The qubits "used" by instructions and programs aren't calculated correctly

[mingyoungjeng]

1. Instruction::get_qubits and Instruction::get_qubits_mut miss the qubits contained in certain instructions.
2. Program::add_instruction should also only track the qubits used by body instructions.
   • For example, it is possible to extract qubits used in CalibrationDefinitions, but the qubits in a definition should not be considered "used" by the Program.