resolved.git!.worktreeRoot : resolved.canonicalPath;
@@ -835,6 +832,30 @@ export async function resolveProjectLocation(input: {
   };
 }
 
+/**
+ * A directory the user picked in the add/relink chooser.
+ *
+ * `resolveProjectLocation` still walks to the enclosing Git worktree so a
+ * historical session cwd inside a repository stays on that repository.
+ * The chooser must not do that: selecting `repo/child` would otherwise
+ * silently become `repo` and reopen the parent project.
+ */
+async function resolveUserSelectedProjectLocation(path: string): Promise<ResolvedProjectLocation> {
+  const resolved = await resolveProjectLocation({ path });
+  if (
+    resolved.kind !== 'git' ||
+    !resolved.git ||
+    resolved.canonicalPath === resolved.git.worktreeRoot
+  ) {
+    return resolved;
+  }
+  return {
+    canonicalPath: resolved.canonicalPath,
+    identity: `folder:${resolved.canonicalPath}`,
+    kind: 'folder',
+  };
+}
+
 async function resolveGitLocation(
   canonicalPath: string,
 ): Promise<NonNullable<ResolvedProjectLocation['git']>> {