Add 'mode' parameter to compile_to_hardware()

Use mode='branching' when using control flow. Mode='linear' will give the old
behavior. For now, the basic effect of this is to turn of SSB.

This pull request also patches a couple other methods to accept 'branches' in
addition to 'linkList' in an awgChan dict.
Revert "Modify higher level compile functions to accept branch sequences in return"

This reverts commit fe60e9d44b9bc257a37e0f9cfd6c46cac641ef03.

Conflicts:
QGL/Compiler.py
Restore a couple of good changes from the revert.
Flatten branches in-place.
Add WAIT instruction.

Will convert this into trigger bits on following APS instruction.