Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/integration_manifest.json

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+          "missing scores/ye2026_sepsis/disease/draw4/score/summary.json"
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+          "missing scores/imperial_eskd/disease/draw4/score/summary.json"
+        ],
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+          "missing scores/giroux2022/disease/draw1/score/summary.json",
+          "missing scores/giroux2022/disease/draw2/score/summary.json",
+          "missing scores/giroux2022/disease/draw3/score/summary.json",
+          "missing scores/giroux2022/disease/draw4/score/summary.json"
+        ],
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+          "missing scores/ji2025_chili/disease/draw1/score/summary.json",
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+          "missing scores/ji2025_chili/disease/draw3/score/summary.json",
+          "missing scores/ji2025_chili/disease/draw4/score/summary.json"
+        ]
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+      "contrast_missing": [
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+      "deconvolution_deg": "donor-aware continuous-expression limma sensitivity primary where estimable; historical Welch separate"
+    },
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+  },
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+    "Figure 2 needs 20/20 strict healthy support units",
+    "Figure 3 needs 5/5 folds, visual, extras and time receipts",
+    "Figure 4 needs 5/5 strict draws per cohort and contrast/deconvolution evidence",
+    "Figure 2 strict CSV has incomplete fold/size units",
+    "Figure 3 strict per-sample CSV has incomplete folds",
+    "Figure 4 strict CSV has incomplete or mixed-design draws",
+    "fig4_strict_per_sample.csv lacks source-bound support hashes",
+    "Figure 5 needs all 20 strict rare-state receipts",
+    "Figure 5 rare-state CSV is absent, diagnostic or incomplete",
+    "Figure 5 strict arms incomplete: giroux2022/draw3",
+    "Figure 5 strict support hash mismatch: ye2026_sepsis/draw0",
+    "missing strict figure: fig3_realism_metrics.pdf",
+    "missing strict figure: fig3_canonical_marker_dotplot.pdf",
+    "missing strict figure: fig3_umap_by_celltype.pdf",
+    "missing strict figure: fig3_composition_fractions.pdf",
+    "missing strict figure: fig3_runtime_components.pdf",
+    "missing strict figure: fig4_deconvolution_strict.pdf",
+    "missing strict figure: fig4_deconvolution_expression_strict.pdf",
+    "missing strict figure: fig5_rare_states_strict.pdf",
+    "missing strict figure: fig5_rare_visuals_strict.pdf",
+    "missing strict figure: fig5_all_states_strict.pdf",
+    "missing strict figure: fig5_behcet_rules_strict.pdf"
+  ],
+  "figure6": "waiting_user_prepared_data; unchanged placeholder",
+  "git_push": false,
+  "overleaf_sync": false
+}

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/macros.tex

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+% Shared macros for main.tex and supplementary.tex.
+\newcommand{\method}{PBISC-Diffusion}
+\newcommand{\todo}[1]{\textcolor{red}{[TODO: #1]}}
+% Figures are typeset in place after the references (not as floats), so a figure can run over more than one page.
+\newcommand{\figureprefix}{Figure}
+\newcommand{\mainfigure}[2]{\clearpage\refstepcounter{figure}\label{#1}%
+  \noindent{\large\textbf{\figureprefix~\thefigure\ $|$ #2}}\par\medskip}
+\newcommand{\suppfigure}[2]{\clearpage\refstepcounter{figure}\label{#1}%
+  \noindent{\large\textbf{Supplementary Fig.~\thefigure\ $|$ #2}}\par\medskip}
+\newcommand{\figpanel}[2]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=\textwidth,height=0.31\textheight,keepaspectratio]{#2}\par}\medskip}
+\newcommand{\figpanelh}[3]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=\textwidth,height=#3\textheight,keepaspectratio]{#2}\par}\medskip}
+\newcommand{\figpanelpair}[5]{\par\noindent\textbf{#1}\par\nopagebreak
+  {\centering\includegraphics[width=#4\textwidth,height=0.31\textheight,keepaspectratio]{#2}\hfill
+  \includegraphics[width=#5\textwidth,height=0.31\textheight,keepaspectratio]{#3}\par}\medskip}
+\newcommand{\tbcpanel}[1]{\par\noindent\fbox{\parbox{\dimexpr\textwidth-2\fboxsep-2\fboxrule\relax}{\centering
+  \vspace*{1.5cm}{\Large\textbf{To be continued}}\par\medskip #1\par\vspace*{1.5cm}}}\par\medskip}
+\newcommand{\figlegend}[1]{\par\medskip\noindent{\small #1}\par}

paper-releases/pbisc-diffusion/updates/20261012T130738Z-strictpairs-implementation/diffusion/dataset/server_1/model8/plans/paper_figures_strictpairs_20261012/archive/20261012T130738Z-strictpairs-implementation/snapshot/manuscript/main.blg

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+Database file #1: references.bib
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