Anyone find the positional script arguments confusing?

[kyleabeauchamp]

So my one beef with the current scripts is how the meaning of various flags changes as you move from left to right. I know we're short on characters, but I bet a lot of people are troubled by the following example:

Cluster.py rmsd kcenters -k 5 -p Project.yaml  # Fails
Cluster.py -p Project.yaml rmsd kcenters -k 5  # Runs

[schwancr]

This has caused quite a few people coming to me with a failed run.

It's actually more than just a lack of characters, because it's a feature of argparse, since we're using subparsers, each subparser is not aware of the parent parser

[rmcgibbo]

I'm all ears if anyone has a "solution", but I don't see how to change this.