psyclaw 0.27.22 → 0.28.0

package/vendor/ars/deep-research/references/mode_selection_guide.md

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+# Mode Selection Guide
+
+## Overview
+
+deep-research provides 8 modes suited to different research stages and needs. This guide helps users select the most appropriate mode.
+
+---
+
+## Decision Flowchart
+
+```
+User Input
+    │
+    ├── Have a clear research question?
+    │   ├── Yes ──→ Have a text to review?
+    │   │            ├── Yes ──→ review mode
+    │   │            └── No ───→ Need PRISMA-compliant systematic review / meta-analysis?
+    │   │                         ├── Yes ──→ systematic-review mode
+    │   │                         └── No ───→ Need a complete report?
+    │   │                                     ├── Yes ──→ full mode
+    │   │                                     └── No ───→ Only need literature?
+    │   │                                                 ├── Yes ──→ Need rapid paper comparison?
+    │   │                                                 │            ├── Yes ──→ three-way-scan mode
+    │   │                                                 │            └── No ───→ lit-review mode
+    │   │                                                 └── No ───→ quick mode
+    │   │
+    │   └── No ──→ Want guided thinking?
+    │              ├── Yes ──→ socratic mode
+    │              └── No ───→ full mode
+    │                          (Phase 1 interactive RQ clarification)
+    │
+    ├── Only need to verify specific facts?
+    │   └── Yes ──→ fact-check mode
+    │
+    └── Not sure what you need?
+        └── Describe your situation → System auto-recommends a mode
+```
+
+---
+
+## Detailed Mode Information
+
+### full mode (Complete Research)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need to conduct complete academic research from scratch, producing a citable research report |
+| **Not Applicable** | Just need a quick understanding of a topic; already have complete research and only need review; only need a bibliography |
+| **Typical Users** | Graduate students preparing thesis proposals, policy researchers writing analysis reports, scholars exploring new fields |
+| **Expected Output** | Complete APA 7.0 report (3,000-8,000 words), including literature review, methodology, analysis, conclusions |
+| **Expected Dialogue Rounds** | 2-5 rounds (Phase 1 interaction + checkpoints) |
+| **Agents Activated** | All 9 |
+| **Time Required** | Longer; suitable for in-depth research without time pressure |
+
+**Trigger Examples**:
+```
+"Research the impact of AI on higher education quality assurance"
+"Deep research on the impact of declining birth rates on Taiwan's higher education"
+"Research the current state of SDGs implementation in Asian universities"
+```
+
+---
+
+### quick mode (Quick Research)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need a quick understanding of a topic's core viewpoints and key literature, under time constraints |
+| **Not Applicable** | Need complete methodology design; need in-depth critical analysis; need publication-quality reports |
+| **Typical Users** | Administrative staff preparing meeting background materials, researchers needing a quick literature scan, preliminary exploration before writing a proposal |
+| **Expected Output** | Research brief (500-1,500 words), including key summary, major literature, preliminary viewpoints |
+| **Expected Dialogue Rounds** | 0-1 round (typically direct output) |
+| **Agents Activated** | 4 (RQ + Biblio + Verification + Report) |
+| **Time Required** | Shorter |
+
+**Trigger Examples**:
+```
+"Quick research on blockchain in education"
+"Quick research on the latest trends in educational technology"
+```
+
+---
+
+### review mode (Text Review)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Already have a paper/report/draft that needs professional review and feedback |
+| **Not Applicable** | No text to review yet; need to write research from scratch; need literature search |
+| **Typical Users** | Graduate students who finished a paper and need peer review feedback, self-check before journal submission, peer review |
+| **Expected Output** | Review report with Editorial Verdict (Accept/Revise/Reject), specific revision suggestions, ethics review |
+| **Expected Dialogue Rounds** | 0-1 round |
+| **Agents Activated** | 3 (Editor + Devil's Advocate + Ethics) |
+| **Time Required** | Medium, depends on text length |
+
+**Trigger Examples**:
+```
+"Review this paper"
+"Help me review this paper's methodology"
+"Check this manuscript before submission"
+```
+
+---
+
+### lit-review mode (Literature Review)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need systematic literature search and synthesis analysis, but not a complete research report |
+| **Not Applicable** | Need a complete report with original analysis; only need to verify a few facts; need methodology design |
+| **Typical Users** | Graduate students writing the literature review chapter of their thesis, research teams conducting systematic reviews, coursework assignments |
+| **Expected Output** | Annotated bibliography + synthesis analysis (1,500-4,000 words), including thematic classification, evidence matrix, research gaps |
+| **Expected Dialogue Rounds** | 1-2 rounds (confirm search scope) |
+| **Agents Activated** | 3 (Biblio + Verification + Synthesis) |
+| **Time Required** | Medium |
+
+**Trigger Examples**:
+```
+"Literature review on SDGs in higher education"
+"Literature review: the evolution of quality assurance in Taiwan's higher education"
+"Systematic review of AI-assisted assessment"
+```
+
+---
+
+### three-way-scan mode (WHY / HOW / WHAT paper comparison)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need a disciplined shortlist of papers compared in a stable WHY/HOW/WHAT frame, lighter than a full literature review |
+| **Not Applicable** | Need a complete evidence matrix, thematic synthesis, or PRISMA-like coverage (escalate to `lit-review` / `systematic-review`); need to verify specific facts (`fact-check`) |
+| **Typical Users** | Researchers scoping a new area, students triaging a reading list, anyone deciding which papers to read in depth |
+| **Expected Output** | Per-paper WHY/HOW/WHAT shortlist + cross-paper synthesis (common WHY, divergent HOW, strongest WHAT, unresolved gap) (800-2,000 words) |
+| **Expected Dialogue Rounds** | 1-2 rounds (confirm candidate set) |
+| **Agents Activated** | 2 (Biblio + Verification, retrieval + compact extract) |
+| **Time Required** | Low-Medium |
+
+**Trigger Examples**:
+```
+"Compare these papers in WHY/HOW/WHAT format"
+"Quick 3W scan of recent LLM-evaluation papers"
+"Which of these should I read first?"
+```
+
+---
+
+### fact-check mode (Fact-Checking)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need to verify the truthfulness and source quality of specific factual claims |
+| **Not Applicable** | Need complete research analysis; need literature synthesis; need to produce a research report |
+| **Typical Users** | Verifying data cited in meetings, checking factual accuracy in reports, checking policy claims |
+| **Expected Output** | Verification report (300-800 words), including source rating, factual accuracy assessment, credibility determination |
+| **Expected Dialogue Rounds** | 0 rounds (direct output) |
+| **Agents Activated** | 1 (Source Verification) |
+| **Time Required** | Shortest |
+
+**Trigger Examples**:
+```
+"Fact-check these claims about Taiwan's university enrollment"
+"Fact-check: Is the number of universities in Taiwan really declining?"
+"Verify: 'OECD countries average 50% tertiary attainment rate'"
+```
+
+---
+
+### socratic mode (Guided Research)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Interested in a topic but unsure how to start research; want to clarify thinking through dialogue; need research guidance |
+| **Not Applicable** | Already have a clear research question and methodology; need quick report output; only need literature or fact-checking |
+| **Typical Users** | Master's students encountering research for the first time, scholars transitioning research fields, doctoral students brainstorming research proposals |
+| **Expected Output** | Research Plan Summary with extracted INSIGHTs, research question direction, methodology suggestions |
+| **Expected Dialogue Rounds** | 8-15 rounds (multi-round dialogue is the core feature) |
+| **Agents Activated** | 2-3 (socratic_mentor + research_question + devils_advocate as needed) |
+| **Time Required** | Longer, but the focus is on the thinking process rather than output speed |
+
+**Trigger Examples**:
+```
+"Guide my research on higher education topics"
+"Guide my research on educational technology"
+"Help me think through my thesis direction"
+"Help me think through my research topic"
+「引導我的研究：高教品保」
+「幫我釐清我的研究方向」
+「幫我想想，我對少子化議題有興趣但不確定要研究什麼」
+「我有個模糊的想法，想找研究題目」
+「帶我做研究」
+```
+
+---
+
+### systematic-review mode (Systematic Review / Meta-Analysis)
+
+| Item | Description |
+|------|------|
+| **Applicable Scenario** | Need a PRISMA-compliant systematic review, potentially with meta-analysis; evidence synthesis for policy or clinical decisions |
+| **Not Applicable** | Exploratory research without a focused PICOS question; narrative literature review; quick overview of a topic |
+| **Typical Users** | Researchers conducting Cochrane-style reviews, doctoral students writing systematic review chapters, policy teams synthesizing evidence for guidelines |
+| **Expected Output** | PRISMA 2020 report: protocol, flow diagram, risk of bias assessment, forest plot data (if meta-analysis), GRADE evidence table, full reference list |
+| **Expected Dialogue Rounds** | 3-6 rounds (protocol review + screening decisions + synthesis decisions) |
+| **Agents Activated** | 8-10 (RQ + Architect + Biblio + Verification + RoB + Meta-Analysis/Synthesis + Report + Editor + Ethics) |
+| **Time Required** | Longest; systematic reviews are inherently comprehensive |
+
+**Trigger Examples**:
+```
+"Systematic review of AI-assisted assessment in higher education"
+"Meta-analysis of the effect of active learning on STEM outcomes"
+"PRISMA review of quality assurance frameworks in Asian universities"
+"Evidence synthesis on the impact of accreditation on institutional improvement"
+```
+
+---
+
+## Common Misselection Scenarios
+
+| What the User Says | What They Probably Need | Recommended Mode | Reason |
+|-----------|------------------|---------|------|
+| "Help me do a complete literature review" | Complete report (with analysis and conclusions) | `full`, not `lit-review` | lit-review only produces bibliography and synthesis, no original analysis |
+| "Quickly check the situation with X" | Fact-checking | `fact-check`, not `quick` | If only needing to verify specific facts, fact-check is more precise |
+| "I want to research X" / 「我想研究X」(but can't articulate what they want to know) | Research thinking clarification | `socratic`, not `full` | full mode's Phase 1 also offers interaction, but socratic goes deeper |
+| "Help me fix this paper" | Paper revision guidance | `review`, not `full` | Already has text, needs review not research from scratch |
+| "I need APA-formatted references" | Reference formatting | `lit-review`, not `full` | If only a reference list and formatting is needed, no complete research required |
+| "Help me think of a research topic" / 「幫我想研究題目」 | Research direction exploration | `socratic` | Best suited for users without a clear direction |
+| "Systematic review of X" | PRISMA-compliant review | `systematic-review`, not `lit-review` | lit-review is a narrative survey; systematic-review follows PRISMA protocol with risk of bias and optional meta-analysis |
+| "I need a meta-analysis" | Quantitative evidence synthesis | `systematic-review` | Meta-analysis is a component of systematic review, not a standalone mode |
+| "Literature review for my thesis chapter" | Narrative literature review | `lit-review`, not `systematic-review` | Thesis lit review chapters are typically narrative, not PRISMA-compliant |
+
+---
+
+## Mode Transitions
+
+### Common Transition Paths
+
+```
+socratic → full              Continue with complete research after Socratic completion
+socratic → academic-paper    Write paper directly after Socratic completion
+lit-review → full            Want complete analysis after literature review
+lit-review → systematic-review  Need formal PRISMA compliance after initial lit survey
+fact-check → full            Need deeper research after fact-checking
+quick → full                 Worth going deeper after quick research
+review → full                Need to re-research after review
+systematic-review → academic-paper  Write up systematic review as a paper
+```
+
+### deep-research to academic-paper Mode Mapping
+
+| deep-research Mode | Output | Maps to academic-paper Mode | Description |
+|-------------------|------|--------------------------|------|
+| `full` | Complete research report | `full` or `revision` | Research complete, proceed to paper writing |
+| `socratic` | Research Plan Summary | `plan` | Research direction determined, plan paper structure |
+| `lit-review` | Annotated bibliography + synthesis | `full` (literature-based) | Literature review complete, start writing paper |
+| `quick` | Research brief | `plan` (needs expansion) | Preliminary exploration complete, plan full paper |
+| `review` | Review report | Does not map | Review concluded, revise original paper |
+| `fact-check` | Verification report | Does not map | Fact-checking concluded |
+| `systematic-review` | PRISMA report + forest plots + GRADE table | `full` (systematic review paper) | Systematic review complete, write as a journal article |
+
+### deep-research vs academic-paper-reviewer Mode Mapping
+
+| deep-research `review` mode | academic-paper-reviewer |
+|------------------------------|------------------------|
+| 3 agents (Editor + DA + Ethics) | Dedicated paper review skill |
+| Suitable for quality review of any text | Designed specifically for academic paper review process |
+| Produces Editorial Verdict | Produces structured review comments |
+| Recommended for: initial draft screening, non-academic texts | Recommended for: formal pre-submission review |
+
+---
+
+## Complete Academic Research Pipeline
+
+```
+Step 1: deep-research (socratic/full)
+          ↓ Research Plan / Full Report
+Step 2: academic-paper (plan/full)
+          ↓ Paper draft
+Step 3: academic-paper-reviewer (full/guided)
+          ↓ Review comments
+Step 4: academic-paper (revision)
+          ↓ Revised paper
+Step 5: [Repeat Steps 3-4 until passed]
+          ↓ Final paper
+```
+
+---
+
+## Mode Transition Matrix
+
+Rules for switching between modes mid-research. Not all transitions are safe.
+
+### Transition: quick → full
+- **When**: Quick brief reveals the topic is more complex than expected
+- **Reusable**: RQ Brief (as-is), initial keyword list
+- **Must Redo**: Full literature search (quick only uses 5-8 sources), synthesis, verification
+- **Quality Delta**: Full mode requires 15+ sources, 3+ databases, formal methodology design
+
+### Transition: lit-review → full
+- **When**: Literature review reveals a gap worth investigating with original methodology
+- **Reusable**: Complete bibliography, synthesis themes, evidence gap analysis
+- **Must Redo**: Research design (methodology_patterns), data collection plan, ethics review (if primary research)
+- **Quality Delta**: Full mode adds original research design; lit-review is secondary analysis only
+
+### Transition: socratic → full
+- **When**: Socratic dialogue produces a well-formed RQ and user wants autonomous research
+- **Reusable**: RQ Brief (with socratic_insights), accumulated INSIGHTs, scope definition
+- **Must Redo**: Everything after RQ formulation (bibliography, synthesis, verification, report)
+- **Quality Delta**: socratic mode only produces RQ Brief; full mode executes the complete pipeline
+
+### Transition: fact-check → full
+- **When**: Fact-checking reveals a claim is part of a larger contested topic worth researching
+- **Reusable**: Verified/debunked claims, source verification results
+- **Must Redo**: RQ formulation (reframe from verification to inquiry), full bibliography, synthesis
+- **Quality Delta**: Fact-check is binary (true/false/mixed); full mode produces nuanced analysis
+
+### Transition: lit-review → systematic-review
+- **When**: Literature review reveals the topic warrants formal PRISMA compliance (e.g., for publication in a journal that requires it)
+- **Reusable**: Initial keyword strategy, some identified sources (need re-screening)
+- **Must Redo**: Protocol registration, formal inclusion/exclusion criteria, dual screening, risk of bias assessment, meta-analysis feasibility assessment
+- **Quality Delta**: systematic-review requires protocol, RoB assessment, GRADE; lit-review has none of these
+
+### Transition: systematic-review → academic-paper
+- **When**: Systematic review is complete and user wants to write it up as a journal article
+- **Reusable**: Everything — PRISMA report is essentially the paper draft
+- **Must Redo**: Formatting to target journal requirements, abstract restructuring
+- **Quality Delta**: Minimal — systematic review output is already structured per PRISMA 2020
+
+### Prohibited Transitions
+- **full → quick**: Cannot downgrade a full research to quick brief (loss of rigor)
+- **Any → socratic**: Socratic mode is an entry point only; cannot transition into it mid-pipeline
+- **paper-review → full**: Paper review evaluates existing work; full mode creates new research. These are fundamentally different tasks

package/vendor/ars/deep-research/references/openalex_api_protocol.md

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+# OpenAlex API Verification Protocol
+
+**Status**: v3.9.0; #495 auth/backoff refresh (2026-07)
+**Used by**: `bibliography_agent`, `migrate_literature_corpus_to_v3_9_0.py`
+**API base**: `https://api.openalex.org`
+**Rate limit**: freemium daily budget (https://developers.openalex.org/api-reference/authentication) — single-entity GETs effectively unmetered, searches budget-metered; a free API key gives 10× the keyless budget. Burst cap 100 req/s. Client pacing: 10 req/s (authenticated — API key or legacy `mailto`), 1 req/s (anonymous).
+**API key env var**: `OPENALEX_API_KEY` (preferred; free key from openalex.org/settings/api)
+**Polite email env var**: `OPENALEX_POLITE_EMAIL` (legacy; the polite pool is no longer in OpenAlex's docs, but the client still sends `mailto` when configured and treats it as an authenticated-tier credential for pacing)
+
+---
+
+## Purpose
+
+Provides a second bibliographic-index lookup for v3.9.0 cross-index triangulation per spec v3.9.0 §3.4. Mirrors the structure of `semantic_scholar_api_protocol.md` so adapters and migration tools can swap clients with minimal contract divergence. Used by `bibliography_agent` at ingest time and by the v3.9.0 migration tool for legacy backfill.
+
+OpenAlex coverage complements Semantic Scholar for OA venues, monographs, and works without DOIs. Per Zhao et al. arXiv:2605.07723 §3, cross-index triangulation reduces false-positive rate vs. single-index detection (e.g., a paper unmatched in S2 but matched in OpenAlex is high-coverage-gap evidence, not fabrication evidence).
+
+## Query Patterns
+
+### Pattern 1: DOI Lookup with Title Cross-Check (primary when DOI is available)
+
+```
+GET /works/doi:{doi}?select=id,title,authorships,publication_year,doi,primary_location,is_retracted
+```
+
+**Matching rule (mirrors S2 `DOI_MISMATCH` pattern):** DOI lookup hits are gated by a Levenshtein 0.70 title cross-check. If the returned `title` field fails the threshold against the entry's canonical title, the DOI hit is rejected (DOI_MISMATCH — a known hallucination pattern where a fabricated DOI resolves to an unrelated paper). The caller falls through to title search.
+
+### Pattern 2: Title Search (fallback when DOI absent or DOI_MISMATCH)
+
+```
+GET /works?search={url_encoded_title}&per-page=5&select=id,title,authorships,publication_year,doi,primary_location,is_retracted
+```
+
+**Matching rule:** Compute Levenshtein similarity between query title and each result title (case-insensitive, punctuation stripped) per `_normalize_title` in the client. Accept if similarity >= 0.70 (matching PaperOrchestra threshold). If multiple candidates pass, prefer matching-year tiebreaker, then highest similarity, then candidate with populated DOI.
+
+## `openalex_unmatched` derivation
+
+`true` if and only if:
+- DOI present: DOI lookup either misses or fails the title cross-check, AND title search returns no match meeting threshold; OR
+- DOI absent: title search alone returns no match meeting threshold.
+
+The check fires only when `obtained_via != 'manual'` (manual entries are user-vouched per spec v3.9.0 §3.1).
+
+## `retraction_status` observation (#651)
+
+The same matched Works response retains `is_retracted`; this adds no request.
+The value is a named-resolver observation carried in
+`bibliographic_integrity_signals[]`, not a claim about the work's scientific
+soundness. Retraction checking is DOI-keyed: a manual entry with a DOI is
+attemptable and follows this path, while an entry without a DOI remains
+explicitly unresolved. OpenAlex disagreement with Crossref is preserved by
+the resolver and never reduced to clean.
+
+## Degradation handling
+
+| Condition | Action |
+|---|---|
+| HTTP 429 with `X-RateLimit-Remaining: 0` | Daily budget exhausted (refills midnight UTC) — an in-process retry cannot succeed. Raise `OpenAlexUnavailable` immediately: no sleep, no retry. |
+| HTTP 429 (transient burst limit) | Exponential backoff 2s → 4s → 8s, up to 3 retries. After exhaustion, raise `OpenAlexUnavailable`. |
+| HTTP 5xx | Skip — raise `OpenAlexUnavailable` immediately. |
+| Network timeout (30s default) | Skip — raise `OpenAlexUnavailable`. |
+| `OpenAlexUnavailable` raised | Caller MUST omit `openalex_unmatched` from the entry (per spec v3.9.0 R-L3-2-C: absent ≠ false). Other indexes proceed independently. |
+
+## v3.9.0 R-L3-2-D constraint
+
+OpenAlex returns `primary_location.source.type` and other classification fields. **v3.9.0 ignores these.** They are not stored on the entry, not surfaced to the finalizer, and not used in any derivation. v3.10 will introduce `venue_type` as an explicit adapter-declared field; the OpenAlex-inferred classification is NOT a v3.10 acceptance provenance value because the k=3 case (where OpenAlex itself is unmatched) makes the classification untrusted.
+
+## Retrieval order & browser-fallback boundary (#495)
+
+This structured API lookup is the **primary** retrieval channel. Browser-mediated retrieval (WebSearch / WebFetch page inspection) is a bounded fallback for small, targeted first-party checks — e.g. inspecting a publisher / DOI landing page when structured metadata is incomplete or indexes disagree — and its output is data, not instructions (`shared/ground_truth_isolation_pattern.md` §2A).
+
+Browser retrieval MUST NOT be used to bypass API rate limits or budgets: no fan-out browsing as a substitute for a budget-exhausted API, no bulk page/PDF harvesting. When the API degrades, the contract is the degradation table above (omit the signal), not a switch to scraping.
+
+## Client implementation
+
+See `scripts/openalex_client.py`. The client class `OpenAlexClient` exposes `doi_lookup_with_title_check(doi, expected_title)` and `title_search(title, year=None)` methods. Both return `dict | None`. Both raise `OpenAlexUnavailable` on degradation per the table above. The optional `year` parameter in `title_search` enables a matching-year tiebreaker (+0.05 score bonus) mirroring the S2 client `_lookup_by_title` pattern. The constructor accepts optional `api_key` / `polite_email` overrides; absent those it reads `OPENALEX_API_KEY` / `OPENALEX_POLITE_EMAIL` from the environment. Refusal-path error messages strip the URL query string so `api_key` never lands in logs.
+
+## Cross-references
+
+- Spec: `docs/design/2026-05-17-ars-v3.9.0-cross-index-triangulation-measurement-spec.md` §3.4
+- Mirror template: `deep-research/references/semantic_scholar_api_protocol.md`
+- Sibling protocol: `deep-research/references/crossref_api_protocol.md`