Create Overwrite Sys and User folders

[r2dliu]

The structure of the ini files and content of these folders in general is obviously going to be different for mainline dolphin. Need to update all of these things

[WyldeLaRue]

The gecko code loading issue can be fixed by using copying the codehandler.bin found in Data/Sys instead of the one in Overwrite/Sys

I think that's the only change that needs to go into Overwrite/Sys to keep everything running the same as it is on the Ishiiruka fork. Figuring out what defaults should go into User will probably take a little more tinkering.

[r2dliu]

Getting rid of overwrite, move folders into data/sys

[ehandal]

Looks like PollingMethod = OnSIRead can be removed from the ini files. The rest of the Core settings still do something, but the PollingMethod was something added by Hannes to Ishii.