Q: Migration Assistant without php/mysql/apache settings

My existing setup (Yosemite) has become borked after trying to upgrade to PHP 5.6. Way back when (a few migrations ago), I was using MacPorts. More recently, someone tried to "help" by moving some things over to Homebrew. Bottom line: I've not been using the stock OS X versions of Apache, MySQL, or PHP for a long time. Trying to upgrade from PHP 5.5 to PHP 5.6 has horribly broken PHP.

This seems like a good time for me to do a clean re-install and start over. The problem is, I have so many 3rd party apps that it would be a real pain to have to re-install them all, track down the serial numbers, etc.

I tried using Migration Assistance once already, but it brought over *everything*, including my borked PHP install.

Is there a way to have Migration Assistant bring over ONLY the applications in the Applications folder(s) (and possibly user settings), without touching anything in the various lower level directories (/opt/local, /etc/, etc.)?

I just want to have all my "stuff" back without any of the lower level stuff (PHP/MySQL/Apache).