Emulator

Dolphin currently does not make any assumption on where the DOL and the disc contents are relative to each other. Which is the correct way to do it IMO, because having the .dol in the same directory means that it will be contained on the emulated disc image, which is not "correct" (.dol is not part of the main partition, it's stored separately).

I don't offer you to change whole thing.

You can make special exception for new menu item "Boot CG game from folder" or "Boot Wii game from folder" (since those use different folders structure).

Then after choosing the folder, Dolphin can temporary set it's DVD root patch and Apploader to automagically determined ones and that's until emulation stop.

delroth: I agree that it's difficult to make something that's both user-friendly and correct. One possibility could be looking for the &&systemdata directory that GameCube Rebuilder creates, but that would obviously fail if the disc is extracted using some other method that creates directories/files with different names.

Is correctness really that important for this, though? It's not like a directory disc image looks identical to a real disc image the way things are now...

I think that setting all that paths right after choosing the dol to run is still more user-friendly, than setting those in settings.

In that case, Dolphin should remember the paths used the last time, so that it isn't necessary to select three paths every time you want to launch a DOL.

There is still some tricky logic can be done based on that apploader is usually in same folder as dol.
if dol name is start.dol, then apploader name is AppLoader.ldr
if dol name is main.dol, then apploader name is apploader.img

if dol is in "&&systemdata" folder, then DVD Root folder is the parent directory of "&&systemdata".
if dol is in "sys" folder, then DVD Root folder is "files" directory that is in same dir as "sys". This is the case if game extracted by WIT

This is all easy to break, through.

Actually, if non of patters math, then you can ask to choose those dirs manually.

Another thing to consider is how to handle accurately emulate disk read speeds. Since files will no longer be on a disk image, there needs to be an alternative means of determining the physical position of files as they were on the disk.