Transfer Data between Macs

I have a local web development environment setup with Brew, Nginx, PHP, MySQL, Ruby, Gem, Sass, and so many other packages out there that it would probably be a nightmare to set it up again with the same exact versions on a new machine. These packages are usually installed outside of the /Users directory.

So my question is, does the built-in OS X transfer Mac feature support transferring these type of files, and configurations that are located outside of the /Users/ folder and in system directories such as /usr/local or /etc, etc..?

If you make and then restore a complete Time Machine backup or use Migration Assistant you should have no problem moving everything to a new machine and having it work as expected. Otherwise I'm afraid you'll have to reinstall all of your tools and libraries.