Standardize behaviors and designs in rdock-utils

[ggutierrez-sunbright]

Some of the tools in rdock-utils differ in their behavior (toward or from configuration parameters) and the look and feel.

before the official release, we need to make the experience more homogeneous.

this includes, but is not limited to:

• having all configuration dataclasses separated from parsing (probably in the same file as the tool)
• having a subpackage for each tool (right now the most simple ones are single files)
• descriptions and help messages