Update Makefile to accommodate to new directory structure.

[impeeza]

Description

A set of small changes to accommodate to new directory setup.

Now builds Switch version without problem, and solves https://github.com/snesrev/zelda3/issues/266

Thanks a lot to @GodReborn to help diagnose the problem here and SMW repo.

Will this Pull Request break anything?

No, instead resolve the problem of build switch version introduced when directories was reorganized.

Suggested Testing Steps

Build Switch Version on MSYS.

[Mraulio]

This helped me build the Switch version.

[impeeza]

Hello there, anybody has been able to review this PR? any ETA for apply? regards.

[hgue]

Can confirm this is working when building on Linux, please merge