clean up repo for publication

[sr320]

No description provided.

[yaaminiv]

place files to be deleted in the trash so we can review before deleting: https://github.com/sr320/ceabigr/tree/main/trash

[kubu4]

I don't think they need to be deleted, do they? I mean, I guess we could recover them by rolling back to earlier commits if needed, but we might want to reference/access various scripts for other projects/uses without having to perform that step.

[sr320]

big goal now is making repo understandable by someone reading the paper.

[yaaminiv]

i think the place to start are the code and output READMEs.

i moved miscellaneous code and output directories to the misc directory (formerly trash) and updated the code README with all scripts i used for the analysis and output README with the output directories related to information discussed in the paper.

@sr320 @kubu4 @AHuffmyer can y'all do the same?

once we nail down the READMEs, we can move all other files to the misc directory then decide what to do with them.

[yaaminiv]

(and if i mistakenly moved something we needed into the misc directory...sorry!)

[sr320]

reminder "real" code is already noted with "00" https://github.com/sr320/ceabigr/tree/main/code

[yaaminiv]

reminder "real" code is already noted with "00" https://github.com/sr320/ceabigr/tree/main/code

welp, some of mine that i used for the manuscript was not noted with a "00"!