Fix Control Unit in TPUv2

[WilliamZhang20]

When this PR is merged, the result is:

• The TPU can clear outputs and still have correct outputs.
• The TPU can run at 100 Million FLOPS with no correctness issues.

This is done by:

• Fixing clear logic and timing inside PE
• Fixing control orchestration + mark with comments so it isn't so hard next time :(