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Frida is a very complicated piece of software, with many abstraction layers and inherited functionality. It also utilizes different languages, such as C, C++, javascript and vala to name a few. My plan is to update the information here as I better understand myself. Here's a limited breakdown of what is in what repo:

 

Component Repo What
Frida https://github.com/frida/frida This repo is pretty much for combining all the pieces of frida together. It does not contain much functionality itself.
Frida-core https://github.com/frida/frida-core

Static linkings for frida's bindings

Loaders for frida (preload, injection, etc)

vala for handling things like what to do when a process forks

Frida-gum https://github.com/frida/frida-gum

This is where most of the magic is

v8/duk js bindings

code to bind together js with low level access

specific handling of linux vs windows vs darwin