Return non-help prompts from help_prompt and add robust species archetype updater; include workshop_mod source files

[hubertdungen]

Motivation

• Prevent the help handler from producing misleading errors when the user input is not a help/tutorial request and allow caller menus to handle numeric shortcuts and other inputs.
• Ensure Stellaris species archetype trait point edits work with both legacy MPP variable declarations and newer archetype block-only files.
• Provide a small, repository-tracked Workshop mod source so editable defaults are preserved and can be uploaded from the repo.

Description

• Modified help_prompt to return None for inputs that are not help/tutorial requests and added a fallback help_parent when history is missing.
• Added update_species_archetype_values(file_path, machine_points, machine_traits, biological_points, biological_traits) which updates both @-prefixed MPP variables and in-place BIOLOGICAL/PRESAPIENT/MACHINE archetype blocks so values are applied even when variables are absent.
• Replaced direct modify_value_in_file edits to 00_species_archetypes.txt with calls to update_species_archetype_values in modify_mod_files_with_defaults, modify_mod_files_custom, and update_mod_files.
• Added a workshop_mod folder with common/defines/00_defines.txt, common/species_archetypes/00_species_archetypes.txt, descriptor.mod, docs/SOURCE_NOTES.md, and workshop_item.vdf.example to track and restore editable Workshop mod source and default FLEX preset values.

Testing

• No automated tests were executed as part of this rollout.

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Codex Task