restoreConfigFromBase and setupBranch pass --depth to every git fetch. On a
checkout made with fetch-depth: 0 that does not just cap the download: it
truncates the history already present and marks the repository shallow, which
drops the merge base with the base branch. `git log origin/<base>..HEAD` then
silently includes commits that are already merged, and
`git diff origin/<base>...HEAD` fails with "no merge base" — the two commands
the prompt tells Claude to run to scope its work to the PR.
Gate the flag on `git rev-parse --is-shallow-repository`, so a checkout that is
already shallow (the fetch-depth: 1 default) keeps the same depth behaviour and
the fetch savings it was added for, while a full checkout stays full.
Fixes#1642
