How to actually use Unreal include tool?

I have the 4.26 branch of UE4 cloned in one folder, while my project is placed in a completely separate folder. I’ve spent a better part of my day trying to run the include tool, but with no luck. It either has files missing (which I then merge from the engine) or it generates the improper UE4RulesManifest.json or something else.

The documentations sucks because it explains nothing, it looks like the include tools expects everything to be in one place instead of in two separate folders, which baffels me since, to my knowledge, most project are created separately. I have no idea how to merge my project into the engine (or vice versa), so any help would be appreciated.
Maybe there is some way to tell the tools to look in multiple folders?

If I have engine in C:\Engine (which contains Binaries, Build, Config, etc folders) and my project in C:\Project (which also contains Binares, Build, Config, etc folders), what are the arguments that I have to give to the include tool to have it analyse/optimise my project? Do I have to somehow merge the two folders together? How do I do that? Do I have to modify some files so engine knows how it’s merged?

Is there anyone who knows how to run the tool properly?