gh stack sync --prune for a completed stack deletes the branch but leaves stack in gh stack checkout metadata

gh stack sync --prune for a completed stack deletes the branch but leaves stack in gh stack checkout metadata.

Repro steps:
1. Create a stack with 1 branch.
2. Submit PR
3. Complete PR
4. Run gh stack sync --prune
5. Branch is synced and deleted
6. Run `gh stack checkout`
7. Observe

Expected: Stack should be deleted
Actual: Stack is not deleted, and cannot be selected because the branch no longer exists.
Workaround: Create a branch with the same name as one that doesn't exist. Run `gh stack untrack`, delete branch.

使用一個包含一個分支的 stack 重現該問題：在其 PR 完成後執行 `gh stack sync --prune`，然後執行 `gh stack checkout`。追蹤 sync prune 路徑以及 checkout 中繼資料處理；完成標準是，已完成的 stack 從中繼資料中移除，且不再作為無效的可選 stack 顯示。

由索引模型根據 Issue 內容生成。