Update docs: challenges.md (training bias + scene text approach), vam/multimodal/trainers docs sync

reorganize configs into subdirs lm/vlm/vam, remove runs/, add interview docs for pretrain & full_sft

refactor(docs): restructure docs with modular organization

Restructure docs to mirror src/ module layout

Update docs for tokenizer training script and checkpoint save path

Add modular development docs under docs/ for learning and interviews