Fix handling of output permutation and initial layout

[martin-fink]

Description

Output permutation and initial layout need to be applied after the circuit is parsed completely.

This fixes an issue where an output permutation is declared with less qubits than are used in the circuit.

// i 0 2 1 3
// o 3 0
qubit[4] q;

Would result in an output permutation of

0: 1
1: 1
2: 2
3: 0

instead of

0: 1
3: 0

The issue is fixed by applying the output permutation after parsing the complete circuit.

Checklist:

• The pull request only contains commits that are related to it.
• I have added appropriate tests and documentation.
• I have made sure that all CI jobs on GitHub pass.
• The pull request introduces no new warnings and follows the project's style guidelines.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (8881fb0) 91.0% compared to head (6ba80dc) 91.0%.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #509   +/-   ##
=====================================
  Coverage   91.0%   91.0%           
=====================================
  Files        128     128           
  Lines      13706   13709    +3     
  Branches    2143    2145    +2     
=====================================
+ Hits       12485   12488    +3     
  Misses      1221    1221           

Flag	Coverage Δ
cpp	90.8% <100.0%> (+<0.1%)	⬆️
python	99.7% <ø> (ø)

Files	Coverage Δ
src/parsers/QASM3Parser.cpp	90.5% <100.0%> (+<0.1%)	⬆️

[burgholzer]

Looks good. Many thanks for the quick fix 😎