File taxonomy and possible re-organization

[mhearne-usgs]

A taxonomy of the folders/files created/used by WASP would be helpful - first step to maybe trying to re-organize a little, identify any extraneous files. I'd like to see

1. demarcation of input/output files
2. combination of metadata into fewer (maybe 1?) JSON files
3. plots going into "plots" folder, etc.
4. Use of file extensions to indicate the format of the file.