Linting & cleanup

[diegodoimo]

This PR updates the linter configuration to process all main modules.

Previously, the following modules were excluded from linting:

• data_sets.py
• id_discrete.py
• kstar.py
• plots.py
• density_advanced.py
• causal_graph.py
• diff_imbalance.py
• feature_weighting.py
• hamming.py
• neigh_graph.py

With this change, the linter runs on the entire main codebase.

I also removed three empty functions in metric comparisons, a useless project.toml file, and the dev_scripts/whitelist.py, which contained only dead (commented out) code.