I can understand the confusion. Especially since I’ve accidently pointed the link at my overview instead of right to the Repositories tab, sorry, it’s fixed now. Each repository is a mod or program. For the most part, all the cdda mods I’ve personally updated have ‘M_’ at the beginning. The ones I’ve included in the pack at any rate. This is my repositories page:

It’s a lot to take in. Let’s assume you want to install the M_Secronom mod:

Notice this file, modinfo.json, that’s required by every cataclysm mod and indicates that this IS in fact a mod for cataclysm. They won’t all be right on the top level like this, but if you’ve navigated directories in (x)windows, you can navigate a github repository.
That’s all well and good, you’re saying, but how do I install it? Easy, click here:

Click download zip and enjoy. I assume you can handle it from there, correct? Just make sure you’re dropping the correct folder in your mods directory.
I think the only weird install on there is Kawaiimaidmod, it comes with soundset files for a soundpack. Oh, if you see ‘forked from yadda yadda’:
That means I’ve copied another coders repository. I may or may not have made changes, but you can choose to use the original version by clicking on the origin, in this case Regularitee/KawaiiiMaidMod. Mine has working teleporters, I’m just saying…
Several mods were only available as a dropbox download or the like, I’ve put them in my repositories for ease of access and version control. Expanded Archery and dda-lua-mop are 2 such examples.