Ask HN: How do you manage trigger-happy installing and file-bloat

This is probably a newbie question. I'm using a mac, and getting into development, you tend to install a lot of stuff. While there are some nice package managers out there, their scope is limited, and since when is hacking a =). Hence, I'm pretty sure my trigger-happy installing and trying to stay up to date with the latest versions of everything has left my root directory littered with now useless stuff. From now on, I guess I'll be more selective with what I install, but the problem still needs to be fixed. Because I'm not a UNIX-wiz, and the fact that so many shell scripts share the same name. eg: I've got a node script in /usr/local/bin corresponding to v0.2.0, and another corresponding to v0.2.3 in another dir, but I'm hesitant to move things around or delete things, in fear that something may break. I probably need to get a much better familiarity with the file system. Basically, things like bash paths and all the stuff that goes on when you call "make install" . As such, what resources would be good? Thanks.