[Dependency] Data-structure layer `source_cell` depending back on higher layers

[Critsium-xy]

Describe the Code Quality Issue

• Symptom: cell reverse-includes
  • estate/read_orb.h, estate/cal_nelec_nband.h, estate/module_charge/charge.h (magnetism.cpp, read_atoms_helper.cpp);
  • hamilt/module_xc/exx_info.h (read_atom_species.cpp, bcast_cell.cpp);
  • pw/module_pwdft/soc.h, lcao/module_ri/serialization_cereal.h, io/module_unk/berryphase.h.
• Root cause: cell carries responsibilities that do not belong to a data-structure layer — reading pseudopotentials / reading orbitals / computing electron counts (read_orb/read_pseudo logically belong to L3).
• Fix: return cell to a pure "geometry + atoms + k-points" container; relocate read_orb/read_pseudo to upper layers and let them inject into cell after construction; pass exx_info, soc, serialization in from above.
• Acceptance: source_cell retains only edges to source_base/module_parameter (Note: better not, but considering that PARAM may be hard to deal with, so this is an expedient measure).

Additional Context

No response

Task list for Issue attackers (only for developers)

• Identify the specific code file or section with the code quality issue.
• Investigate the issue and determine the root cause.
• Research best practices and potential solutions for the identified issue.
• Refactor the code to improve code quality, following the suggested solution.
• Ensure the refactored code adheres to the project's coding standards.
• Test the refactored code to ensure it functions as expected.
• Update any relevant documentation, if necessary.
• Submit a pull request with the refactored code and a description of the changes made.