[Bug]: Folders added from inside one repository merge into a single project, so I cannot start a thread in a specific folder

[VIPlearner]

Before submitting

• I searched existing issues and did not find a duplicate.
• I included enough detail to reproduce or investigate the problem.

Area

apps/web

Steps to reproduce

I work in a monorepo. Different parts of it are effectively separate projects, and I want a
session per part, each starting in its own folder.

1. Take a repository with a git remote, for example acme-corp/platform, containing apps/web
   and services/api.
2. Add the repository root as a project.
3. Add apps/web as a project.
4. Add services/api as a project.
5. Open the project picker in the sidebar.

Expected behavior

Three projects, one per folder I added. I added them separately because I want to start a
thread in a specific folder and have the agent work there.

Actual behavior

One entry, named after the repository: acme-corp/platform.

The folders I added are not listed anywhere in the picker, so there is no way to choose one.
Opening the single entry puts me in one of the three folders, and a thread I start from it runs
in that folder rather than the one I meant. Nothing indicates this happened, so the agent just
works in the wrong directory.

Threads I already have in those folders also show under that one repository entry, so I cannot
tell which folder a thread belongs to by looking at the sidebar.

Adding the projects works fine, which is what makes it confusing: T3 Code accepts all three
paths, then behaves as though I only added one.

Impact

Major degradation or frequent failure

Version or commit

main @ 6c58362, run from source.

Environment

macOS 15, Chrome.

Screenshots, recordings, or supporting files

Four projects added: the acme-platform repository root, its apps/web and services/api
folders, and a separate toolbox repository. Only three entries appear, and the two monorepo
folders are not among them.

Workaround

Two, both with a cost:

• Set the grouping override to Keep separate on each folder individually. This works, but
  you have to know the setting exists and repeat it for every folder you add.
• Turn project grouping off globally. This also splits up worktrees and second checkouts of the
  same repository, which is the thing grouping is for.

---

Related: #4188 was about the ungroup control being hard to find, and was fixed by #5768. This is
a different problem: the folders inside a repository cannot be selected at all, whatever the
grouping setting is called.

I have opened #10922 with a proposed fix.