Variable connections in the configuration file are ignored for indep variables when generating the input file

[ScottDelbecq]

Describe the bug In the presence of IndepVarComp and if these are connected to component inputs directly in the configuration file, the connections are ignored when generating the input file. Though, it seems when a run_model is achieved the connections are not ignored.

To Reproduce I added a unit test here: https://github.com/fast-aircraft-design/FAST-OAD/blob/22e52d93b784fb92e9cefbbaea305111c5625491/src/fastoad/io/configuration/tests/test_configuration.py#L159-L201

The test uses this configuration file:

title: Sellar

module_folders:
  - conf_sellar_example
  - d:/path/does/not/exist  # will only trigger a warning

input_file: ../results/problem_definition_with_indep/inputs.xml
output_file: ../results/problem_definition_with_indep/outputs.xml

driver: om.ScipyOptimizeDriver(optimizer='SLSQP')
model:
  indep:
    id: configuration_test.sellar.indeps
  connections:
    - source: system:x
      target: x
    - source: y1
      target: yy1
    - source: y2
      target: yy2
  cycle:
    nonlinear_solver: om.NonlinearBlockGS(iprint=1)
    linear_solver: om.ScipyKrylov()
    disc1:
      id: configuration_test.sellar.disc1
    disc2:
      id: configuration_test.sellar.disc2
  functions:
    id: configuration_test.sellar.functions

Expected behavior x that is connected to system:x should not appear in the generated input file. In the unit test provided we should obtain:

<FASTOAD_model>
  <z units="m**2" is_input="True">[5.0, 2.0]</z>
  <system>
    <x is_input="True">2</x>
  </system>
</FASTOAD_model>

Instead of:

<FASTOAD_model>
  <x is_input="True">1.0</x>
  <z units="m**2" is_input="True">[5.0, 2.0]</z>
  <system>
    <x is_input="True">2</x>
  </system>
</FASTOAD_model>

Environment

• Operating System: macOS 12.3.1
• Python environment: Anaconda Python 3.8.13
• Packages: FAST-OAD > 1.3.2 (master)