Read more about PiTrex in general at: PiTrex Wiki.
Read more about PiTrex Baremetal at: Malbans PiTrex baremetal pages (and the pages accessable by the menu).
To develop baremetal PiTrex you can download a prepared virtual machine for Virtual box (Ubuntu 16.04). Don't forget to update the sources with the ones found here (on github): PiTrex baremetal development virtual machine.
All stuff under the directory "pitrex" is the actual "baremetal boot source" to build baremetal programs. For a short description of the "bootup" look at: PiTrex – Baremetal knowledge.
All stuff under the directory "pitrex/vectrex" is the actual "interface" to the vectrex. For a short description at: PiTrex baremetal: vectrexInterface.c.
All other "single" directories within the repository represent single "programs" runnable under the baremetal environment. Within each directory is a single Makefiles.baremetal to create baremetal images.