CLAUDE.md keeps the rules; the reference sections move to docs/ so they load on demand - #5
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… docs/, loaded on demand
The always-loaded file keeps the project overview, the pipeline
architecture, how to run the scripts, data_source.R configuration, the
storage table, experimental design, R packages, data files, the figure
script rules and the common variables, plus one pointer line per moved
topic. Moved verbatim (one header line added, heading levels adjusted)
into docs/, beside the static results site:
Storage layout: 00_FILE_MAP.md, artifact regeneration, drive-sync
checker (the section's second half) -> docs/storage_layout.md
PyMOL 3D Structure Visualization (Figure 5E/5F) -> docs/pymol_structure_figures.md
MS/MS Spectrum Annotation (Python) -> docs/spectrum_annotation.md
Key Data Insights -> docs/key_data_insights.md
Revision / presentation notes -> docs/revision_notes.md
Markdown to PDF, DOCX to PDF, PDF to TIFF,
PDF to Text -> docs/document_conversion.md
(notes that the pandoc recipe also lives in the global ~/.claude/CLAUDE.md)
Line accounting: all 283 non-blank lines of the previous CLAUDE.md are
present in CLAUDE.md or docs/ afterwards; 0 unaccounted.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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CLAUDE.md keeps the rules; the reference sections move to docs/ so they load on demand