Replace click with argparse

We use argparse everywhere else, and aren't using anything special about click. It should be possible to (carefully) replace it in molecule.

Start by locating Molecule's click-based command-line entry points and compare them with the existing argparse usage elsewhere in the project. Carefully replace the click integration while preserving current command-line behavior, then run the project's tests to confirm the migration is complete.

Written by the indexing model from the issue text.