Fix references so they account for inheritance correctly

[PiTheGuy]

Fixes #148

[modmuss50]

Please can you explain the changes here, I am struggling to understand what has changed/what this is fixing. I dont see how this can work when split across many isolated workers.

[PiTheGuy]

The idea is to split the finding of references into a separate pass so it can use member to data to normalize the references to the class the methods are actually defined.

As to how this works with multiple workers, it doesn't. I tested this before I submitted the PR, but I think I just got lucky with the workers were split up. I'm converting this to a draft while I figure the best way to fix this.