Remove deleted files from records file when `--stage-record-file` flag is used

[frankieyan]

Currently, because we throw when a non-existant path is encountered, we are unable to remove deleted files from the records file.

This was introduced in #21, where we used to read deleted files directly from git prior to that change. Since requiring a file list, it no longer checks for deleted files.

[frankieyan]

lint-staged by default doesn't pass in deleted file paths. It'd be better UX to have the tool check all paths for existance and remove those that no longer exist.