How to fix this error:
Edit cpw.mods.fml.common.discovery.JarDiscoverer.java to include the following: (the first few lines are context and are in the discover method)
After you have modified the source, run the recompile script from mcp and you should have no more errors.
This is from Forge making sure that net.minecraft.src packages are only inside the minecraft jar. I am assuming you are recompiling the whole Minecraft source in IDEA, so the Minecraft jar is actually your output folder. You need to reorder the dependencies of this module so that the <module source> is the first entry, not the java JDK. In any other child modules that depend on this module, you will need to make sure this module comes first on the dependency list before the child's <module source>.
This works very well for the other errors. Thank you!
I now have a completely clean run (except for the LWGL error and the 1.6 release flag error, but those can be ignored)