clarify the structure of analysis directories

[adamcantor22]

Is your feature request related to a problem? Please describe.
The intended structure of the analysis directories is unclear. Similarly to as in #457, the definition of what goes in an analysis dir and what becomes a separate or child analysis dir. Directories are also not well named ("{Tool}_#", particularly so once multiple analyses have been run) and are poorly organized, leading to cases of having to comb through many results and manually organize them.

Describe the solution you'd like
We should meet at some point to discuss this and #457, determine any modifications to the design