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 Remove outdated figures and images that are no longer relevant to the current manuscript.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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---
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description: JFM manuscript terminology and dangerous scientific boundaries
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globs: "{docs/JFM_WYQ/**/*.md,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.tex,docs/JFM_WYQ/MANUSCRIPT/**/*.tex}"
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alwaysApply: false
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---
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# JFM Knowledge and Terminology Scaffold
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- Use the current round controls, global decision ledger, owning dossier, named authorities/manifests, and immutable artifacts. Memory and literature do not override them. This rule is a guardrail, not a substitute for exact section authorities.
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- In reader-facing prose name the `parabolic-inflow/no-slip-wall channel configuration` and `uniform-inflow/free-slip-wall channel configuration`. Keep `Legacy` and `V5` only in provenance paths/ledgers; never merge, continue, validate, pool, or imply equivalence across their evidence chains.
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- Spell `Kármán` exactly.
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- Use article-wide $Re_D=U_{ref}D/\nu$: bulk/mean inlet speed for the parabolic configuration, uniform inlet speed for the uniform configuration; state $U_{max}\simeq1.5U_{ref}$ where needed. Convert authoritative $2D$ code labels by one half, verify every inherited label, and prohibit bare `Re100`.
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- Bind every result to configuration, case/seed/role, comparator, metric/estimand, ROI/mask/window, and artifact. Periodic mean/phase, event-relative, mean-only, steady-profile, spatial L2, and native/normalized DTW estimands are non-equivalent; do not pool near-colliding values or call them replication, agreement, validation, or triangulation without exact authority.
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- Positive symbolic regression is Kármán/cloaking-only. Illusion SR is historical/negative.
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- CCD is descriptive and noncausal; use exactly `action-correlated correction-field modes`. Do not imply response, authority, causality, uniqueness, or superiority to POD.
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- OID remains claim-free. Steady evidence is separate-chain context, not mechanism, stability, optimum, or cross-configuration validation. Experiment is qualitative, open-loop, author-owned, and provenance-gated; it is not quantitative validation.
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- Kan99b K2 retains the authority's exact overall `partial pass`. Its opposite mean-lift sign follows the CFD coordinate/force-direction convention; never call it unresolved physics or suspected wrong rotation.
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---
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description: DynamisLab JFM research, decision, and drafting workflow
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description: General JFM startup, authority, memory, literature, and safety routing
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alwaysApply: true
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---
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# JFM Research and Manuscript Workflow
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# JFM Research Start and Tool Routing
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## Round-aware operating mode
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- Identify the active round and output before work. R1 indexes evidence; R2 designs the manuscript; R3 builds section dossiers; R4 settles author-facing arguments, ownership, displays and section freezes; R5 drafts prose only from frozen R4 packets and authorities.
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- Keep evidence states distinct: `mapped` is not `read`; `read` is not independently verified or artifact-audited. Use a compact ledger (`read`, `mapped`, `not-covered`, `external-inaccessible`) proportional to the round; do not let governance overwhelm argument/design.
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- In R4/5 prioritize the section question, bounded answer, paragraph jobs, display logic, ownership, interfaces, author choices and manuscript value. Do not recreate R1 inventories or rediscover the project.
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## Start from the assigned unit
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- Name the project, active round, exact unit, deliverable, output, and exclusions. R1 indexes evidence; R2 designs; R3 builds dossiers; R4 freezes arguments/displays; R5 writes admitted section prose and controls from frozen R4 packets.
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- Read fresh supplied context once. Follow the coordinator packet's exact reads, ownership, limits, questions, and acceptance checks; do not rediscover the project or recreate R1 coverage.
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## Continuation and context
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- When prior decisions matter, continuation agents begin with targeted Nowledge `memory_search`; use thread recall for exact prior discussion. Then verify every operative decision against current repository authorities. Memory aids discovery/history and never overrides authorities, manifests, code/configuration or immutable artifacts.
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- Before launching section agents, the coordinator creates a minimum context packet containing: exact controlling reads; accepted author feedback; available material/artifact inventory with readiness; requested output decision; exclusions; target length/section share; paragraph jobs; concrete display layout; ownership; and exact questions. Agents stay within that packet and perform only targeted authority checks.
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- Cadence after the initial architecture: present two detailed section packets together; receive author feedback; launch two tightly scoped continuation agents in parallel; then perform a coordinator second audit before either section is frozen or handed to R5.
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## Recall, then verify
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- Use 2–3 narrow Nowledge `memory_search` queries containing `DynamisLab JFM` plus round, section/unit, and decision/claim/term. Use `thread_search` and scoped `thread_fetch_messages` only when exact prior wording or conversation history is needed.
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- Memory navigates decisions; `mem_fs` may locate source/original text only when actually stored, with source state retained. It is not a general full-text corpus.
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- R1–R4 indexes, dossiers, plans, controls, and figure plans route architecture, ownership, ceilings, and fallbacks; they do not establish a new internal fact or verify/promote an artifact.
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- Bind internal facts/numbers to current package authority, manifest, code/configuration, or immutable artifact. If unbound, omit, use the frozen fallback, mark an authorized placeholder, or report the gate. Current authority overrides memory and summaries.
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- Search before `memory_add`; update rather than duplicate. Save only durable decisions, procedures, or lessons.
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## Tool routing and execution safety
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- Nowledge: decisions, preferences and discussion history. Undermind: external literature only, after `get_orientation` and `list_workspaces`; literature cannot establish internal results. Repository read/search tools: internal evidence, authorities, code, manifests and artifacts.
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- For read-only derivations or scripts, discover the designated conda environment from current repository authority or environment listings and record it; never guess an environment. Do not run CFD, training, artifact generation or expensive analysis unless explicitly authorized.
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## Literature and tool routing
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- For Undermind: run `get_orientation`, list/select the DynamisLab workspace, inspect existing folders/files/searches, search the library first, and broaden only if needed. Confirm identity, DOI, and availability with `get_paper_info`.
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- Keep each `read_pdfs` request bounded and self-contained: identify the papers/pages or question, request only necessary passages, and preserve `full-PDF`, `full-report`, `mapped`, `snippet`, or `inaccessible` state. Mapped/snippet evidence cannot support detailed wording or structural claims.
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- Literature supports external propositions and rhetorical/structural diagnosis only; it never verifies internal results, numbers, artifacts, priority, readiness, or claim ceilings.
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- Before any authorized read-only script, discover and use the repository-designated environment and documented entry point; do not guess an environment or install/change dependencies.
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## Evidence and claim boundaries
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- Trace claims to current authorities and preserve solver, geometry/configuration, Reynolds convention, case/seed/role, comparator, metric/estimand, ROI/window and artifact. Keep internal Legacy and modern V5 chains separate; use physical configuration names in manuscript prose.
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- Use case-specific periodic, transient and steady metrics. Distinguish sourced fact, bounded observation, interpretation, historical/negative result and open question; report gaps and conflicts without inventing citations or numbers.
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- Image work inventories existing data/scripts before proposing panels; inventory is not panel readiness. Label existing derivations, independent checks and new conjectures separately.
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## Fixed scientific cautions
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- Bound positive SR to Kármán/cloaking. Illusion SR is historical/negative; CCD is descriptive/noncausal and uses `action-correlated correction-field modes`; OID is claim-free; steady results are contextual; experiment is qualitative/provenance-gated.
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- Kan99b K2 retains the authority's exact overall `partial pass`. Its opposite mean-lift sign is explained by the CFD coordinate/force-direction convention, not unresolved physics or suspected wrong rotation; do not call the sign unresolved.
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- Never promote claims across chains, alter evidence packages/archive/history, or inflate solver qualification into controller or mechanism validation.
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## Safety and closeout
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- Do not run CFD, training, artifact generation, or expensive/new analysis without explicit authorization. Never fill an evidence gate by inference.
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- Close out whether Working Memory, durable memory, thread recall, `mem_fs`, scripts, and literature were used, distinguishing `read`, `mapped`, and independently verified/audited evidence.
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---
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description: Current Round-5 admission status, outputs, and hard boundaries
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globs: "{docs/JFM_WYQ/ROUND4_TOP_DOWN/**/*.md,docs/JFM_WYQ/FIGURE_PLANS/**/*.md,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.tex,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.md,docs/JFM_WYQ/MANUSCRIPT/**/*.tex,docs/JFM_WYQ/MANUSCRIPT/**/*.md}"
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alwaysApply: false
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---
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# Current JFM Stage: Round 5
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## Goal and admission
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- R5 produces near-final section-by-section TeX prose plus Markdown audit/control sidecars for later final main-TeX assembly. Do not write directly into the submission master, redesign the paper, reopen frozen R4 decisions, create evidence, or silently fill gates.
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- Start with R5 controls. Record confirmed workflow decisions in repository ledgers/packets as assigned; confirmation does not close source, provenance, caption, artwork, or production-readiness gates.
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- Sections 1, 2, 4–7, and 10 are admitted under their listed local gates.
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- Section 3 is admitted with the author-accepted R4 safe default: a two-figure interface comprising the steady profile and a Kármán-dominant wake composition with one source-bound Vortex and one 0.75-radius Illusion preview. Exact source/provenance/caption and production readiness remain gated.
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- Section 8 is admitted with the author-accepted R4 recommendation: the multi-cylinder Hodge/period outer-solution main equation beside the one-circle incompatibility, plus an integrated CFD, prescribed-circulation outer-reference, and sign/closure-failure figure composition. Exact artwork/source/provenance and production readiness remain gated.
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- Section 9 permits clearly marked placeholder TeX with author fields only. Do not invent apparatus facts, execution details, trial IDs, provenance, or morphology observations; placeholders are not admitted experimental results.
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## Scope boundaries
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- Work one assigned section at a time and normally one paragraph job at a time. Change only named outputs; do not edit neighboring sections or interfaces.
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- Draft from the owning current/admitted R4 packet and named current authorities. Preserve jobs, ownership, imports/exports, claim ceilings, displays, equations, fallbacks, and author-only slots.
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- Missing internal authority blocks the dependent factual sentence or number, not unrelated licensed drafting: omit it, mark an explicit placeholder, or use the frozen fallback.
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- Missing artifact readiness allows textual argument only where R4 licenses it; never claim that the artifact exists, is approved, or is production-ready.
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- No agent may promote a section, gate, display, equation, source, artifact, or author-only choice beyond the confirmed workflow decisions and controlling authorities.
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---
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description: Controlled lifecycle for Round-5 section TeX and audit production
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globs: "{docs/JFM_WYQ/ROUND4_TOP_DOWN/**/*.md,docs/JFM_WYQ/FIGURE_PLANS/**/*.md,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.tex,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.md,docs/JFM_WYQ/MANUSCRIPT/**/*.tex,docs/JFM_WYQ/MANUSCRIPT/**/*.md}"
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alwaysApply: false
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---
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# JFM Round-5 Production Workflow
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## Controls and unit contract
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- Initialize R5 controls before prose and record confirmed decisions in the assigned ledger/packet without representing unresolved artifact gates as closed.
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- The coordinator contract names the section, owning packet, authority/evidence reads, paragraph jobs, claim ceiling, output paths, provisional length/share budget, exclusions, local gates, and acceptance checks.
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- Each paragraph requires an evidence card binding its job, claim, comparator, metric/estimand where relevant, authority, caveat, display/equation dependency, and fallback or placeholder.
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- Maintain a live section/article length-and-share ledger; derive provisional budgets from R4 jobs, argument centrality, display burden, and the authorized article target. Historical percentages are context, not quotas.
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## Section production
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1. Draft the assigned section as near-final `.tex` prose from paragraph evidence cards; create its audit/control `.md` sidecar and update the live ledger.
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2. After the complete first draft, use bounded full-PDF Undermind evidence for section-level diagnosis of logic, proportion, comparator placement, caveats, and JFM rhetoric.
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3. Perform one integrated rewrite; synthesize cross-paper patterns without imitating one paper. Literature cannot authorize internal content or raise claim ceilings.
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4. Audit contract compliance, source state, paragraph logic, TeX ownership, unresolved gates/fallbacks, word count, and section share in the sidecar.
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5. At each production wave boundary, audit interfaces, ownership, bridges, terminology, displays/equations, duplication, and budget before starting the next wave.
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6. After all eligible sections, run three global passes: structure/logic; evidence/data; length/display. Then run terminology, style, and TeX preflight before later main-TeX assembly.
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## Stop conditions and deliverable
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- Bind internal facts/numbers to current package authority, manifest, code/configuration, or immutable artifact. Missing binding blocks only dependent sentences/numbers: omit, use the frozen fallback, or insert an explicit authorized placeholder.
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- Missing artifact readiness permits only R4-licensed textual argument and prohibits claims that a panel, equation artwork, caption, source package, or approval exists.
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- Do not run CFD, training, artifact generation, or new/expensive analysis. Stop only the affected unit when admission, claim license, author choice, or required fallback is absent; report the gate and continue independent licensed work.
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- Deliver the section `.tex`, audit `.md`, updated controls/ledger assigned by the contract, unresolved gates and fallbacks, and knowledge-use closeout. Do not assemble or format the final submission master.
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---
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description: Operational JFM Round-5 paragraph and TeX drafting protocol
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globs: "{docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.tex,docs/JFM_WYQ/ROUND5_BOTTOM_UP/**/*.md,docs/JFM_WYQ/MANUSCRIPT/**/*.tex,docs/JFM_WYQ/MANUSCRIPT/**/*.md}"
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alwaysApply: false
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---
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# JFM Round-5 Paragraph Drafting Protocol
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## Authority and paragraph contract
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- Draft from the owning current R4 section packet and paragraph evidence card. Obey jobs, ownership, imports/exports, claim ceiling, terminology, display/equation plan, author slots, gates, and fallbacks; current authorities control scientific facts.
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- Literature supports external propositions and rhetorical diagnosis only; it never verifies a DynamisLab result, number, artifact, priority, or readiness. Retain source state and do not use mapped/snippet evidence for detailed wording or structural claims.
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- Order paragraphs as `claim/question → comparator/definition → evidence → bounded interpretation → local caveat → consequence/bridge`. Put the dangerous limitation beside its claim and keep distinct configurations, acquisitions, estimands, masks, windows, and evidence chains separate.
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- Use green wording directly, amber only with the named test/object and adjacent qualifier, and delete red wording unless a dedicated authority licenses it. Avoid causal, mechanism, necessary, sufficient, stable, optimal, robust, general, transferable, validating, or independently confirming claims unless explicitly earned.
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## Displays, equations, and TeX
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- Keep prose-ready and artifact-ready separate. Use only licensed displays and captions; otherwise use the recorded textual fallback or clearly marked placeholder. Never imply a planned artifact exists or is approved.
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- Display equations only when owned, source-bound, licensed, and used immediately or repeatedly. Define symbols, normalization, units, sign, and domain at first use; import owner notation rather than re-deriving or duplicating it.
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- Clearly mark every placeholder and name the author-supplied field needed. Do not fabricate `\ref`, `\label`, `\cite`, or bibliography keys; labels, citations, and equations must be owned and source-bound.
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- Produce section TeX only. Do not perform final-master formatting, template integration, submission metadata, or global preamble work.
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## Style and self-audit
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- Use concrete physical subjects and verbs. Remove throat-clearing, generic AI promotion, package chronology, inventories, panel narration, repeated templates, decorative lists, unsupported intensifiers, method catalogues, roadmap endings, and heading-repeating conclusions.
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- Keep a number only when it changes the inference. Let captions decode conditions and metadata while body prose carries comparison, inference, limitation, and consequence. Define an acronym once and do not rename fixed terms for variety.
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- Before acceptance verify one paragraph job; authorized claim and exact evidence; comparator before inference; local caveat; valid citation source state; display/equation ownership; no chain pooling or duplication; intended bridge; and no filled author-only slot, invented key, or promoted artifact.
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