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 Remove outdated figures and images that are no longer relevant to the current manuscript.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.
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Frank14f
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\documentclass[lineno]{JFM-FLM_Au}
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\usepackage{amsmath,amssymb,bm,booktabs}
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\title{Interpreting learned hydrodynamic cloaking and illusion in a fluidic pinball}
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% R5 review assembly only; not a submission master.
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% Review status is documented in README.md and is intentionally not rendered.
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\begin{document}
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\maketitle
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\input{../sections/SECTION_01_INTRODUCTION.tex}
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\input{../sections/SECTION_02_PROBLEM_METHOD_EVALUATION.tex}
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\input{../sections/SECTION_03_CAPABILITY_PROGRESSION.tex}
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\input{../sections/SECTION_04_KARMAN_RESULTS.tex}
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\input{../sections/SECTION_05_KARMAN_SR_LAW.tex}
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\input{../sections/SECTION_06_KARMAN_FIELD_CCD.tex}
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\input{../sections/SECTION_07_CROSS_CASE_EXTENSIONS.tex}
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\input{../sections/SECTION_08_STEADY_THEORY.tex}
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% SECTION_09_EXPERIMENT_PLACEHOLDER.tex is intentionally not input.
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% Current safe branch: no author-supplied, provenance-audited experimental prose is admitted.
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\input{../sections/SECTION_10_DISCUSSION_CONCLUSION.tex}
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\bibliographystyle{jfm}
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\bibliography{../R5_REFERENCES}
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\end{document}
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# R5 safe review master
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## Status and scope
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This directory contains a review-only assembly master, not a submission master. `R5_REVIEW_MASTER.tex` inputs the current Round-5 section files S1--S8 and S10 in numerical order. S9 is explicitly omitted under the active safe branch because its current file is an author-field placeholder and its substantive author/provenance gates remain open.
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The article title is the current provisional controlling title: *Interpreting learned hydrodynamic cloaking and illusion in a fluidic pinball*. It remains provisional and is not represented as author-final.
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Citation integration is now enabled from the R5-owned `../R5_REFERENCES.bib`. Only S1, S2, S5, S6 and S8 contain reader-facing external citations under the authoritative citation ledger; no source is used to support an internal result.
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## Inherited template mechanics
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The old `My_JFM/FLMguide.tex` was read only to identify mechanics. The new master inherits only:
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- the `JFM-FLM_Au` document class with the `lineno` option;
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- the preamble package set `amsmath`, `amssymb`, `bm` and `booktabs`;
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- the standard `\title`, `\begin{document}`, `\maketitle`, section `\input`, and `\end{document}` assembly pattern.
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The JFM support files remain at `../../My_JFM/JFM-FLM_Au.cls` and `../../My_JFM/jfm.bst`; they were neither copied nor edited. Compilation therefore uses `TEXINPUTS` to expose that template directory.
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## Excluded old content and metadata
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No manuscript prose, abstract, keywords, claims, equations, figures, captions, labels, citations, acknowledgements, declarations, author names, affiliations, correspondence details, ORCIDs, funding text, submission metadata, running titles or bibliography keys were copied from `My_JFM/FLMguide.tex`.
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No figure environments or references were added. Review-draft status and the safe-branch S9 omission are documented only in non-rendering master comments and this README; they introduce no typeset notice.
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## Bibliography state and integration
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The review master uses the JFM class citation commands (`\citep` in the section prose), `\bibliographystyle{jfm}`, and `\bibliography{../R5_REFERENCES}`. The bibliography is owned by Round 5 and contains only the externally needed sources approved in `../00_CITATION_CANDIDATE_LEDGER.md`; the legacy `../../My_JFM/jfm.bib` is not loaded.
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The JFM support files remain at `../../My_JFM/JFM-FLM_Au.cls` and `../../My_JFM/jfm.bst`. Compile from `master/` with `TEXINPUTS=../../My_JFM//:` so both the class and `jfm.bst` are discoverable; the bibliography database itself is reached by the explicit relative path `../R5_REFERENCES`.
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## Compile environment and command
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TeX discovery on 2026-08-11 found none of `latexmk`, `pdflatex`, `lualatex`, `xelatex`, `bibtex`, `biber` or `kpsewhich` on `PATH`. A full compile was therefore unavailable and only static preflight was run.
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Once a TeX distribution is available, compile from this directory:
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```bash
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cd docs/JFM_WYQ/ROUND5_BOTTOM_UP/master
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TEXINPUTS=../../My_JFM//: latexmk -pdf -interaction=nonstopmode -halt-on-error R5_REVIEW_MASTER.tex
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```
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If `latexmk` is unavailable but `pdflatex` and `bibtex` are available:
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```bash
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cd docs/JFM_WYQ/ROUND5_BOTTOM_UP/master
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TEXINPUTS=../../My_JFM//: pdflatex -interaction=nonstopmode -halt-on-error R5_REVIEW_MASTER.tex
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TEXINPUTS=../../My_JFM//: bibtex R5_REVIEW_MASTER
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TEXINPUTS=../../My_JFM//: pdflatex -interaction=nonstopmode -halt-on-error R5_REVIEW_MASTER.tex
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TEXINPUTS=../../My_JFM//: pdflatex -interaction=nonstopmode -halt-on-error R5_REVIEW_MASTER.tex
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```
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## Static preflight contract
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Static preflight checks the master structure, exact input order, explicit S9 omission, active R5 bibliography/style paths, exact citation-key resolution, existence of every input and template-support file, and absence of imported author/submission metadata. Static checks cannot establish class/package compatibility, font availability, overfull boxes, page layout, undefined control sequences or other runtime diagnostics; those remain compile-gated.
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# R5 review master static TeX preflight
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**Project / round / unit:** DynamisLab JFM / Round 5 / independent final static TeX preflight.
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**Scope:** current `master/R5_REVIEW_MASTER.tex`, all ten files under `sections/`, and `R5_REFERENCES.bib`.
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**Exclusions:** no section science edits; no edit to `My_JFM/FLMguide.tex`; no CFD, training, artifact generation, dependency installation or TeX compilation.
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## Overall status
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**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.
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No clear mechanical defect was found in `R5_REVIEW_MASTER.tex`, so neither the master nor section science was edited in this preflight.
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## Exact findings
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### PASS — inputs, order and Section 9 omission
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- The master has exactly nine active inputs in exact numerical order: S1, S2, S3, S4, S5, S6, S7, S8 and S10.
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- Every active `\input` resolves from `master/` to the named file under `../sections/`.
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- `SECTION_09_EXPERIMENT_PLACEHOLDER.tex` exists but is not actively input.
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- The master explicitly records both the S9 omission and its safe-branch reason.
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- The omitted S9 placeholder contains a `\subsection` but no top-level `\section`; omission avoids introducing orphaned section structure.
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### PASS — citation and bibliography integration
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Static inventory reports:
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- **49 bibliography entries, 49 unique keys** in `R5_REFERENCES.bib`;
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- **64 citation-key occurrences, 49 unique cited keys** across the section TeX;
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- **49/49 active-citation resolution:** every cited key exists in `R5_REFERENCES.bib`;
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- zero unresolved keys;
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- zero uncited bibliography entries;
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- zero duplicate bibliography keys;
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- zero legacy keys among active citations.
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The master has exactly these active bibliography commands:
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- `\bibliographystyle{jfm}`;
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- `\bibliography{../R5_REFERENCES}`.
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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.
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### PASS — braces, environments and math delimiters
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A comment-aware Python scanner checked the master plus all ten section files, 11 TeX files total:
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- balanced unescaped `{...}` groups;
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- correctly nested and paired `\begin{...}` / `\end{...}` environments;
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- even unescaped `$` delimiter counts;
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- paired `\(...\)` and `\[...\]` math delimiters.
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Result: zero structural errors. All displayed `equation` environments close correctly; no environment mismatch or visible equation delimiter defect was found.
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### PASS — section and document ownership
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- Each admitted input S1--S8 and S10 owns exactly one top-level `\section`.
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- No admitted section owns `\documentclass`, document begin/end, bibliography style or bibliography database commands.
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- The master supplies one document wrapper and introduces no duplicate section wrapper.
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- The bibliography appears after S10 and before `\end{document}`.
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### PASS — class and support paths
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- `\documentclass[lineno]{JFM-FLM_Au}` is supported by `../../My_JFM/JFM-FLM_Au.cls` under the documented compile-from-`master/` `TEXINPUTS=../../My_JFM//:` assumption.
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- The class's `lineno` option requests `lineno-FLM`; `../../My_JFM/lineno-FLM.sty` exists.
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- `\bibliographystyle{jfm}` is supported by `../../My_JFM/jfm.bst` under the same `TEXINPUTS` assumption.
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- The class statically supplies author--year `natbib`; no manuscript-local citation command definition is needed.
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### PASS — no superseded citation condition
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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.
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## Runtime-only condition
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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.
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## Final gate
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- **Static TeX structure:** PASS.
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- **Input order and existence:** PASS.
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- **Safe S9 omission:** PASS.
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- **Braces/environments/math delimiters:** PASS.
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- **Active R5 citation resolution:** PASS, 49/49; zero uncited bibliography entries.
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- **Bibliography activation/path/style:** PASS.
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- **Master mechanical correctness:** PASS; no edit required.
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- **Section science:** untouched.
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- **Full runtime compile:** CONDITIONAL only because no TeX/BibTeX toolchain is available.
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## Evidence-use closeout
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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.
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