Add line-by-line citations mapping code to algorithms in ./docs/rf3_si.pdf:

- Algorithm 1 (inference_sampler.py): Main inference diffusion loop
  - Lines 1-12 annotated for the denoising diffusion process
  - Includes gamma modulation, noise injection, and coordinate updates

- Algorithm 2 (inference_sampler.py): Symmetric inference diffusion loop
  - Lines 1-13 annotated for homo-oligomer design
  - Key difference: symmetry operations applied during diffusion

- Algorithm 3 (encoders.py): Token initializer
  - Lines 1-12 annotated for token-level feature generation
  - Includes 1D embedding, pair features, and Pairformer processing

- Algorithm 4 (encoders.py): Atom initializer
  - Lines 1-8 annotated for atom-level feature generation
  - Includes motif/reference embeddings and MLP processing

- Algorithm 5 (RFD3_diffusion_module.py): Diffusion forward pass with recycling
  - Lines 1-18 annotated for the main diffusion module
  - Includes encoder, transformer, decoder, and recycling loop

All annotations follow the format "Algorithm X - line Y" to match
the user's requested style for easy cross-referencing with the paper.