Ensure pre-commit hook scans staged files

[mtdowling]

This commit updates the pre-commit hook to scan staged files instead of files in the working directory.

This ensures that if a staged file was invalid, then the working directory version of the file was fixed, that the --scan command will still detect the error in the staged file rather than thinking the problem is fixed due to the modified working directory file. See here for the added test case.

In order to achieve this, I introduced the --cached option to scan. This matches the --cached option from git grep. I also added --no-index and --untracked. With the addition of these changes, I added more validation to the provided arguments of the tool to ensure that the user only supplies arguments related to the subcommand they are running, and that mutually exclusive arguments are not present. For example, --recursive cannot be used alongside --cached because --recursive is only relevant when working with files outside of the git repository.

Closes #12

@trevorrowe @jamesls @jeskew

[jeskew]

LGTM