This is nothing to worry about. Homebrew is designed to play well with other things that are installed on /usr/local/ , which is the standard place for software designed for the user. There are many other things. The brew list --unbrewed simply lists all the files under /usr/local that were not placed there by Homebrew. This is not a diagnosis of an actual problem, it is more for identifying things that you might want to put in the Homebrew formula, or to help developers help checking stray files during installation work. Any normal system is likely to have a non-empty brew list --unbrewed .
Make a brew doctor instead. This checks files in specific places under /usr/local , which can be problematic. If a brew doctor complains about something, you should probably go for it. Otherwise, do not worry about them and do not try to clean them - you will probably place these files for some reason.
Here is an example of what my test 10.8.3 reports. Many files --unbrewed , but doctor happy. Homebrew is functioning just fine.
$ brew list
So:
1) No, do not worry about this or correct it, unless the brew doctor tells you. Removing these files may lead to a breakdown of what you installed.
2) These paths refer to brew --prefix , which is probably /usr/local .
3) Hypothetically, in order to βcleanβ, for each file, you simply determine that it was installed, and delete it by reinstalling it using the Homebrew formula, if you really need it, or came to the conclusion that it was a mistake or no longer needed and delete it. There is no standard or easy way to do this. And this is exactly the problem that Homebrew and other package managers are facing.
Some of them may be useful if you want to use Homebrew more widely to manage your installations. Every time you are going to install some software other than Homebrew, which is located in /usr/local/ , instead of following normal installation instructions, use brew create to create a formula for it. Then homebrew will track the files that it installs.
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