You can modify any game files you find in your install folder.
assets\archetypes has some of the most commonly modified files
assets\gui\layouts is self explanatory
assets\textures has some textures, more spread out in other folders
Most config files are .json that can be modified with notepad, textures are sometimes .png, sometimes .dds files which often require image editing software and/or plugins to modify (photoshop has https://developer.nvidia.com/nvidia-texture-tools-adobe-photoshop, gimp https://code.google.com/archive/p/gimp-dds/). Msgpack files aren’t human readable and will require you to convert them somehow, but these are rarely edited anyway since they contain mostly just static data like items etc. https://github.com/willcrutchley/boundless-msgpack To convert between .msgpack to .json and back.
There was an attempt to make applying modifications to files easier, but I never moved it past the testing stage. Mod Manager and Mod Collection The op has a cmd version that I built the GUI on.