This fixes two problems when VirtRegMap encounters bundles:
- When substituting a vreg subregister def with an actual register the internal read flag must be cleared.
- Removing an identity COPY from a bundle needs to use removeFromBundle() and a newly introduced function to update SlotIndexes.
No testcase here, because none of the in-tree targets trigger this, however an upcoming commit of mine will need this and the testcase there will trigger this.