Is there anywhere I can find documentation on starting the edit these things?
Ask the developers of your project(s) of interest. Usually, if they really want contributions, they will have build instructions. The GitHub app does as part of its project README. The newly-released StackExchange app is not open source.
Is there a master repo somewhere where I can grab all of the code for Cyanogen (I know, this is probably ridiculous) to make sure I have all the imports?
CyanogenMod has a wiki which contains lots of project documentation, including a set of pages for how to build CM and so forth. They even have dedicated build guides for how to build from source for various device models. There is also a page describing their GitHub hosting model.
Please bear in mind that many of the apps that came to CyanogenMod from the Android Open Source Project (AOSP) are not Android SDK apps that you can build with an IDE and the SDK alone. Most have many hooks into the rest of the OS and as such need to be built as part of a larger OS build. As such, this is not what I would recommend somebody "getting back into Java programming" to get involved with as their first order of business. The being said, for further assistance in developing for CyanogenMod, contact their community through their various channels.