API implementation fix

Fix: replace removed gr.update() with component constructors for Gradio 5.x

docs: add Gradio 4.x breaking changes to LEARNINGS.md

docs: add HuggingFace deployment lessons to LEARNINGS.md

Fix HuggingFace Spaces deployment

docs: consolidate documentation and add working patterns

refactor: cleanup repo, add SLURM scripts, document reproducibility

docs: update verification notes with FDR calibration results

feat: add verification scripts and multi-model embedding support

feat: add CLI, fix FDR bug, verify paper result (59/149 = 39.6%)

feat: add test infrastructure, docs, and modern packaging