document files added to user homedirs and whether they should/n't be backed up
I've personally just removed everything in ~/.travis while cleaning up because I don't still have the CLI installed at the moment, but I had trouble finding any succinct acknowledgement of the files (currently config.yml and travis.sh) in it, where they came from, and context on whether a user would want to back them up or not.
Some people assume these files, particularly ~/.travis/config.yml, are something they should bother keeping, store them in backups or dotfile repos, and of course potentially restore them.
Since dotfiles are commonly stored in git or git-related tools, I think this could be as simple as writing a .gitignore to this directory. It can ignore anything you don't think the user should try to preserve, and have short comments explaining where they came from and why they should/shouldn't be saved. I think most people who "care" will notice this (and appreciate its proximity to the decision they're trying to make).
This is also a good place to warn people about the caution with which they should treat these files if they maintain a public dotfiles repo. (Here's an example that leaps to mind--weechat maintains a table of these).