Finally fixed the store delay hazard bug.

Created by: rosethompson

• On the way to solving the store delay hazard.
• Progress on reducing store stall in d cache.
• More progress towards store delay reduction.
• Closer.
• Got it working for the cache.
• DTIM works without the store delay stall. Still a bit of work remaining. The DTIM needs cleanup. The cache needs a bit of clean up and the chapter needs updates. The controller needs to be updated to remove the store delay hazard for cmo instructions.
• Added comments to finish store delay stall removal.
• Updated wavefile.
• I think I solved the AMO/store hazard issue introduced by removing the store delay hazard.
• Get's the fpga building again after the git history rewrite.
• Fixed the AMO hazard.