Code cleanup: many files directly below `bin/`

@weissenh suggests:

Review the large bin directory and clean it up (duplicated scripts, very old one-off code) and add meaningful structure (readme, folders)

See also #352

Start by reviewing the files directly below the bin directory and compare the scope with issue #352. Identify duplicated scripts and old one-off code, then define a meaningful folder structure and README; done means the bin contents are organized, documented, and unnecessary duplication or obsolete scripts have been addressed.

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