Slash-command popup overlaps and bleeds through the branch/checkout repo dialog (z-index/layering bug)

### Summary

The slash-command (`/`) autocomplete popup renders **on top of and bleeds through** the "Pick a branch and checkout mode for each repo" dialog. Both layers are visible at the same time — the command list (`/inbox`, `/chronicle`, `/docx`, …) overlaps the repo rows and their branch dropdowns, making both unreadable. Looks like a z-index / layering (modal stacking) issue.

### Steps to reproduce

1. Open the "Pick a branch and checkout mode for each repo" screen (multi-repo branch selection).
2. With that dialog open, focus the prompt box and type `/` to trigger the slash-command menu.
3. The slash-command dropdown appears over the dialog, and the two layers visibly overlap / show through each other.

### Expected

The slash-command menu should either be suppressed while that dialog is open, or render in its own opaque layer that doesn't overlap/bleed through the repo+branch list.

### Actual

Both UIs render in the same space simultaneously — text from the repo list (e.g. "FE.MSecSCC", "WDATP.Infra.App.Tenant…", branch "main" dropdowns) shows through the slash-command popup, and vice versa.

### Environment

- GitHub Copilot desktop app, macOS (Apple Silicon).

### Additional context

Screenshot attached showing the overlap (repo/branch dialog behind, slash-command list in front, both visible through each other).

Start by reproducing the multi-repo branch-selection dialog and then opening the slash-command menu from the prompt box. Inspect the dialog and popup layering to determine whether the menu should be suppressed or rendered as an opaque, non-overlapping layer; done means the repo rows, branch dropdowns, and command list remain separately readable.

Written by the indexing model from the issue text.