Clarify QQnote input boundary

SKILL.md

@@ -13,10 +13,10 @@ English polish, but a materials-specific argument that connects composition,
 structure, properties, mechanism, device/application performance, and limits.
 
 It can also route through the user's Zotero/Obsidian literature-note workflow:
-extract keywords from the manuscript topic or draft, use DeepSeek to screen
+extract keywords from the manuscript topic or draft, use QQnote-generated
-existing Zotero child notes or Obsidian-linked notes, separate strongly related
+Zotero child notes or paper tables as literature inputs, separate strongly
-and weakly related papers, then use those papers to improve positioning,
+related and weakly related papers inside QQsci, then use those papers to improve
-introduction logic, comparison, novelty framing, and citations.
+positioning, introduction logic, comparison, novelty framing, and citations.
 
 ## Core stance
 
@@ -46,7 +46,7 @@ introduction logic, comparison, novelty framing, and citations.
 | [references/submission-package-audit.md](references/submission-package-audit.md) | User provides or mentions a submission package with manuscript, Supporting Information, highlights, cover letter, figures, SI figures, TOC, graphical abstract, or related Word/PPT files |
 | [references/literature-routing.md](references/literature-routing.md) | User wants Zotero/Obsidian/DeepSeek note search, strong/weak related-paper screening, keyword extraction, or literature-grounded rewriting |
 | [references/word-citation-comments.md](references/word-citation-comments.md) | User wants citation insertion guidance in Word, reference placement, DOI-only comments, or annotated `.docx` citation suggestions |
-| [references/zotero-obsidian-subskill.md](references/zotero-obsidian-subskill.md) | User asks to generate new Zotero notes, batch process newly imported papers, summarize papers as comparison tables, link Zotero notes into Obsidian, or operate QQnote/QQnote-skill |
+| [references/zotero-obsidian-subskill.md](references/zotero-obsidian-subskill.md) | User asks QQsci to obtain or refresh literature-note inputs through QQnote, including Zotero child-note summaries or paper comparison tables |
 | [references/journal-positioning.md](references/journal-positioning.md) | Target journal is missing, uncertain, or needs recommendation and writing-position adjustment |
 
 ## Intake
@@ -96,15 +96,15 @@ placeholders.
 ## Literature-note routing workflow
 
 Use this when the user wants the manuscript optimized using previous
-DeepSeek/AwesomeGPT Zotero notes.
+DeepSeek/AwesomeGPT Zotero notes generated by QQnote or equivalent sources.
 
 1. Extract manuscript keywords from the topic, draft, abstract, figures, or SI:
    material names, material family, device/application, mechanism, performance
    metrics, synthesis strategy, target journal, and competing concepts.
 2. If the target journal is absent, ask the author for it. If they want advice,
    open `references/journal-positioning.md` and recommend several tiers.
-3. Open `references/literature-routing.md` and prepare a DeepSeek screening
+3. Open `references/literature-routing.md` and perform QQsci's own relevance
-   brief for existing notes.
+   screening against the existing notes or QQnote-generated comparison tables.
 4. Screen notes into:
    - `strongly related`: same material, same material family plus same device,
      same mechanism, same target journal/neighbor journal, or direct benchmark.
@@ -180,15 +180,16 @@ Rules:
 
 ## Zotero/Obsidian child-note subskill
 
-When the user imports new papers and asks to generate notes, summarize selected
+When the user imports new papers and asks to generate Zotero child-note
-papers, audit missing notes, or operate QQnote, use
+summaries or paper comparison tables with QQnote, use
 `references/zotero-obsidian-subskill.md`.
 
 Important defaults:
 
-- Prefer the installed `QQnote-skill` as the source of truth for Zotero child
+- QQnote is only the note/table generation tool.
-  note generation, note audits, paper-to-table summarization, Obsidian cleanup,
+- QQsci owns keyword extraction, strong/weak related-paper screening, target
-  and Dataview dashboards.
+  journal positioning, comparative review, submission-package audit, and
+  DOI-only Word citation comments.
 - Generate or update Zotero child notes first.
 - Obsidian comes second through Zotero Integration links and Dataview.
 - Keep API keys in local private config, not in chat.

references/zotero-obsidian-subskill.md

@@ -1,139 +1,94 @@
-# QQnote Subskill Boundary
+# QQnote Input Boundary
 
-Use this file when the user asks QQsci to use QQnote, the Zotero/Obsidian
+Use this file when QQsci needs literature-note inputs from QQnote.
-workflow, newly imported papers, batch DeepSeek note generation, paper summary
-tables, missing-note audits, Obsidian literature notes, or Dataview dashboards.
 
-The installed `QQnote-skill` is the source of truth for note generation and
+QQnote is only the tool for summarizing papers into Zotero child notes or
-Obsidian maintenance. QQsci consumes the resulting notes and tables for
+compact Markdown comparison tables. QQsci owns all manuscript-facing reasoning:
-materials-manuscript writing, strong/weak related-paper screening,
+keyword extraction, strong/weak related-paper screening, target-journal
-submission-package audit, and DOI-only Word citation comments.
+positioning, comparative review, submission-package audit, figure/format
+checks, terminology checks, and DOI-only Word citation comments.
 
-If QQnote-skill changes, follow QQnote-skill rather than this file for script
+Do not ask QQnote to decide whether a paper is strongly related, weakly related,
-arguments and operational details.
+necessary for citation, or sufficient as reviewer evidence. QQnote supplies
+structured paper information; QQsci makes the manuscript decision.
 
 ## Core order
 
-1. QQnote first: identify Zotero items and generate/update Zotero child notes
+1. QQsci identifies what literature input is needed from the manuscript topic,
-   through `QQnote-skill`.
+   draft, figures, target journal, or missing evidence.
-2. Optional QQnote table: summarize selected papers into a Markdown comparison
+2. QQnote generates or refreshes Zotero child-note summaries for selected papers
-   table when QQsci needs compact strong-paper comparison axes.
+   when the notes are missing or stale.
-3. Obsidian second: link Zotero notes into the vault through Zotero Integration
+3. QQnote may summarize selected papers into a Markdown comparison table when
-   and Dataview.
+   QQsci needs compact data for side-by-side comparison.
-4. QQsci third: use screened notes/tables to rewrite positioning,
+4. QQsci performs relevance classification, manuscript comparison, audit,
-   introduction, comparison, discussion, and citation placement.
+   rewriting, and Word DOI-comment placement.
 
 Do not default to creating standalone Obsidian markdown notes when the user says
-`文献笔记`; the default target is Zotero child notes generated by QQnote.
+`文献笔记`; the default input source is Zotero child notes generated by QQnote.
 
-## QQnote-skill entrypoints
+## QQnote entrypoints
 
-Use these installed scripts through QQnote-skill, not reimplemented QQsci logic:
+Use the installed `QQnote-skill` scripts only for note/table generation:
 
 ```powershell
 py "$env:USERPROFILE\.codex\skills\QQnote-skill\scripts\generate_zotero_ai_note.py" --vault "C:\Users\qyh15\Documents\Obsidian Vault" --item-key SXAIQUJT --skip-existing
-py "$env:USERPROFILE\.codex\skills\QQnote-skill\scripts\audit_zotero_ai_notes.py" --vault "C:\Users\qyh15\Documents\Obsidian Vault" --keys-only
 py "$env:USERPROFILE\.codex\skills\QQnote-skill\scripts\summarize_zotero_table.py" --vault "C:\Users\qyh15\Documents\Obsidian Vault" --item-keys "SXAIQUJT X7GJZ627" --batch-size 3 --out "C:\Users\qyh15\Documents\Obsidian Vault\99 misc\literature-comparison-table.md"
 ```
 
 Use `generate_zotero_ai_note.py` when new or selected papers need Zotero child
 notes.
 
-Use `audit_zotero_ai_notes.py` when QQsci needs to know which papers lack
-generated notes before manuscript screening.
-
 Use `summarize_zotero_table.py` when QQsci needs a compact comparison table for
-strongly related papers, benchmark comparison, figure/storyline audit, or
+papers it has already selected or is about to classify.
-target-journal positioning.
+
+Do not use QQnote's audit, cleanup, or Dataview workflows as QQsci decision
+logic unless the user explicitly asks for QQnote maintenance.
 
 ## Safety and config
 
 - Do not ask the user to paste API keys into chat.
-- Follow QQnote-skill's current config rules. It loads Zotero/LLM credentials
+- Follow QQnote's current config rules for DeepSeek/AwesomeGPT and Zotero
-  from environment variables, private local config, or AwesomeGPT preferences.
+  credentials when generating notes or tables.
 - Keep private config ignored and local-only.
 - Do not print secret-bearing config or preference lines.
 - Treat Zotero local API at `127.0.0.1:23119` as read-oriented.
-- For child-note writes, require QQnote's configured write path. It may require
+- For child-note writes, use QQnote's configured write path.
-  `ZOTERO_API_KEY` for Zotero Web API writes.
 
-## Preflight
+## When to call QQnote
 
-Before writing notes:
+Call QQnote when:
 
-1. Check Zotero is running and the local/connector route is available.
+- a candidate paper has no generated Zotero child note
-2. Confirm the target collection, selected items, tags, or explicit item keys.
+- the user imports new papers and wants note generation
-3. Check whether notes already exist and skip or update according to the user's
+- QQsci needs a compact table for a selected set of papers
-   instruction.
+- the existing notes are too thin and the user asks for deeper notes
-4. Prefer QQnote dry-run or audit mode for first-time validation.
-5. Confirm the write route for Zotero child notes.
-6. Confirm the DeepSeek/AwesomeGPT config is available without exposing secrets.
 
-## Batch behavior
+Do not call QQnote when:
 
-Batch work must be resumable:
+- the task is only to classify strong/weak related papers from existing notes
+- the task is target-journal positioning
+- the task is manuscript/package audit
+- the task is Word DOI-only citation comments
+- the task is figure, format, spelling, or terminology checking
 
-- use QQnote's existing duplicate detection and note audit behavior
+## QQsci-owned manuscript integration
-- skip items with successful existing notes unless the user asks to regenerate
-- for deep regeneration, follow QQnote's replace/update behavior instead of
-  creating duplicate child notes
-- process long runs in 20-30 item batches
-- preserve UTF-8 output for Chinese templates and notes
 
-## New paper flow
+After QQnote outputs notes or a table:
 
-When the user says they introduced new papers:
+1. QQsci extracts the manuscript keyword pack.
-
+2. QQsci uses `literature-routing.md` to classify strong and weak papers.
-1. Identify new Zotero items by collection, tag, selected items, import time, or
+3. QQsci builds a source map linking paper -> useful claim -> manuscript
-   explicit keys.
+   section.
-2. Use QQnote-skill to gather metadata, abstract, attachment text if available,
+4. QQsci uses `comparative-review-audit.md` and
-   and existing child notes.
+   `submission-package-audit.md` for missing-evidence and package checks.
-3. Use QQnote-skill to send the note-generation prompt to DeepSeek/AwesomeGPT
+5. QQsci adds Word native comments containing DOI strings only when requested.
-   using the user's template.
-4. Create or update the Zotero child note through QQnote-skill.
-5. Refresh or instruct Obsidian Zotero Integration linking only after Zotero
-   notes are created.
-6. Report successes, skips, and failures using QQnote's audit output.
-
-## Paper comparison table flow
-
-When QQsci needs to compare strong related papers before revising or auditing a
-manuscript:
-
-1. Use `literature-routing.md` to choose candidate strong papers.
-2. Ask QQnote-skill to summarize those Zotero items into a Markdown table.
-3. Use columns relevant to materials manuscripts: title, year, journal, DOI,
-   material system, device/application, mechanism, key performance, controls,
-   figure logic, and useful comparison point.
-4. Use the table as the comparison basis for `comparative-review-audit.md` and
-   `submission-package-audit.md`.
-
-## Manuscript integration flow
-
-After notes exist:
-
-1. Extract manuscript keyword pack.
-2. Use `literature-routing.md` to classify strong and weak papers.
-3. Use QQnote notes or QQnote-generated comparison tables to build a source map
-   linking paper -> useful claim -> manuscript section.
-4. For Word citation help, add native Word comments containing DOI strings only,
-   one DOI per line.
-5. Rewrite the manuscript section with citation placeholders only if the user is
-   not using the DOI-comment workflow.
-6. Flag missing evidence, missing citations, and overclaim risks.
 
 ## Output template
 
-`QQnote preflight:`
+`QQnote input used:`
 
-`Processed Zotero items:`
+`Generated or refreshed notes:`
 
-`Generated or updated child notes:`
+`QQnote table path:`
 
-`QQnote comparison table:`
+`QQsci screening/audit next step:`
-
-`Skipped existing notes:`
-
-`Failed items and reason:`
-
-`Next QQsci manuscript-use step:`