Fix PLUMED: use API for plumed.dat check and preview (avoid cache); add update note on Protein Loading

Fix: Move superimposed viewer controls (Reset, Surface, Spin) inside the viewer box

Fix: Create combined ligand file (4_ligands_corrected.pdb) for separate ligand download

Fix: Properly handle errors from prepare_structure in API endpoint

Fix: Require chain selection for structure preparation (no default to all chains)

Rename project from AmberFlow to AmberPrep