[FEATURE] Desktop app: configure persistent working directories per project

Problem

In the Claude Code desktop app, a project maps to a single folder. Many real projects span several directories: a backend repo, a frontend repo, shared libraries, infra/config repos, and so on. Today the extra folders have to be attached to each session by hand, every time a new session starts.

The existing workarounds don't cover this well:

• --add-dir is a CLI flag and only lasts for one launch.
• permissions.additionalDirectories in settings.json needs manual JSON editing, isn't visible or editable in the desktop UI, and lives in one checkout instead of on the project. #92582 also reports that it isn't always honored.

Proposed solution

Let users configure working directories per project:

1. Project settings get a list of working directories: one primary directory and any number of additional ones, with add, remove, reorder and "set as primary" in the UI.
2. Every new session in the project starts with all of these directories attached: file pane, tool permissions, @-mentions and search.
3. Per-directory worktree option: when a session runs in a worktree, choose for each directory whether it gets its own worktree or is shared as-is.
4. Optionally keep the list in sync with permissions.additionalDirectories in .claude/settings.local.json, so the CLI and the IDE extensions pick it up too.

Why

Multi-repo work is common, and re-adding the same folders to every session is repetitive and easy to forget. When a folder is missing, Claude can't read or edit the related code.

Related

• #36949: claudeCode.workingDirectory setting for VS Code multi-root workspaces
• #89094: pin a session to a root folder in a multi-root VS Code workspace
• #92453: iPad app has no way to select or change the working folder
• #92582: additionalDirectories from project settings ignored by blockReadsOutsideWorkingDirectories

Environment

• Claude Code desktop app (Code tab), Linux