Draft: Resolve "Refine building process of docker image"

This MR suppose to fix multiple issues with the building process of the noamd docker image.

• Fix the python package dependency conflicts
  • get rid of the circular dependencies of the submodules (closing: !1579 (merged), @ahmil , @himanel1 ) solution: Adding the submodules dependency directly to the main pyproject.toml file. This way we do not rely on the submodules' dependencies. This method might change when these submodules are going to be a proper plugins.
  • fix the issue with the pybis package (@amgo) Solution: remove it from the dependency and install it without its deps later. pip install --no-deps pybis
  • remove unused/probelmatic pyscf package dependency (@ladinesa )
• explicitly defining nomad user and using it propertly for the kubernetes' security context (@afekete) solution: using nomad user for both of the docker build stages
• Using develop stage for debugging or as a replacement for the production image (closing: #1598 (closed), @mscheidg ) solution: combining the python and node build stage into a single stage to represent better a full dev environment. It can be used for running the test or the full application if needed.
• Pynxtools as dependency (closing: !1629 (closed), @dflor )

Update: all python dependency related fix has been removed from this MR.

Closes #1848