See README files in different catalogs to learn what are the files in them for.
Files can be installed automatically using install sh scripts. Each sub-directory contains one such script, which when ran, will install the files from that sub-directory. There's also one in the main directory that will run all other, installing everything.
Install scripts use cp -pi to copy files, so they will ask to replace files (so it's safe to run).
Note the script for stylish is an update script. See stylish/README.md for details.