Sync CpptrajAI: updated code, README, agent flow diagram

Fix conda create syntax: -c flag must precede package names

Fix: use valid miniconda3 tag + isolated Python 3.11 env for ambertools

Fix Dockerfile: use Python 3.11 + ambertools (cpptraj is bundled in ambertools)

Fix: install cpptraj in isolated conda env to bypass Python 3.12 pin

Fix: install cpptraj from bioconda channel

Fix Docker: use mambaforge + mamba; add PDB test data

Deploy CpptrajGPT to HuggingFace Spaces