I recently got a proxmark3 for RFID testing and had to get the environment set up properly. I downloaded the precompiled client tools the manual suggests, but it kept asking for a specific version of GLIBC which i could not find packages for for the life of me. I ended getting their source code off their github and compiling the client tools right there. Works perfectly.
1. Download the 64bit version of kali
2. Set up a virtual machine (or install to disk) with kali on it
3. git clone https://github.com/Proxmark/proxmark3
4. cd into the proxmark3/client directory
5. run make to compile the files
6. call the client interface with ./proxmark3 /dev/ttyACM0 (or whatever device it shows up as for you)
Now it should drop you into the proxmark3 interactive shell. Here you can do things like read basic corporate badges with 'lf hid fskdemod' or play it back with 'lf hid sim codehere' or clone the cards onto physical T55x7 cards.
In any case, here are some important links:
Proxbrute and other utilities: http://www.mcafee.com/us/resources/white-papers/foundstone/wp-proxbrute.pdf
Github Wiki: https://github.com/Proxmark/proxmark3/wiki/commands
User Manual (for my version): http://ryscc.com/products/PM3PRD/dl/PM3-UserGuide-20140401.pdf