test(freshness_checksum): enable -Zfreshness-checksum

These tests are modified or renamed to reflect the switch to
checksum fingerprint:

* bust_patched_dep
* modifying_and_moving
* rebuild_on_mid_build_file_modification
* rebuild_sub_package_then_while_package
* skip_mtime_check_in_selected_cargo_home_subdirs
* use_mtime_cache_in_cargo_home

Author: weihanglo