I've been learning vim and messing around with installing certain terminal extensions like zsh and tmux. So far I've been installing everything according to their online instructions, and this has left me with quite the disastrous ~/ folder. Running ls -a vomits up a whole trough of .gobbeldigook and rattles me to my OCD core. Often things do not connect properly or are duplicates, and I'm not even sure where to begin deleting or searching.
Is there some book I could read? Some system I could follow? If I'm going to learn how to use these complex tools, I think I should at least learn how to make them work first.
I know this question is a bit grand in scope, but I have no idea how else to word it. I've googled exhaustively, but found no answers. Books on the Terminal tend to focus on commands and interaction rather than structure. I want to know how I can become comfortable with understanding these terminal applications and how the shell interacts with them, so that I can organize them efficiently and fix problems when they arise.