`bazel mod tidy` removes a transitive Swift package repo from use_repo and breaks builds

With `rules_swift_package_manager` `1.14.0`, `bazel mod tidy` removes a transitive Swift package repo from `use_repo(...)`, and a subsequent Bazel build fails when a target depends on that repo directly. ## Repro https://github.com/bc-lee/rules-swift-package-manager-mod-tidy-repro ```bash git clone https://github.com/bc-lee/rules-swift-package-manager-mod-tidy-repro.git cd rules-swift-package-manager-mod-tidy-repro bazelisk build //... bazelisk mod tidy git diff -- MODULE.bazel bazelisk build //... ``` ## Actual After `bazel mod tidy`, a transitive Swift package repo is removed from `use_repo(...)`. In this repro, `swiftpkg_grdb.swift` is removed, and the next build fails because `//:repro` depends on `@swiftpkg_grdb.swift//:GRDB-dynamic`. ## Expected `bazel mod tidy` should not remove a Swift package repo that is still needed by Bazel targets in the root module. ## Notes In this repro, `swiftpkg_grdb.swift` comes from the resolved transitive SwiftPM dependency graph, not from the root `Package.swift` dependency list.