dsh-aris-panel 0.1.0

package/skills/research-wiki/SKILL.md

@@ -0,0 +1,461 @@
+---
+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, mcp__codex__codex, mcp__codex__codex-reply
+---
+
+# 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 hygiene (anti-self-poisoning)
+
+Before persisting an **idea / claim / experiment** note, screen it for
+operational noise that would harden into a self-cited falsehood (see
+[`shared-references/capture-antipatterns.md`](../shared-references/capture-antipatterns.md)).
+Resolve the helper via the canonical chain (integration-contract §2):
+`.aris/tools/capture_filter.py` → `tools/capture_filter.py` →
+`$ARIS_REPO/tools/capture_filter.py` (warn-and-skip if unresolved). Run
+`python3 <capture_filter> -` on the note text; if it flags **env-failure /
+transient-error / negative-tool-claim**, do NOT store it as a durable node —
+rewrite it to the *fix / missing config / workaround*, or drop it. Never store
+"codex/gemini/the reviewer can't do X" — that gets loaded into every future
+session and cited against the agent long after the real cause is gone. (The wiki's
+"failed ideas → anti-repeat memory" is the GOOD inverse: a class-level *research*
+finding, not operational noise.)
+
+## 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
+
+## Helper resolution (run before any subcommand below)
+
+All wiki operations except plain directory bootstrap go through a single
+canonical helper, `tools/research_wiki.py`. Skills that touch the wiki
+must resolve `$WIKI_SCRIPT` via the chain below — never hard-code
+`python3 tools/research_wiki.py …`. Hard-coding silently fails when
+the project does not have `tools/` on disk (the post-`install_aris.sh`
+default), which is exactly the failure mode that left a real user's
+`research-wiki/` empty for a week.
+
+```bash
+cd "$(git rev-parse --show-toplevel 2>/dev/null || pwd)" || exit 1
+ARIS_REPO="${ARIS_REPO:-$(awk -F'\t' '$1=="repo_root"{print $2; exit}' .aris/installed-skills.txt 2>/dev/null)}"
+if [ -z "${ARIS_REPO:-}" ] && [ -f "$HOME/.aris/repo" ]; then
+  ARIS_REPO=$(cat "$HOME/.aris/repo" 2>/dev/null) || true
+fi
+WIKI_SCRIPT=".aris/tools/research_wiki.py"
+[ -f "$WIKI_SCRIPT" ] || WIKI_SCRIPT="tools/research_wiki.py"
+[ -f "$WIKI_SCRIPT" ] || { [ -n "${ARIS_REPO:-}" ] && WIKI_SCRIPT="$ARIS_REPO/tools/research_wiki.py"; }
+[ -f "$WIKI_SCRIPT" ] || {
+  echo "ERROR: research_wiki.py not found at .aris/tools/, tools/, \$ARIS_REPO/tools/, or via ~/.aris/repo." >&2
+  echo "       Fix one of:" >&2
+  echo "         1. rerun 'bash tools/install_aris.sh' from the ARIS repo (creates .aris/tools symlink, refreshes ~/.aris/repo)" >&2
+  echo "         2. rerun 'bash tools/smart_update.sh' (refreshes ~/.aris/repo)" >&2
+  echo "         3. export ARIS_REPO=<path-to-ARIS-repo>" >&2
+  echo "         4. cp <ARIS-repo>/tools/research_wiki.py tools/" >&2
+  exit 1
+}
+```
+
+`/research-wiki` itself is the wiki tool — if the helper is missing the
+skill **hard-fails**. Caller skills that update the wiki as a side
+effect (`/idea-creator`, `/result-to-claim`, `/research-lit`, `/arxiv`,
+`/alphaxiv`, `/deepxiv`, `/semantic-scholar`, `/exa-search`) use the
+same chain but **warn-and-skip** instead of hard-failing — their
+primary output (idea list, claim verdict, paper summary) must still be
+delivered to the user.
+
+### `/research-wiki init`
+
+Initialize the wiki for the current project. After resolving
+`$WIKI_SCRIPT` per the chain above:
+
+```bash
+python3 "$WIKI_SCRIPT" init research-wiki/
+```
+
+The helper creates `research-wiki/{papers,ideas,experiments,claims,graph}/`
+plus `index.md`, `log.md`, `gap_map.md`, **`query_pack.md`**, and
+`graph/edges.jsonl`, then appends `"Wiki initialized"` to `log.md`.
+
+(Earlier versions of this skill described a prose-only init that
+omitted `query_pack.md` — that drifted from the helper and made
+`/idea-creator`'s Phase 0 query-pack check fall through to a
+`rebuild_query_pack` invocation that, under the old hard-coded path,
+silently failed. Delegating init to the helper is the single source of
+truth for the wiki schema.)
+
+### `/research-wiki ingest "<paper title>" — arxiv: <id>`
+
+Add a paper to the wiki. This subcommand is thin wrapping around
+`python3 "$WIKI_SCRIPT" ingest_paper …`, which is the single
+implementation of paper ingest in ARIS (per
+[`shared-references/integration-contract.md`](../shared-references/integration-contract.md)
+— one helper, no copies). The helper does all of:
+
+1. **Fetch metadata** — queries the arXiv Atom API when `--arxiv-id` is given
+2. **Generate slug** — `<first_author_last_name><year>_<keyword>`
+3. **Check dedup** — skip an existing page unless `--update-on-exist`
+4. **Create page** — `papers/<slug>.md` with the schema below
+5. **Rebuild `index.md`** and `query_pack.md`
+6. **Append `log.md`**
+
+Edge extraction (step 5/8 in the old manual flow) is **not** in
+`ingest_paper`; do it as a follow-up with `add_edge` per relationship
+identified:
+
+```bash
+# arXiv-known paper
+python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+    --arxiv-id 2501.12345 --thesis "One-line claim from abstract."
+
+# Venue paper with no arXiv mirror
+python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+    --title "Attention Is All You Need" \
+    --authors "Ashish Vaswani, Noam Shazeer, …" --year 2017 --venue "NeurIPS"
+
+# Manual edge after ingest
+python3 "$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
+python3 "$WIKI_SCRIPT" sync research-wiki/ \
+    --arxiv-ids 2310.06770,1706.03762
+
+# From a file (one id per line, # comments ok)
+python3 "$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 | full sections | Structured extraction from `RESEARCH_BRIEF.md` by `## ` heading (Problem / Constraints / Direction / Background / Non-Goals / Domain Knowledge / Existing Results), in priority order. No per-field char cap — the 8000-char assembly loop is the only safety net. Falls back to a flat 600-char slice if the brief uses no known headings. |
+| 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 "$WIKI_SCRIPT" ingest_paper …` after resolving `$WIKI_SCRIPT` via the chain at the top of this SKILL
+- 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 AND $WIKI_SCRIPT resolved (chain at top of this SKILL):
+    for paper in top_relevant_papers (limit 8-12):
+        python3 "$WIKI_SCRIPT" ingest_paper research-wiki/ \
+            --arxiv-id <id> [--thesis "..."] [--tags "..."]
+        for each explicit relation to existing wiki paper:
+            python3 "$WIKI_SCRIPT" add_edge research-wiki/ \
+                --from "paper:<slug>" --to "<target>" \
+                --type <extends|contradicts|addresses_gap|...> \
+                --evidence "..."
+    log "research-lit ingested N papers"
+elif research-wiki/ exists but $WIKI_SCRIPT did not resolve:
+    warn "wiki update skipped — research_wiki.py unreachable; rerun install_aris.sh"
+```
+
+Each paper-reading skill ships its own Step "Update Research Wiki (if
+active)" that calls the same helper once per paper it touched. The
+business logic is not duplicated — only the loop over that skill's
+specific result set differs.
+
+### Hook 2: `/idea-creator` reads AND writes wiki
+
+**Before ideation:**
+```
+if research-wiki/query_pack.md exists (and < 7 days old):
+    prepend query_pack to landscape context
+    treat failed ideas as banlist
+    treat top gaps as search seeds
+    still run fresh literature search for last 3-6 months
+```
+
+**After ideation (CRITICAL — without it, `ideas/` stays empty; runs on EVERY
+generation, including a re-run with updated constraints):** the page write is a
+**deterministic helper command**, not a freehand step the model can skip:
+```
+for idea in all_generated_ideas (recommended + killed):
+    python3 "$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
+    # existing 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 the deterministic helper (verdict owner
+# → --update-on-exist). This is the experiment BIRTH point. add_edge does NOT verify
+# node existence, so GATE the supports/invalidates edges below on the node having been
+# born (EXP_NODE_OK) — else they'd dangle off a missing exp node.
+EXP_NODE_OK = (python3 "$WIKI_SCRIPT" add_experiment research-wiki/ --slug <exp_id> \
+  --idea idea:<active_idea> --verdict <yes|partial|no> --confidence <high|medium|low> \
+  --metrics <...> --reasoning <...> --provenance <run dir> --update-on-exist) succeeded
+  # writes page + idea--tested_by-->exp edge + rebuilds index/query_pack
+
+# Record empirical support as EDGES ONLY, and ONLY if EXP_NODE_OK — never overwrite the
+# claim's `status`. A claim's `status` is the PROOF axis (verified / sound-modulo-imports
+# / refuted / unproven / drafted / retracted), owned by /proof-checker (the claim birth
+# point). Experiment support is a SEPARATE axis carried entirely by supports/invalidates
+# edges; writing "supported"/"invalidated" into status is rejected by the validator.
+if EXP_NODE_OK:
+    for claim_id in resolved_claims:
+        if verdict == "yes":
+            add_edge(exp_id, claim_id, "supports")
+        elif verdict == "partial":
+            add_edge(exp_id, claim_id, "supports")   # partial — qualify in --evidence
+        else:
+            add_edge(exp_id, claim_id, "invalidates")
+
+# Update idea outcome
+update_idea(active_idea_id, outcome=verdict)
+
+# If failed, record WHY for future ideation
+if verdict in ("no", "partial"):
+    update_idea failure_notes with specific metrics and reasons
+
+rebuild query_pack
+log "result-to-claim: exp_id updated, verdict=..."
+```
+
+### Hook 4: Claim birth — from `/proof-checker` (the ONLY birth point)
+
+Wiki **claim nodes are born here.** `/proof-checker` Phase 5.5 calls `add_claim`
+for each top-level theorem/headline after writing `PROOF_AUDIT.json`, stamping an
+honest PROOF-axis `status` and a `provenance` pointer to the audit trace. No other
+skill creates a claim node: `/result-to-claim` (Hook 3) only adds empirical
+`supports`/`invalidates` *edges* to an already-born claim and never edits its `status`.
+
+```bash
+# (run by /proof-checker; shown here for the wiki's record)
+python3 "$WIKI_SCRIPT" add_claim research-wiki/ --slug thm-main-ub \
+  --name "Main upper bound" --status verified \
+  --provenance ".aris/traces/proof-checker/<run>/" --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 entirely 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 independence applies.** When the wiki is read by cross-model review skills, pass file paths only — do not summarize wiki content for the reviewer.
+- **The wiki is UTF-8.** All wiki files are read and written as UTF-8 so a `research-wiki/` stays portable across platforms and collaborators. A wiki created by an older ARIS on a non-UTF-8 locale (e.g. cp936 on Chinese Windows) must be converted to UTF-8 once — back it up first; the helper reports the offending file by name instead of guessing.
+
+## 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."