mc-modules is a repository containing "modules" (mods without mods) for Minecraft 1.9. The modules are created using CPM, available here: http://energyxxer.com/cpm/
The "sources" directory contains raw CPM code, able to be modified. The "commands" directory contains "compiled" modules in the form of one or more commands, which you can install by copying and pasting the commands in order into a command block and actiating it after each paste. The "special" directory contains truly single-command modules, ones which do not need installation. You'll see what I mean.