[FEATURE] Desktop app: remember additional folders per project across sessions

Preflight Checklist

• [x] I have searched existing requests and this feature hasn't been requested yet
• [x] This is a single feature request (not multiple features)

Problem Statement

Environment

• Claude Code Desktop app 2.110.0, Windows 11 Pro
• Working folder is a git repository; two sibling repositories are used in every session as additional folders

What happens now
Additional folders added to a session are lost as soon as a new session is started in the same working folder.

I tested three ways on 16 Sep 2026:

1. Added both folders via "+" → "Add folder" in the new-session composer, sent a message. The next new session in the same working folder started with only the working folder on the bar.
2. Claude added them itself via the request_directory tool. Access was granted, but no folder chip appeared on the session bar.
3. Listed both folders in .claude/settings.json under permissions.additionalDirectories. This grants file access, but the folders are not shown on the bar.

In each case the folders are stored only in that one session's record (sessionPermissionUpdates). There is no project-level or app-level setting that keeps them.

What I expect
When I add additional folders to a session, the app should offer or restore the same folders for every new session in the same working folder, until I remove them. Whether a folder is on the bar or not should be my choice, made once, not repeated at the start of every session.

On my previous computer, with an earlier version of the app, folders added once stayed in place for later sessions. After moving to a new computer with 2.110.0 this no longer happens.

Suggested behaviour

• Remember additional folders per working folder (for example next to permissions.additionalDirectories, or as an app-side per-project setting).
• Show them on the session bar from the first message of every new session.
• Let the user remove them from the bar; removal should also persist.

Related: #3146 (settings-file support for additional directories, which grants access but does not show folders on the Desktop session bar).

Proposed Solution

Remember additional folders per working folder and show them on the session bar from the first message of every new session. Let the user remove them; removal should also persist.

Alternative Solutions

_No response_

Priority

Critical - Blocking my work

Feature Category

CLI commands and flags

Use Case Example

_No response_

Additional Context

_No response_