Make sure all instructions are in the ordered list.

Currently, some instructions will be missing from the list of
ordered_instructions. This will cause issues due to the debug change
which passed the last instruction into subsequent passes.

This CL moves the addition to the ordered list out of the
RegisterInstruction method into AddOrderedInstruction. This method is
called first in ProcessInstruction and the CapabilitiesPass and IdPass
are updated to take an Instruction parameter.