docs: remove phase labels and organize guides by topic - #17
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Make the entire documentation phase-agnostic. Rename public guides to
prediction-confidence.md,structural-verification.mdandvalidation-results.md; give the independent wwPDB protocol a descriptive heading; add a topic-baseddocs/README.md; update the main README and all cross-links. Preserve implementation and verification worklogs separately indocs/development/, with descriptive titles and a historical index. Rename phase-labelled test scripts and update the browser and independent-validation workflows so CI remains intact. Current screenshots stay in place, and screenshot curation accepts older CI artifact names for backward compatibility. Verified user-facing and archived Markdown links and scanned all renamed documents/workflows for remaining phase references.