gh stack modify: modify fails when merged branches have been pruned

Looks like modify can't deal with pruned branches once they have been merged.

See below output:

```
➜ token-scanning-service git:(aerendel/fix-generic-secrets-metadata) gh stack modify
✗ failed to apply modifications: building snapshot: resolving branch SHAs: failed to run git: fatal: ambiguous argument 'aerendel/mixed-content-types1': unknown revision or path not in the working tree.
Use '--' to separate paths from revisions, like this:
'git [...] -- [...]'
```

### Observed behavior:
The bottom of my stack has been merged and the branch pruned so it doesn't exist locally or remotely anymore (not unusual once a branch is merged), and all `gh stack modify` operations fail to save. Any operation will fail, wether it's renaming a branch, reorganizing, dropping a branch, etc.

### Repro:
1. Make a stack with 2 or 3 layers
2. Merge the first layer
3. Delete the first layer's branch locally (or just answer Yes to gh stack's prune prompt)
4. Run `gh stack modify` and try to save any modify operation

Start at the gh stack modify flow and the snapshot step that resolves branch SHAs, then reproduce the issue by pruning the bottom branch of a two- or three-layer stack. Done means renaming, reorganizing, dropping, and other modify operations can save successfully after the merged branch is deleted locally and remotely.

Written by the indexing model from the issue text.