[BUG] Claude Desktop: primary working directory locked to a different folder than the one selected when opening a session

What's Wrong?

In Claude Desktop (macOS), there is no way to set the primary working directory of a new session to the folder I actually want to work in. When I try to open a session for one project folder, a different folder is forced as the primary cwd, and the folder I selected ends up only as an "additional working directory" — visible to tools, but not the real cwd.

In my case the symptom is: I want to open a session in ~/Documents/sites/peugeot, but every new session opens with ~/Documents/admin-module as the primary cwd and ~/Documents/sites/peugeot only attached as an additional working directory. The session's environment header confirms this:

Primary working directory: /Users/.../Documents/admin-module
Additional working directories:
  - /Users/.../Documents/sites/peugeot

The user-facing problem is that the primary cwd cannot be changed from the UI. Tools that key off cwd (e.g. Claude Preview's preview_start, which reads .claude/launch.json from the primary cwd, and any model behavior that pivots on the primary directory) end up operating on the wrong project. From inside a session there is no way to fix it — --add-dir-style "additional directories" exist but there is no equivalent mechanism for changing the primary cwd, and the Desktop UI does not appear to expose one either.

I have two related project folders (a template and a per-site instance copied from it). Once Desktop has decided one is "the" project, opening the other from the picker keeps the first as primary.

What Should Happen?

When I pick a folder in Claude Desktop's project picker / "Open Folder" / new-session flow, that folder should become the primary working directory of the new session. Other folders should only be attached as additional working directories if I explicitly add them.

At minimum, the UI should let me see and change the primary cwd before/at session start, so I'm not stuck with the wrong one.

Steps to Reproduce

1. Have two project folders on disk, e.g. ~/projA and ~/projB. (projB being a copy/derivative of projA may or may not matter — needs verification.)
2. Open projA in Claude Desktop and use it for a while (so it becomes the "remembered" project).
3. From Claude Desktop, try to open a new session in projB (via the project picker / open folder UI).
4. In the new session, ask the assistant or check the env header for the primary working directory.
5. Observed: primary cwd is projA; projB is attached as an additional working directory.
6. Expected: primary cwd is projB.

I have not yet been able to find a UI control that changes the primary cwd, hence the report.

Environment

• Claude Desktop (macOS) — Claude.app 1.6259.1
• Bundled claude-code: 2.1.128
• macOS: Darwin 25.4.0 (arm64)
• Entry point: claude-desktop (per session metadata in ~/.claude/sessions/*.json)

Notes / Workarounds tried

• Cleaning up cross-project references in .claude/launch.json files so neither project's launch config cds into the other folder. This avoids one source of cross-pollution but does not fix the underlying Desktop bug — the primary cwd is still forced to the wrong folder when opening a new session from the picker.
• The only reliable workaround is launching the bundled CLI directly from a terminal with cd <correct folder> && claude, bypassing the Desktop project picker entirely. This is not discoverable for users who installed Claude via the Desktop app, since no claude binary is placed on PATH by default.