refactor: relocate configs and enforce import rules

[dest1n1s]

This PR refactors the configuration structure, making config classes live alongside the methods and classes that consume them. It also enforces a strict rule set for internal module imports to ensure consistency:

• Top-level modules (e.g., trainer.py): Must use absolute imports.
• Submodules (e.g., factory.py): Use absolute imports for dependencies outside the submodule, and relative imports for internal references. Parent directory traversal (e.g., from ..module import) is prohibited.
• __init__.py files: Must always use relative imports.
• Internal code within lm_saes must use fully qualified paths. External code (e.g., server or tests) is permitted to import directly from the root lm_saes package.