What file/files is the hierarchy saved inside the project folder?

This might be a little bit complicated to explain. I'm working on something that automatically builds Unity projects based on pre-determined instructions (avatars for VR games). A character builder that then automatically creates a Unity project. I need to remove/edit some objects from the hierarchy by editing files within the Unity project folder (without even opening unity, if possible).

I understand the file system for Unity projects quite well, but I can't seem to locate where data for the hierarchy is saved. The actual file/files where that data is stored. These projects are not compiled, just the raw original project folder.

To be VERY clear; these projects ONLY contain assets (models, textures, etc) that I have created myself, or assets that I have 100% written permission to distribute. I am NOT trying to reverse engineer Unity itself, or any existing 3rd party projects or games. I am simply working on a web-based character builder (think the Sims game) that then creates a project with a ready to upload/export avatar for VR games.

 

The "hierarchy" is the scene files, so the .unity files. The .prefab files have a similar layout.

The files are yaml, so editing simple values internally in an object should be pretty simple, as well as deleting them. Changing references to other objects and to assets is a bit more tricky, as that gets into file/asset ID's.