Ensure user-provided PDBs are used for clustering

[keithchev]

Overview

This PR makes two changes to fix bugs that may prevent user-provided PDB files from being used for clustering:

• it makes copy_pdb and make_pdb ambiguous rules with precedence given to copy_pdb; this prevents make_pdb from being called if a user-provided PDB is present for a given input protid
• it removes the input protids from the list of protids for which to download PDBs from alphafold so that either copy_pdb or make_pdb is always called for all of the input protids

This should (hopefully) address #82.

This behavior is not currently covered by automated testing, but I tested manually that copy_pdb is called when a PDB is present in the input directory, whether or not its protid was among the aggregated hits for which alphafold PDBs are downloaded.

PR checklist

• [x] Tag the issue(s) or milestones this PR fixes (e.g. Fixes #123, Resolves #456).
• [x] Describe the changes you've made.
• [x] Describe any tests you have conducted to confirm that your changes behave as expected.
• [x] If you've added new software dependencies, make sure that those dependencies are included in the appropriate conda environments.
• [x] If you've added new functionality, make sure that the documentation is updated accordingly.
• [x] If you encountered bugs or features that you won't address, but should be addressed eventually, create new issues for them.