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

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 `CalibrationDefinition`s, but the qubits in a definition should not be considered "used" by the `Program`.