psyclaw 0.28.0 → 0.28.2

package/vendor/nature-skills/skills/nature-polishing/references/writing-strategy.md

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+# Writing Strategy
+
+## Contents
+
+- [Core stance](#core-stance)
+- [Hourglass structure](#hourglass-structure)
+- [Writing order is not reading order](#writing-order-is-not-reading-order)
+- [Claim, evidence, boundary](#claim-evidence-boundary)
+- [Section responsibilities](#section-responsibilities)
+- [Citation as positioning](#citation-as-positioning)
+- [Fairness to earlier work](#fairness-to-earlier-work)
+- [Overclaim control](#overclaim-control)
+
+
+Use this file when the user is not just asking for cleaner English, but for better scientific writing logic. This is the layer that should govern all paragraph- and section-level rewriting.
+
+## Core stance
+
+Academic polishing is not only about style. It is also about making the reasoning legible. A polished paragraph that still performs the wrong rhetorical job is a failed edit.
+
+## Hourglass structure
+
+Most strong research writing follows a `broad -> narrow -> broad` pattern:
+
+- `Introduction`: open the territory, narrow to the gap, then state the study
+- `Discussion/Conclusion`: start from the specific findings, then widen to implications and limits
+
+Use this pattern when deciding paragraph order and section scope. If a draft jumps between background, results, and implications without control, rebuild the progression first.
+
+## Writing order is not reading order
+
+The author may draft in one order and the reader may consume in another. A useful planning sequence is:
+
+1. results
+2. introduction and conclusion
+3. title
+4. discussion
+5. methods
+6. abstract
+
+The practical rule for this skill is simple: organize around evidence and argumentative function, not around the chronology of the raw draft.
+
+## Claim, evidence, boundary
+
+Every important scientific statement should have three parts:
+
+1. `claim`: what is being said
+2. `evidence`: what supports it
+3. `boundary`: where the claim stops, or what uncertainty remains
+
+Typical failures:
+
+- claim without evidence
+- data without an explicit point
+- implication without a scope condition
+- correlation rewritten as mechanism
+
+When polishing, repair these failures before polishing rhythm.
+
+## Section responsibilities
+
+### Introduction
+
+The Introduction should answer four questions:
+
+1. What is already known?
+2. What remains unresolved?
+3. What exact question does this study ask?
+4. How does the study address it?
+
+Do not summarize results or conclusions here.
+
+### Results
+
+Results state what was observed. They should provide:
+
+- object or system
+- condition
+- quantitative support
+- direct result
+
+Do not turn Results into a Discussion section by adding long mechanistic interpretation.
+
+### Discussion
+
+Discussion explains what the findings mean. It should address:
+
+- how the work fits the broader field
+- what has been added to understanding
+- which earlier work is being supported, revised, or complicated
+- which explanations are plausible
+- which limitations constrain the interpretation
+
+Discussion is the natural home for hedging.
+
+### Methods
+
+Methods should pass a reproducibility test: could another group repeat the work from this description, or from this description plus a clearly cited prior protocol?
+
+Reject vague writing such as:
+
+- `under standard conditions`
+- `using routine methods`
+- `data were analysed statistically`
+
+### Conclusion
+
+Conclusion is not a mini-discussion. A strong closing usually does three things:
+
+1. restates the central contribution
+2. identifies the decisive evidence
+3. states the implication with a boundary
+
+Do not introduce new data here.
+
+### Abstract
+
+The abstract is a mini-paper:
+
+1. context or problem
+2. gap
+3. approach
+4. key result
+5. implication
+
+It should help the reader decide whether the paper is relevant, credible, and potentially important.
+
+## Citation as positioning
+
+Citation is not just a formatting issue. It tells the reader how the current work stands relative to earlier work.
+
+Useful categories:
+
+- `support`: prior work supports the premise
+- `borrow`: current work adopts a method, framework, or protocol
+- `contrast`: current work differs in result, setting, or interpretation
+- `reuse/adaptation`: material, data, code, or images come from elsewhere
+
+Always cite the source actually read and verified. Do not cite a paper as direct support if you only know it through another paper's summary.
+
+## Fairness to earlier work
+
+Do not manufacture novelty by flattening previous studies into a weak baseline. Prefer language like:
+
+- `Although previous studies showed ..., their performance in ... remains unclear.`
+- `Earlier work established ..., but did not address ...`
+
+This preserves intellectual honesty while still making the gap explicit.
+
+## Overclaim control
+
+Watch for:
+
+- `prove`
+- `conclusively`
+- `unprecedented`
+- `best`
+- unqualified `first`
+
+Replace or qualify them unless the evidence is unusually strong and the scope is tightly defined.

package/vendor/nature-skills/skills/nature-polishing/static/core/failure-modes.md

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+# Diagnose failure mode before editing
+
+Before rewriting, identify the main problem:
+
+- wrong paper type logic
+- missing gap or poor positioning
+- claim without evidence
+- evidence without a clear claim
+- missing boundary or limitation
+- Results and Discussion mixed together
+- weak title or abstract signal
+- inconsistent terminology, abbreviations, units, or notation across sections
+- evidence-complete but main-text-bloated Results
+- reviewer-driven additions appended without deleting redundant prose
+- the same claim or full statistical report repeated across Results and captions
+- sentence-level clutter only
+
+Prioritize fixes in this order:
+
+`paper type -> section job -> evidence placement -> paragraph necessity -> claim/evidence/boundary -> sentence polish`
+
+Do not sentence-polish a draft whose section job is wrong. Surface the structural problem first, then polish.
+
+For Results or full-main-text work, load
+`../../../nature-shared/core/main-text-discipline.md`. Resolve evidence placement,
+revision accretion, explanatory recursion, and claim repetition before editing
+sentence rhythm.
+
+Terminology consistency is a cross-cutting check that runs at every level: build the Terminology Ledger on first contact (see `../../../nature-shared/core/terminology-ledger.md`) and enforce its canonical forms throughout the polish.

package/vendor/nature-skills/skills/nature-polishing/static/core/output-format.md

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+# Output format
+
+Default output:
+
+1. The polished text as plain prose, not in a code block.
+2. `Revision notes:` with `3-5` short bullets on the major structural and stylistic changes.
+3. If the rewrite changed section logic, say so explicitly.
+
+If the user asks for side-by-side revision, provide:
+
+- `Original`
+- `Polished`
+- `Why changed`
+
+If any paragraph's structural problem could not be fixed without inventing content, say so under `Revision notes:` instead of papering over it.
+
+When the main-text discipline is triggered, add a compact
+`Main-text discipline audit:` that identifies material kept, replaced,
+compressed, relocated to SI/caption, or deleted; states which descriptive and
+primary inferential quantities remain in the main text; and reports the
+before/after word count. Do not bury the polished prose under the audit.

package/vendor/nature-skills/skills/nature-polishing/static/core/stance.md

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+# Default stance
+
+- Language serves argument. Do not polish sentences while leaving the reasoning broken.
+- Write with empathy for the reader: relevance first, then novelty, then trust, then reuse, then meaning.
+- There should be no mystery for the writer, but there may be one for the reader.
+- Do not invent data, references, mechanisms, or novelty claims.
+- Do not let AI draft the paper's core scientific argument from scratch.
+- If the draft is Chinese or structurally rough, reconstruct the logic first and the prose second.
+- On first contact with the draft, build a Terminology Ledger and keep terms, abbreviations, units, and notation consistent across every section. Do not introduce synonyms to vary the prose. See `../../../nature-shared/core/terminology-ledger.md`.
+- Avoid em dashes in polished output by default. Prefer commas, parentheses, or full stops. Use colons sparingly unless the user explicitly asks to preserve dash-based punctuation or wants a colon-led style.
+
+## Reader workflow
+
+See `../../../nature-shared/core/reader-workflow.md` (loaded via manifest `always_load`) for the 5-step reader question sequence. Polishing should help the paper answer those questions in order.
+
+## Protect the core argument
+
+The paper's core argument includes:
+
+- the scientific question the paper actually answers
+- why that question matters
+- how the work differs from existing research
+- what the results imply
+- how the main line of reasoning unfolds
+
+AI may help polish, structure, or compare phrasings. AI should not invent or author the core argument. If the argument is weak or unclear, expose that weakness rather than hiding it under polished language.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/generic.md

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+# Journal: generic
+
+Used when the user has not named a target journal, or the journal is not specifically modeled by another fragment.
+
+## Defaults
+
+- Apply Nature-leaning style without enforcing Nature's strictest length or significance-framing demands.
+- Keep the em-dash and hedging defaults from `core/stance.md`.
+- If the user later names a journal, apply that journal's fragment to the ongoing request; ask only if the intended scope of revision remains materially ambiguous.
+
+## Optional context
+
+Use these details when supplied; otherwise proceed with the generic defaults and state material assumptions. Ask only when missing information changes scientific meaning or a required deliverable. Do not turn these preferences into an intake checklist.
+
+- Target journal and section format (structured vs unstructured abstract; word limits; reference style).
+- Audience breadth: subfield vs broad readership.
+- Whether the draft will go through a separate copy-edit pass (affects how aggressively to rewrite vs flag).

package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-comms.md

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+# Journal: Nature Communications (polishing)
+
+## Read the shared facts first
+
+Open `../../../../nature-shared/journal-formats/nat-comms.md` for the authoritative formatting facts: word limits, abstract rules, figure specs, reference style, mandatory statements, and common desk-rejection patterns.
+
+The notes below are the **polishing action layer** on top of those facts.
+
+## Audience
+
+Open-access, broader than a subfield journal but more specialist-tolerant than Nature. The reader is typically an active researcher in an adjacent area.
+
+## Polishing priorities
+
+- Significance framing matters, but a less aggressive opening than Nature is acceptable.
+- Word count is more forgiving than Nature, but **the ~5,000-word cap includes Methods**. If polishing brings the manuscript near the limit, surface a word-budget check rather than just compressing prose.
+- Methods can stay more detailed in-line; do not strip reproducibility content just to hit length.
+- Same em-dash and hedging defaults as Nature.
+- Abstract is unstructured, 150 words, no citations. If the user's abstract has citations or is structured (Background/Methods/Results), restructure before sentence polishing.
+
+## Length-aware polishing checks
+
+When polishing a Nature Communications Article, run these word-budget checks before sentence-level work:
+
+1. Estimate total word count **including Methods**. Verify the current journal limit when submission compliance is requested. If over the applicable limit, continue meaning-preserving polishing and flag the gap in Revision notes. Obtain approval before substantive cuts to results, methods, or argument; length diagnosis does not block language edits.
+2. If display items > 10, flag for redistribution into Supplementary Information before deeper edits.
+3. If references > ~60, flag for trimming or consolidation.
+4. If the abstract is > 150 words or contains citations, restructure first.
+
+These are diagnostic, not destructive — surface the problem in `Revision notes:` rather than silently cutting.
+
+## Things the shared facts already cover
+
+Do not restate facts that live in `nature-shared/journal-formats/nat-comms.md`. Reference them when the user asks. Examples Claude should respond by reading shared facts:
+
+- "What's the reference style?" → cite the format example from shared
+- "How many figures can I have?" → cite the 10-item cap from shared
+- "What's the abstract limit?" → 150 words, unstructured, no citations

package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nat-mach-intell.md

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+# Journal: Nature Machine Intelligence — polishing
+
+## Read the shared contract first
+
+Open
+`../../../../nature-shared/journal-formats/nature-machine-intelligence.md` for
+the exact, stage-aware NMI facts. This fragment controls polishing decisions,
+not the submission numbers themselves.
+
+For Results or Discussion, also open
+`../../../../nature-shared/core/nature-results-discussion.md`. It is
+corpus-derived Nature-style writing guidance, not an official NMI requirement.
+
+For Introduction polishing, also open
+`../../../../nature-shared/core/nature-introduction.md`. It is corpus-derived
+Nature-style writing guidance, not an official NMI requirement.
+
+For abstract polishing, also open
+`../../../../nature-shared/core/nature-abstract.md`. It is corpus-derived
+Nature-style writing guidance, not an official NMI requirement.
+
+## Audience and stance
+
+Polish for readers across AI, robotics, machine learning and the scientific or
+societal application domain. Preserve technical precision while making the
+question, evidence and consequence understandable outside one specialist
+benchmark community.
+
+## Structure before sentence polish
+
+For an Article, check these before line editing:
+
+1. Count Introduction + Results + Discussion against the 3,500-word main-text
+   limit; exclude abstract, Methods, references and legends.
+2. Keep the unreferenced abstract at or below 150 words.
+3. Check that figures and tables total no more than six.
+4. Keep the introduction unheaded; allow topical subheadings in Results and
+   Methods but not in Discussion.
+5. Preserve enough Methods detail for replication; NMI does not publish a
+   fixed Methods word limit on the current pages.
+
+Report an over-limit or wrong-structure manuscript under `Revision notes:`.
+Do not silently delete evidence, uncertainty or reproducibility detail to make
+the prose fit.
+
+## Claim calibration
+
+- Replace benchmark-only claims of general intelligence or deployment
+  readiness with the evaluated scope.
+- Separate gains due to architecture from data, supervision, compute or tuning
+  differences.
+- Name robustness and transfer boundaries when the prose currently hides them.
+- Do not convert association, retrospective performance or simulation results
+  into causal, clinical or societal effectiveness.
+- Define specialist abbreviations and remove jargon that is not needed for
+  technical accuracy.
+
+## Results–Discussion calibration
+
+- Preserve a claim-escalating Results sequence rather than flattening related
+  subsections into parallel experiment reports.
+- Keep a bounded local inference in Results when it directly resolves the
+  current experiment; move cross-result synthesis and broader implications to
+  Discussion.
+- Keep conclusion-changing robustness and failure boundaries visible in the
+  main text; move reassurance-only variants to SI.
+- Permit a brief finding anchor in Discussion, but remove repeated evidence,
+  effect sizes, and tests that merely re-demonstrate the Results claim.
+
+## Introduction calibration
+
+- Compress broad context until the specific unresolved problem appears early.
+- Replace vague limitation language with the exact unknown, condition,
+  mechanism, boundary, or literature tension.
+- Reorganize citation catalogues into a known–unknown argument.
+- Replace novelty adjectives with the research question and the design that can
+  answer it.
+- Check that each Introduction question maps to a Results answer and that the
+  closing paragraph previews this route without replaying the paper.
+
+## Abstract calibration
+
+- Rebuild the abstract around one main discovery rather than a list of
+  datasets, models, metrics, and completed analyses.
+- Keep only enough method information to show why the design answers the gap.
+- Retain no more than one or two decisive supporting claims or boundaries.
+- Keep a number only when it defines, supports, or bounds the main discovery.
+- Make the final sentence state the bounded conceptual or field-level payoff,
+  not merely superior performance.
+
+## Submission-sensitive checks
+
+- Preserve explicit disclosure of a substantially extended conference paper.
+- Preserve Data Availability and the separate Code availability section.
+- Flag missing reviewer access or a missing Software Submission Checklist when
+  new code is central to the conclusions.
+- Do not apply a flagship Nature title, Methods or legend limit. NMI's current
+  public pages state no current fixed number for those items. For figure
+  legends, use the official 2018 NMI below-300-word instruction only as a
+  historical advisory ceiling: count the complete legend, not each panel, aim
+  for 150–250 English words, and obey any newer editor or submission-system
+  instruction.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/journal/nature.md

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+# Journal: Nature (and Nature subjournals)
+
+## Audience
+
+A broad, multi-disciplinary readership. A reader outside the immediate subfield must be able to grasp the claim, the gap, and the significance from the first paragraph and the abstract.
+
+## Polishing priorities
+
+- The opening sentence must signal significance for a non-specialist audience without overclaiming.
+- Avoid jargon that does not appear in the headline of a typical Nature News piece. Define or replace.
+- Abstract is unstructured prose for many Nature titles; check the target journal's current guideline if the user names one.
+- Length discipline: Nature articles are unforgiving on word count. Prefer cuts to compressions.
+- No em dashes in body prose. Use commas, parentheses, or shorter sentences.
+- Hedging should be calibrated. Avoid both overclaim (`proves`, `definitive`) and timidity (`might possibly suggest`).
+
+## Things to flag, not silently fix
+
+- If the manuscript leans on a specialist mechanism the broad audience would not follow, flag it for the author rather than over-translate.
+- If significance for a non-specialist is genuinely thin, surface that as a structural problem in `Revision notes:`.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/en.md

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+# Language: English source
+
+## Sentence rules
+
+- In polished prose, aim for sentences in the `10-30` word range.
+- Keep every sentence at `<= 30` words.
+- Do not produce full sentences under `10` words unless the user explicitly asks for terse style or the item is a heading, label, or fixed technical expression.
+- If any sentence exceeds `20` words, check whether it contains more than one main proposition.
+- Split overloaded sentences rather than polishing them cosmetically.
+- The last sentence of a paragraph often becomes the longest and weakest. Check it explicitly.
+- Prefer one core subject-verb proposition per sentence.
+- Do not use em dashes as prose punctuation in the polished version unless the user explicitly requests them. Rewrite with commas, parentheses, or shorter sentences instead. Use colons only when they add clear structural value.
+
+## Paragraph rules
+
+- Each paragraph should have one controlling idea followed by support.
+- Supporting material may include data, comparison, explanation, consequence, literature, or limitation.
+- If a new idea appears, start a new paragraph instead of stacking it onto the old one.
+- Use thematic linking, not repetitive `This suggests ...` openings.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/language/zh-to-en.md

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+# Language: Chinese-to-English
+
+When the source is Chinese or strongly Chinese-influenced English, do not translate clause-by-clause.
+
+## Workflow
+
+1. Extract the core propositions first. List them in plain English before drafting prose.
+2. Reconstruct explicit logical links: contrast, cause, implication, limitation. Chinese academic prose often elides these connectives — restore them.
+3. Verify terminology, causality, and hedging strength against the source.
+4. Keep technical terms, gene/protein names, model names, dataset names, and statistical terms stable; do not "translate" them into rough paraphrases.
+5. Apply the English sentence and paragraph rules from `language/en.md` only after the logic is rebuilt.
+
+## Common Chinese-influenced patterns to fix
+
+- Topic-comment chains rewritten as subject-verb sentences.
+- Strings of short clauses joined by commas — split or add connectives.
+- Vague generalizations (`many studies have shown`) — convert to specific citations or remove.
+- Hedging asymmetry: Chinese drafts often understate; English Nature-style asks for precise hedging matched to evidence strength, neither over- nor under-claiming.
+- Repetition of the topic noun where English would use a pronoun or omit it.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/algorithmic.md

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+# Paper type: algorithmic or device
+
+The argument proposes a procedure, tool, or system and must show that it performs reliably and advantageously.
+
+## What the reader expects
+
+- a clear problem formulation and the precise scope being claimed
+- the proposed procedure or device, described to a level a peer could re-implement
+- a fair comparison against credible baselines under matched conditions
+- ablations or controls that isolate why the new approach works
+- failure modes, runtime/cost characteristics, and applicability boundaries
+
+## Polishing priorities
+
+- Separate "what the system is" from "why it works" from "how well it works"; do not braid them.
+- Performance claims must specify the dataset, metric, baseline, and conditions, not stand as bare numbers.
+- Avoid marketing verbs (`leverages`, `enables`, `empowers`) unless they carry information.
+- The Discussion should name the failure modes the experiments revealed, not only the wins.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/hypothesis.md

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+# Paper type: hypothesis-based
+
+The argument tries to establish or rule out a causal explanation.
+
+## What the reader expects
+
+- a clearly stated hypothesis, framed before the evidence
+- a falsification path: what observations would refute it
+- evidence presented in support, against, or as boundary conditions
+- alternative explanations addressed, not ignored
+
+## Polishing priorities
+
+- Make the hypothesis statement explicit and locatable; do not bury it in the third paragraph of the Introduction.
+- Distinguish supporting evidence from consistent-but-non-discriminating evidence.
+- In the Discussion, address rival explanations before generalizing.
+- Hedging should match the strength of the causal claim. Avoid overclaiming mechanism from correlational data.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/methods.md

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+# Paper type: methods
+
+The reader of a methods paper asks:
+
+- whether the method works
+- whether it is reproducible
+- whether it is better under a fair comparison
+
+## Results section job
+
+The Results section must show the advantages of the method over existing methods. Typical questions are:
+
+- Is it more reliable?
+- Is it faster?
+- Does it require fewer resources?
+- Is the comparison fair and reproducible?
+
+## Methods section detail
+
+The Methods section in a methods paper may need additional detail such as:
+
+- axioms, conditions, and assumptions
+- hardware and software environment
+- mathematical derivations
+- evaluation protocol
+- datasets, baselines, metrics, splits, and hyperparameters
+
+## Productive writing order
+
+1. Methods
+2. Results
+3. Introduction
+4. Conclusion
+5. Discussion
+6. Abstract

package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/research.md

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+# Paper type: research
+
+The reader of a research paper asks:
+
+- why the phenomenon matters
+- what was done
+- what was found
+- what it means
+
+## Hourglass structure
+
+Strong research papers mirror an hourglass:
+
+- `Introduction`: open broadly, then narrow to the specific gap, question, hypothesis, methods, and study
+- `Discussion/Conclusion`: widen again, connecting the findings back to the literature and explaining how the knowledge gap was filled
+
+If a paragraph or section violates this architecture, rebuild it before polishing wording.
+
+## Productive writing order
+
+1. Results
+2. Introduction and Conclusion
+3. Title
+4. Discussion
+5. Materials and Methods
+6. Authors
+7. Abstract
+
+Follow the logic of evidence and argument, not the raw order in which the user drafted sentences.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/paper_type/review.md

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+# Paper type: review
+
+The reader asks: what is the state of the field, where is the disagreement, and what is the path forward.
+
+## What the reader expects
+
+- a clear scope statement (which sub-area, which time window, which inclusion criteria)
+- a synthesis that organizes the literature by argument, not by paper
+- explicit positioning of disagreements and gaps
+- an outlook that names the most informative open questions
+
+## Polishing priorities
+
+- A review is not a survey list. Replace `Author A reported X. Author B reported Y.` with synthesis that groups claims by mechanism, method, or conclusion.
+- Position the reviewer's own stance carefully: a review can take a view, but it must show its reasoning.
+- Avoid generic transitions (`furthermore`, `additionally`). Use connectives that signal the logical relation (`in contrast`, `building on this`, `the remaining disagreement is`).
+- The closing section should leave the reader with a usable map, not a summary of what was just read.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/abstract.md

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+# Section: Abstract
+
+The abstract is the manuscript's shortest evidence chain, not a compressed
+Introduction:
+
+`precise problem/gap -> answer-enabling design -> main discovery -> decisive support/boundary -> implication`
+
+It should answer:
+
+1. What question was addressed?
+2. How was it addressed?
+3. What was found?
+4. Why should anyone care?
+
+Some journals require a strict abstract format. Follow the journal if it conflicts with the generic pattern. (See the loaded `journal/*.md` fragment for journal-specific constraints.)
+
+## Polishing priorities
+
+- Cut sentences that summarize background that the title already implies.
+- Make the gap and the contribution one short, locatable sentence each.
+- Organize the abstract around one main claim and at most one or two decisive
+  supporting claims or boundaries; do not inventory every Results subsection.
+- Keep method detail only when it explains why the question is answerable.
+- Keep a number only when it defines, supports, or materially bounds the main
+  discovery; numeric reporting is not mandatory by itself.
+- The last sentence should state significance, not repeat the result.

package/vendor/nature-skills/skills/nature-polishing/static/fragments/section/conclusion.md

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+# Section: Conclusion
+
+Use the three-part close:
+
+1. restate the central contribution
+2. summarize the key evidence or outcome
+3. state the implication with a boundary
+
+Do not introduce new data in the conclusion. Always run an overclaim check here.
+
+## Overclaim check
+
+- Does each claim trace back to evidence in this paper?
+- Are mechanism words (`demonstrates`, `proves`, `establishes`) backed by the right study design?
+- Is the scope of the implication narrower than or equal to the scope of the evidence?