dsh-aris-panel 0.1.0

package/skills/skills-codex/research-wiki/SKILL.md

@@ -0,0 +1,421 @@
+---
+name: research-wiki
+description: "Persistent research knowledge base that accumulates papers, ideas, experiments, claims, and their relationships across the entire research lifecycle. Inspired by Karpathy's LLM Wiki pattern. Use when user says \"知识库\", \"research wiki\", \"add paper\", \"wiki query\", \"查知识库\", or wants to build/query a persistent field map."
+argument-hint: "[subcommand: init|ingest|sync|query|update|lint|stats]"
+allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, WebSearch, WebFetch
+---
+
+# Research Wiki: Persistent Research Knowledge Base
+
+Subcommand: **$ARGUMENTS**
+
+## Overview
+
+The research wiki is a persistent, per-project knowledge base that accumulates structured knowledge across the entire ARIS research lifecycle. Unlike one-off literature surveys that are used and forgotten, the wiki **compounds** — every paper read, idea tested, experiment run, and review received makes the wiki smarter.
+
+Inspired by [Karpathy's LLM Wiki pattern](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f): compile knowledge once, keep it current, don't re-derive on every query.
+
+## Core Concepts
+
+### Four Entity Types
+
+| Entity | Directory | Node ID format | What it represents |
+|--------|-----------|---------------|--------------------|
+| **Paper** | `papers/` | `paper:<slug>` | A published or preprint research paper |
+| **Idea** | `ideas/` | `idea:<id>` | A research idea (proposed, tested, or failed) |
+| **Experiment** | `experiments/` | `exp:<id>` | A concrete experiment run with results |
+| **Claim** | `claims/` | `claim:<id>` | A theorem/headline with an honest PROOF status — born via `/proof-checker` (see Hook 4) |
+
+### Typed Relationships (`graph/edges.jsonl`)
+
+| Edge type | From → To | Meaning |
+|-----------|-----------|---------|
+| `extends` | paper → paper | Builds on prior work |
+| `contradicts` | paper → paper | Disagrees with results/claims |
+| `addresses_gap` | paper\|idea → gap | Targets a known field gap |
+| `inspired_by` | idea → paper | Idea sourced from this paper |
+| `tested_by` | idea\|claim → exp | Tested in this experiment |
+| `supports` | exp → claim\|idea | Experiment confirms claim |
+| `invalidates` | exp → claim\|idea | Experiment disproves claim |
+| `supersedes` | paper → paper | Newer work replaces older |
+
+Edges are stored in `graph/edges.jsonl` only. The `## Connections` section on each page is **auto-generated** from the graph — never hand-edit it.
+
+### Capture and injection hygiene
+
+Before persisting an idea, claim, or experiment note, screen operational noise
+per [`capture-antipatterns.md`](../shared-references/capture-antipatterns.md).
+Resolve the repo from the Codex manifest, then the helper:
+
+```bash
+if [ -z "${ARIS_REPO:-}" ] && [ -f .aris/installed-skills-codex.txt ]; then
+  ARIS_REPO=$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null) || true
+fi
+CAPTURE_FILTER=""
+[ -n "${ARIS_REPO:-}" ] && [ -f "$ARIS_REPO/tools/capture_filter.py" ] && CAPTURE_FILTER="$ARIS_REPO/tools/capture_filter.py"
+[ -z "$CAPTURE_FILTER" ] && [ -f tools/capture_filter.py ] && CAPTURE_FILTER="tools/capture_filter.py"
+```
+
+Run `python3 "$CAPTURE_FILTER" -` on the note when resolved. If it flags an
+environment failure, transient error, or negative tool-capability claim, store
+the fix/config/workaround instead, or drop the note. Warn-and-skip if the helper
+is unresolved. `research_wiki.py` itself quarantines prompt-injection patterns
+in graph evidence and query-pack rebuilds per
+[`injection-hygiene.md`](../shared-references/injection-hygiene.md); never bypass
+that writer with freehand graph edits.
+
+## Wiki Directory Structure
+
+```
+research-wiki/
+  index.md               # categorical index (auto-generated)
+  log.md                 # append-only timeline
+  gap_map.md             # field gaps with stable IDs (G1, G2, ...)
+  query_pack.md          # compressed summary for /idea-creator (auto-generated, max 8000 chars)
+  papers/
+    <slug>.md            # one page per paper
+  ideas/
+    <idea_id>.md         # one page per idea
+  experiments/
+    <exp_id>.md          # one page per experiment
+  claims/
+    <claim_id>.md        # one page per testable claim
+  graph/
+    edges.jsonl          # materialized current relationship graph
+```
+
+## Subcommands
+
+### `/research-wiki init`
+
+Initialize the wiki for the current project:
+
+1. Create `research-wiki/` directory structure
+2. Create empty `index.md`, `log.md`, `gap_map.md`
+3. Create empty `graph/edges.jsonl`
+4. Log: "Wiki initialized"
+
+### `/research-wiki ingest "<paper title>" — arxiv: <id>`
+
+Add a paper to the wiki. This subcommand is thin wrapping around the
+canonical helper `python3 "$ARIS_REPO/tools/research_wiki.py" ingest_paper …`, which
+is the single implementation of paper ingest in ARIS (per
+[`shared-references/integration-contract.md`](../shared-references/integration-contract.md)
+— one helper, no copies). The helper does all of:
+
+1. **Fetch metadata** — queries the arXiv Atom API when `--arxiv-id` is given
+2. **Generate slug** — `<first_author_last_name><year>_<keyword>`
+3. **Check dedup** — skip an existing page unless `--update-on-exist`
+4. **Create page** — `papers/<slug>.md` with the schema below
+5. **Rebuild `index.md`** and `query_pack.md`
+6. **Append `log.md`**
+
+Edge extraction (step 5/8 in the old manual flow) is **not** in
+`ingest_paper`; do it as a follow-up with `add_edge` per relationship
+identified:
+
+```bash
+ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null)}"
+WIKI_SCRIPT=""
+[ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
+[ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
+[ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"
+
+# arXiv-known paper
+[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+    --arxiv-id 2501.12345 --thesis "One-line claim from abstract."
+
+# Venue paper with no arXiv mirror
+[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+    --title "Attention Is All You Need" \
+    --authors "Ashish Vaswani, Noam Shazeer, …" --year 2017 --venue "NeurIPS"
+
+# Manual edge after ingest
+[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" add_edge research-wiki/ \
+    --from "paper:vaswani2017_attention_all_you" \
+    --to "paper:chen2025_factorized_gap" \
+    --type "extends" --evidence "Section 3.2: adapts the encoder block …"
+```
+
+Other skills (`/research-lit`, `/arxiv`, `/alphaxiv`, `/deepxiv`,
+`/semantic-scholar`, `/exa-search`) call the same helper directly in
+their own last step — they don't re-route through `/research-wiki
+ingest` as a subcommand, so they don't need an LLM roundtrip.
+
+### `/research-wiki sync — arxiv-ids <id1>,<id2>,...`
+
+Batch backfill: ingest one or more arXiv IDs that were read earlier
+without being ingested (e.g., because `research-wiki/` was set up after
+the reading happened, or a hook didn't fire).
+
+```bash
+# Explicit list
+[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" sync research-wiki/ \
+    --arxiv-ids 2310.06770,1706.03762
+
+# From a file (one id per line, # comments ok)
+[ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" sync research-wiki/ --from-file ids.txt
+```
+
+Dedup is handled per-id; already-ingested papers are skipped silently.
+This is the recommended **manual repair** step (see integration
+contract §5 Backfill). `sync` does not scan session traces — callers
+declare the ids explicitly.
+
+**Paper page schema** (exactly what `ingest_paper` emits — do not
+handwrite alternative fields; `lint` will flag drift):
+
+```markdown
+---
+type: paper
+node_id: paper:<slug>
+title: "<full title>"
+authors: ["First A. Author", "Second B. Author"]
+year: 2025
+venue: "arXiv"
+external_ids:
+  arxiv: "2501.12345"
+  doi: null
+  s2: null
+tags: ["tag1", "tag2"]
+added: 2026-04-07T10:12:00Z
+---
+
+# <full title>
+
+## One-line thesis
+
+[Single sentence capturing the paper's core contribution]
+
+## Problem / Gap
+
+## Method
+
+## Key Results
+
+## Assumptions
+
+## Limitations / Failure Modes
+
+## Reusable Ingredients
+
+[Techniques, datasets, or insights that could be repurposed]
+
+## Open Questions
+
+## Claims
+
+[Reference claim pages: claim:C1, claim:C2, etc.]
+
+## Connections
+
+[AUTO-GENERATED from graph/edges.jsonl — do not edit manually]
+
+## Relevance to This Project
+
+[Why this paper matters for our specific research direction]
+```
+
+_Additionally, when the paper was ingested via `--arxiv-id` and the arXiv
+API returned an abstract, the helper appends an `## Abstract (original)`
+section after `Relevance to This Project` containing the raw abstract
+text as a blockquote. Manual ingests (no `--arxiv-id`) do not include
+this section._
+
+### `/research-wiki query "<topic>"`
+
+Generate `query_pack.md` — a compressed, context-window-friendly summary:
+
+**Fixed budget (max 8000 chars / ~2000 tokens):**
+
+| Section | Budget | Content |
+|---------|--------|---------|
+| Project direction | 300 chars | From AGENTS.md or RESEARCH_BRIEF.md |
+| Top 5 gaps | 1200 chars | From gap_map.md, ranked by: unresolved + linked ideas + failed experiments |
+| Paper clusters | 1600 chars | 3-5 clusters by tag overlap, 2-3 sentences each |
+| Failed ideas | 1400 chars | **Always included** — highest anti-repetition value |
+| Top papers | 1800 chars | 8-12 pages ranked by: linked gaps, linked ideas, centrality, relevance flag |
+| Active chains | 900 chars | limitation → opportunity relationship chains |
+| Open unknowns | 500 chars | Unresolved questions across the wiki |
+
+**Pruning priority** (when over budget): low-ranked papers > cluster detail > chain detail. **Never prune** failed ideas or top gaps first.
+
+**Key rule:** Read from short fields only (frontmatter, one-line thesis, gap summary, failure note). Do not summarize full page bodies every time.
+
+### `/research-wiki update <node_id> — <field>: <value>`
+
+Update a specific entity:
+
+```
+/research-wiki update paper:chen2025 — relevance: core
+/research-wiki update idea:001 — outcome: negative
+/research-wiki update claim:C1 — status: refuted
+```
+
+After any update: rebuild `query_pack.md`, update `log.md`.
+
+### `/research-wiki lint`
+
+Health check the wiki:
+
+1. **Orphan pages** — entities with zero edges
+2. **Stale claims** — claims still `status: drafted` or `status: unproven` older than 14 days
+3. **Contradictions** — claims with both `supports` and `invalidates` edges
+4. **Missing connections** — papers sharing 2+ tags but no explicit relationship
+5. **Dead ideas** — `stage: proposed` ideas that were never tested
+6. **Sparse pages** — pages with 3+ empty sections
+
+Output a `LINT_REPORT.md` with suggested fixes.
+
+### `/research-wiki stats`
+
+Quick overview:
+
+```
+📚 Research Wiki Stats
+Papers: 28 (12 core, 10 related, 6 peripheral)
+Ideas: 7 (2 active, 3 failed, 1 partial, 1 succeeded)
+Experiments: 12
+Claims: 15 (8 verified, 4 unproven, 2 refuted, 1 sound-modulo-imports)
+Edges: 64
+Gaps: 8 (3 unresolved)
+Last updated: 2026-04-07T10:12:00Z
+```
+
+## Integration with Existing Workflows
+
+All paper-reading skills follow the same **integration contract** (see
+[`shared-references/integration-contract.md`](../shared-references/integration-contract.md)):
+
+- single predicate — `[ -d research-wiki/ ]`
+- single canonical helper — `python3 "$ARIS_REPO/tools/research_wiki.py" ingest_paper …`
+- concrete artifact — `papers/<slug>.md` + `log.md` entry
+- backfill — `sync --arxiv-ids …`
+- diagnostic — `verify_wiki_coverage.sh` (Policy E; resolved per integration-contract §2)
+
+### Hook 1: After `/research-lit` finds papers
+
+```
+# At end of research-lit, after synthesis:
+if research-wiki/ exists:
+    ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills-codex.txt 2>/dev/null)}"
+    WIKI_SCRIPT=""
+    [ -n "$ARIS_REPO" ] && [ -f "$ARIS_REPO/tools/research_wiki.py" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"
+    [ -z "$WIKI_SCRIPT" ] && [ -f tools/research_wiki.py ] && WIKI_SCRIPT="tools/research_wiki.py"
+    [ -z "$WIKI_SCRIPT" ] && [ -f ~/.codex/skills/research-wiki/research_wiki.py ] && WIKI_SCRIPT="$HOME/.codex/skills/research-wiki/research_wiki.py"
+    for paper in top_relevant_papers (limit 8-12):
+        [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+            --arxiv-id <id> [--thesis "..."] [--tags "..."]
+        for each explicit relation to existing wiki paper:
+            [ -n "$WIKI_SCRIPT" ] && python3 "$WIKI_SCRIPT" add_edge research-wiki/ \
+                --from "paper:<slug>" --to "<target>" \
+                --type <extends|contradicts|addresses_gap|...> \
+                --evidence "..."
+    log "research-lit ingested N papers"
+```
+
+Each paper-reading skill ships its own Step "Update Research Wiki (if
+active)" that calls the same helper once per paper it touched. The
+business logic is not duplicated — only the loop over that skill's
+specific result set differs.
+
+### Hook 2: `/idea-creator` reads AND writes wiki
+
+**Before ideation:**
+```
+if research-wiki/query_pack.md exists (and < 7 days old):
+    prepend query_pack to landscape context
+    treat failed ideas as banlist
+    treat top gaps as search seeds
+    still run fresh literature search for last 3-6 months
+```
+
+**After ideation (CRITICAL — runs on EVERY generation, incl. a re-run with updated
+constraints): the page write is the deterministic `upsert_idea` helper, not freehand.**
+```
+for idea in all_generated_ideas (recommended + killed):
+    python3 "$WIKI_SCRIPT" upsert_idea research-wiki/ --slug <stable-id> --title <title> \
+         --stage <proposed|archived> --outcome pending --thesis <...> --risks <...> \
+         --based-on <paper:slug,...> --target-gaps <G2,...>
+    # one call: writes ideas/<slug>.md, wires inspired_by/addresses_gap edges, rebuilds
+    # index + query_pack, logs. Default skip-on-exist (won't clobber an idea enriched
+    # by /result-to-claim). `outcome` ∈ {unknown,pending,negative,mixed,positive} — the
+    # experiment verdict is set later by /result-to-claim, never guessed at ideation.
+log "idea-creator wrote N ideas to wiki"
+```
+
+### Hook 3: After `/result-to-claim` verdict
+
+```
+# Create/refresh the experiment node FIRST via add_experiment (verdict owner →
+# --update-on-exist). add_edge does NOT verify node existence, so gate the
+# supports/invalidates edges on the node having been born (EXP_NODE_OK).
+EXP_NODE_OK = (python3 "$WIKI_SCRIPT" add_experiment research-wiki/ --slug <exp_id> \
+  --idea idea:<active_idea> --verdict <yes|partial|no> --confidence <high|medium|low> \
+  --metrics <...> --reasoning <...> --provenance <run dir> --update-on-exist) succeeded
+
+# Record empirical support as EDGES ONLY, and ONLY if EXP_NODE_OK — never set a claim's
+# `status`. A claim's `status` is the PROOF axis (verified / sound-modulo-imports /
+# refuted / unproven / drafted / retracted), owned by /proof-checker (Hook 4). The ARIS
+# helper REJECTS "supported"/"partial"/"invalidated" as claim statuses.
+if EXP_NODE_OK:
+    for claim_id in resolved_claims:
+        if verdict == "yes":
+            add_edge(exp_id, claim_id, "supports")
+        elif verdict == "partial":
+            add_edge(exp_id, claim_id, "supports")  # partial — qualify in evidence
+        else:
+            add_edge(exp_id, claim_id, "invalidates")
+
+# Update idea outcome
+update_idea(active_idea_id, outcome=verdict)
+
+# If failed, record WHY for future ideation
+if verdict in ("no", "partial"):
+    update_idea failure_notes with specific metrics and reasons
+
+rebuild query_pack
+log "result-to-claim: exp_id updated, verdict=..."
+```
+
+### Hook 4: Claim birth — from `/proof-checker` (the ONLY birth point)
+
+Wiki **claim nodes are born here.** `/proof-checker` mints a claim node for each
+top-level theorem/headline after writing `PROOF_AUDIT.json`, stamping an honest
+PROOF-axis `status` and a `provenance` pointer. No other skill creates a claim node:
+`/result-to-claim` (Hook 3) only adds empirical `supports`/`invalidates` edges to an
+already-born claim and never edits its `status`.
+
+```
+python3 "$WIKI_SCRIPT" add_claim research-wiki/ --slug thm-main-ub \
+     --name "Main upper bound" --status verified \
+     --provenance "<proof-checker trace dir>" --statement "..." --update-on-exist
+```
+
+Claim `status` ∈ {`drafted`, `unproven`, `sound-modulo-imports`, `verified`, `refuted`,
+`retracted`} — the **proof axis only**. Empirical support is a separate axis carried by
+edges (Hook 3), never written into `status`.
+
+## Re-ideation Trigger
+
+After significant wiki updates, suggest re-running `/idea-creator`:
+
+- ≥5 new papers ingested since last ideation
+- ≥3 new failed/partial ideas since last ideation
+- New contradiction discovered in the graph
+- New gap identified that no existing idea addresses
+
+The system suggests but does not auto-trigger. User decides.
+
+## Key Rules
+
+- **One source of truth for relationships**: `graph/edges.jsonl`. Page `Connections` sections are auto-generated views.
+- **Canonical node IDs everywhere**: `paper:<slug>`, `idea:<id>`, `exp:<id>`, `claim:<id>`, `gap:<id>`. Never use raw titles or inconsistent shorthands.
+- **Failed ideas are the most valuable memory.** Never prune them from query_pack.
+- **query_pack.md is hard-budgeted** at 8000 chars. Deterministic generation, not open-ended summarization.
+- **Append to log.md for every mutation.** The log is the audit trail.
+- **Reviewer context isolation applies.** When the wiki is read by reviewer skills, pass file paths only; base Codex review is same-family provisional.
+
+## Acknowledgements
+
+Inspired by [Karpathy's LLM Wiki](https://gist.github.com/karpathy/442a6bf555914893e9891c11519de94f) — "compile knowledge once, keep it current, don't re-derive on every query."