Dependabot PRs failing due to outdated `pnpm-lock.yaml`

### Description
Dependabot PRs are failing in CI because Dependabot is only updating the `package.json` files but not correctly regenerating the corresponding `pnpm-lock.yaml` files.

Error Message
```
ERR_PNPM_OUTDATED_LOCKFILE  Cannot install with "frozen-lockfile" because pnpm-lock.yaml is not up to date with <ROOT>/sites/xyflow.com/package.json
```