refactor(workflow): update JFM research workflow and remove obsolete figures

Revise the JFM research workflow documentation to clarify project structure, decision-making processes, and tool routing. Remove outdated figures and images that are no longer relevant to the current manuscript. Ensure that the workflow aligns with the latest research objectives and safety protocols.
2026-08-11 21:25:33 +08:00
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+# R5 review master static TeX preflight
+
+**Project / round / unit:** DynamisLab JFM / Round 5 / independent final static TeX preflight.  
+**Scope:** current `master/R5_REVIEW_MASTER.tex`, all ten files under `sections/`, and `R5_REFERENCES.bib`.  
+**Exclusions:** no section science edits; no edit to `My_JFM/FLMguide.tex`; no CFD, training, artifact generation, dependency installation or TeX compilation.
+
+## Overall status
+
+**STATIC PASS; RUNTIME COMPILE CONDITIONAL ONLY.** The current review master, section inputs and Round-5 bibliography pass every requested static check. The post-R5 citation integration is complete: all 49 active citation keys resolve and no legacy key remains. The bibliography contains 49 records, all cited, while the master activates the correct JFM bibliography style and R5 database path. The only remaining condition is engine-based compilation and warning inspection, which is unavailable because no TeX engine, BibTeX executable or TeX resolver is installed.
+
+No clear mechanical defect was found in `R5_REVIEW_MASTER.tex`, so neither the master nor section science was edited in this preflight.
+
+## Exact findings
+
+### PASS — inputs, order and Section 9 omission
+
+- The master has exactly nine active inputs in exact numerical order: S1, S2, S3, S4, S5, S6, S7, S8 and S10.
+- Every active `\input` resolves from `master/` to the named file under `../sections/`.
+- `SECTION_09_EXPERIMENT_PLACEHOLDER.tex` exists but is not actively input.
+- The master explicitly records both the S9 omission and its safe-branch reason.
+- The omitted S9 placeholder contains a `\subsection` but no top-level `\section`; omission avoids introducing orphaned section structure.
+
+### PASS — citation and bibliography integration
+
+Static inventory reports:
+
+- **49 bibliography entries, 49 unique keys** in `R5_REFERENCES.bib`;
+- **64 citation-key occurrences, 49 unique cited keys** across the section TeX;
+- **49/49 active-citation resolution:** every cited key exists in `R5_REFERENCES.bib`;
+- zero unresolved keys;
+- zero uncited bibliography entries;
+- zero duplicate bibliography keys;
+- zero legacy keys among active citations.
+
+The master has exactly these active bibliography commands:
+
+- `\bibliographystyle{jfm}`;
+- `\bibliography{../R5_REFERENCES}`.
+
+From `master/`, `../R5_REFERENCES` resolves to the current Round-5-owned `R5_REFERENCES.bib`. The legacy `My_JFM/jfm.bib` is not loaded. The JFM class loads `natbib` in author--year mode, providing the active `\citep` interface.
+
+### PASS — braces, environments and math delimiters
+
+A comment-aware Python scanner checked the master plus all ten section files, 11 TeX files total:
+
+- balanced unescaped `{...}` groups;
+- correctly nested and paired `\begin{...}` / `\end{...}` environments;
+- even unescaped `$` delimiter counts;
+- paired `\(...\)` and `\[...\]` math delimiters.
+
+Result: zero structural errors. All displayed `equation` environments close correctly; no environment mismatch or visible equation delimiter defect was found.
+
+### PASS — section and document ownership
+
+- Each admitted input S1--S8 and S10 owns exactly one top-level `\section`.
+- No admitted section owns `\documentclass`, document begin/end, bibliography style or bibliography database commands.
+- The master supplies one document wrapper and introduces no duplicate section wrapper.
+- The bibliography appears after S10 and before `\end{document}`.
+
+### PASS — class and support paths
+
+- `\documentclass[lineno]{JFM-FLM_Au}` is supported by `../../My_JFM/JFM-FLM_Au.cls` under the documented compile-from-`master/` `TEXINPUTS=../../My_JFM//:` assumption.
+- The class's `lineno` option requests `lineno-FLM`; `../../My_JFM/lineno-FLM.sty` exists.
+- `\bibliographystyle{jfm}` is supported by `../../My_JFM/jfm.bst` under the same `TEXINPUTS` assumption.
+- The class statically supplies author--year `natbib`; no manuscript-local citation command definition is needed.
+
+### PASS — no superseded citation condition
+
+The earlier condition that section citations used legacy keys and that bibliography integration was disabled is no longer true. It has been removed from this report. Current active-citation resolution and complete 49-entry integration are a PASS.
+
+## Runtime-only condition
+
+No executable was found for `latexmk`, `pdflatex`, `lualatex`, `xelatex`, `bibtex`, `biber` or `kpsewhich`. Therefore the only remaining gate is runtime compilation with the documented class/style search path and subsequent inspection of generated citation/reference warnings, class/package compatibility, fonts, line numbering, layout and bad boxes. No static defect presently predicts a compile failure.
+
+## Final gate
+
+- **Static TeX structure:** PASS.
+- **Input order and existence:** PASS.
+- **Safe S9 omission:** PASS.
+- **Braces/environments/math delimiters:** PASS.
+- **Active R5 citation resolution:** PASS, 49/49; zero uncited bibliography entries.
+- **Bibliography activation/path/style:** PASS.
+- **Master mechanical correctness:** PASS; no edit required.
+- **Section science:** untouched.
+- **Full runtime compile:** CONDITIONAL only because no TeX/BibTeX toolchain is available.
+
+## Evidence-use closeout
+
+This rerun used current repository files and robust static scripts. The current master, all ten section TeX files, R5 bibliography, JFM class and support-file paths were inspected. Nowledge was searched narrowly for navigation; repository files controlled the result. Working Memory, thread recall, `mem_fs`, literature search/PDF read, CFD, training, artifact generation and independent scientific verification were not used. This is a static TeX assembly audit, not a science or evidence audit.