improve documentation for scripts directories

[NewGraphEnvironment]

copy out everything relevant to 01_prep_inputs from the parent directory README.md and put it into that directory with headers for each of the files in there. Then the parent diretory README.md just lists the raw .R files and what they do as well as the three directories (with headers and says generally what they do)

1. getting data ready for reporting
2. creating materials for reporting froom complete dataset
3. Extracting information for permit data submission requirements

This process will help us/others understand/remember what all these scripts do and help us evolve the way we structure these repos.