Summary

Closes #413.

The first full mutation run failed its unmutated baseline in every shard because cargo_update_directories_match_manifests walked the file system for Cargo.toml manifests and found the shared mutation workflow's untracked workflow-src/ checkout, which .github/dependabot.yml legitimately does not list.

This branch implements option 1 from the issue: the test now enumerates manifests with git ls-files -z -- '*Cargo.toml', so only tracked manifests participate in the comparison and untracked content (workflow-src, build artefacts, scratch directories) becomes invisible. The test's intent is unchanged: a newly tracked manifest directory missing from .github/dependabot.yml still fails it. When the source tree is not a git checkout — cargo-mutants builds in a scratch copy that omits .git — the test skips the comparison, since tracked-manifest hygiene is meaningless there.

Review walkthrough

• Start with tracked_cargo_manifest_dirs in tests/dependabot_config_tests.rs: it shells out to git ls-files and maps each tracked manifest's parent directory to Dependabot's POSIX form, returning NotAGitCheckout when the tree has no repository.
• Then see the call site in tests/dependabot_config_tests.rs, where the non-checkout case skips with a captured notice (wrapped in #[expect(clippy::print_stderr)] with a justification).
• The directory-walk helpers remain because local_action_manifest_dirs still uses them for the .github/actions scan, which is confined to tracked configuration.

Validation

• Red check: adding a tracked red_check_crate/Cargo.toml not listed in dependabot.yml makes cargo_update_directories_match_manifests FAIL as intended; reverting restores the pass.
• Pollution simulation: with an untracked workflow-src/rust-toy-app/Cargo.toml inside the checkout (mirroring the shared workflow's fixtures), the full test file passes.
• Non-checkout simulation: in a copy of the tree without .git (mirroring the cargo-mutants scratch copy) and with the workflow-src pollution present, the test prints skipping: source tree is not a git checkout and passes.
• Mutation-baseline verification: cargo test --all-features passes on three consecutive runs (matching the caller's extra-args).
• Repository gates: make check-fmt, make lint, make typecheck, make test, make test-workflow-contracts, make test-typos-config, make markdownlint, and make nixie all pass locally (the Whitaker Dylint suite is unavailable locally and is exercised in CI).