Refactor/qcir flexible gate type

[JoshuaLau0220]

Check List

1. Does your submission pass tests by running make test?
2. If you have specified a [no ci] tag, does your submission also pass tests by running make test-docker?
3. Have you linted your code locally with make lint before submission?

Added

• qcir::QCir::calculate_gate_times() to replace qcir::QCirGate::get_time()
• qcir::QCir::append(GateType, QubitIdList)
• qcir::QCir::prepend(GateType, QubitIdList)

Changed

• qcir::QCir::get_gates() now also returns a topologically sorted list to prevent confusion caused by multiple get-gates APIs.
• qcir::QCir::get_gate(size_t id) now returns the gate in $O(1)$.
• qcir::QCir now automatically maintains its topological gate orders---The user no longer need to update it manually.
• Extraction now outputs $P$ gates rather than $R_Z$ gates. This is to reduce clutteredness in the code.

Fixed

• Tableau and Duostra not reading gates in the topological order
• qcir::QCir not freeing the memory it allocates correctly
• qcir::Optimizer not freeing the memory it allocates correctly

Removed

• qcir::QCirGate::get_time(): the info it returns is always unreliable.
• qcir::QCirGate's traversal pin members.
• qcir::QCir::get_topologically_ordered_gates() and other topological order-related features: rendered useless with the above changes