Clear temp breakpoints off the CPU thread.

This should make it possible to actually clear them.  Fixes #2519.
Fix some sign comparison warnings.
Add an inactive wait just to be safe.
Allow hitting Go on a breakpoint to continue.

Doesn't work for branches though, because of delay slots.
Save flags around conditional breakpoint check.
Merge pull request #2531 from unknownbrackets/jit-minor

Improve breakpoint handling