Keep your workspace tidy from the start, then do like chefs and "clean as you go":
You never have enough time at the end of the project
Don't install anything until you know you need it (and remove anything you don't need ASAP)
Use consistent naming schemes for custom plugins / modules / themes
Keep installers and other archive and backup files out of the web hosting root (or anywhere beneath it)
Store these files in a private directory outside the web root
Simplicity, Abstraction, and the Modern Website: 10 Years Later