Ingest

/ingest

Turn one paper into a fully wired set of wiki pages. Emit well-formed entities and correct cross-references; leave semantic audits (backlink symmetry, dangling nodes, field-value policing) for /check.

Use these local references on demand:

• references/pdf-preprocessing.md — arXiv-ID recovery, tex fetching, prepare-paper handoff for direct PDF drops
• references/dedup-policy.md — merge-vs-create decision rule for concepts and claims, and the line that separates /ingest shape checks from /check semantic audits
• references/cross-references.md — forward/reverse link matrix and paper-to-paper edge-type selection
• references/init-mode.md — manifest-driven handoff from /init and parallel-safety conventions
• references/error-handling.md — source parse, API, and slug-collision fallbacks

Open docs/runtime-page-templates.en.md before drafting any wiki page frontmatter or body sections, and docs/runtime-support-files.en.md for index.md, log.md, and graph/ formats.

Inputs

• source: one of — arXiv URL (e.g. https://arxiv.org/abs/2106.09685), local .tex, local .pdf, or a canonical_ingest_path handed off by /init via .checkpoints/init-sources.json(see references/init-mode.md)
• --discover (optional, default off): after the final report, invoke /discover --anchor <this-paper's-arxiv-id> and append the shortlist to the report as "Related papers you may want to ingest next". Never auto-ingests the suggestions. Skipped automatically in INIT MODE. Treat this as a user-owned flag: do not set it based on repo state.

Outputs

• One fully-wired paper page plus linked entities (concepts, claims, people)
• Graph edges and citations appended via tools/research_wiki.py
• Terminal summary with page counts and suggested follow-up ingests

Wiki Interaction

Reads

• wiki/index.md for existing slugs and tags
• wiki/papers/*.md to detect an already-ingested paper
• wiki/concepts/*.md and wiki/foundations/*.md for dedup matches
• wiki/claims/*.md for dedup matches
• wiki/people/*.md for existing authors
• wiki/topics/*.md to place the paper under existing topics
• wiki/graph/open_questions.md to notice when the paper addresses a known gap

Writes

• wiki/papers/{slug}.md — CREATE
• wiki/concepts/{slug}.md — CREATE (new) or EDIT (append key_papers, aliases, variants)
• wiki/claims/{slug}.md — CREATE (new) or EDIT (append evidence entry)
• wiki/people/{slug}.md — CREATE (importance ≥ 4 only) or EDIT (append Key papers)
• wiki/topics/{slug}.md — EDIT only (no CREATE from /ingest)
• wiki/graph/edges.jsonl — APPEND via tool
• wiki/graph/citations.jsonl — APPEND via tool
• wiki/graph/context_brief.md — REBUILD (skipped in INIT MODE)
• wiki/graph/open_questions.md — REBUILD (skipped in INIT MODE)
• wiki/index.md — APPEND
• wiki/log.md — APPEND via tool

Graph edges created

• paper → concept: introduces_concept / uses_concept / extends_concept / critiques_concept with confidence
• paper → foundation: derived_from (foundation is terminal; no reverse link)
• paper → claim: supports / contradicts
• paper → paper: same_problem_as / similar_method_to / complementary_to / builds_on / compares_against / improves_on / challenges / surveys with confidence
• bibliographic paper → paper: cites in graph/citations.jsonl

tools/research_wiki.py add-edge rejects missing confidence/evidence for paper-paper and paper-concept semantic edges, and rejects legacy paper-to-concept or paper-to-paper types on new writes.

Workflow

Pre-condition: working directory contains wiki/, raw/, and tools/. Resolve the Python interpreter once and reuse it:

# Find the project root via git so worktree subagents can still locate .venv.
# .venv is gitignored, so a subagent whose cwd is ../.worktrees/<branch>/
# doesn't have one — without this lookup it falls back to system python3 and
# misses the .env-loaded API keys plus the installed deps (deepxiv-sdk etc.).
# git rev-parse --git-common-dir returns the main repo's .git regardless of
# which worktree the shell is in; its parent is the project root.
GIT_COMMON_DIR=$(git rev-parse --git-common-dir 2>/dev/null || true)
PROJECT_ROOT=""
if [ -n "$GIT_COMMON_DIR" ]; then
  PROJECT_ROOT=$(cd "$(dirname "$GIT_COMMON_DIR")" 2>/dev/null && pwd)
fi

if   [ -x "$PROJECT_ROOT/.venv/bin/python" ];         then PYTHON_BIN="$PROJECT_ROOT/.venv/bin/python"
elif [ -x "$PROJECT_ROOT/.venv/Scripts/python.exe" ]; then PYTHON_BIN="$PROJECT_ROOT/.venv/Scripts/python.exe"
elif [ -x .venv/bin/python ];                         then PYTHON_BIN=.venv/bin/python
elif [ -x .venv/Scripts/python.exe ];                 then PYTHON_BIN=.venv/Scripts/python.exe
else                                                       PYTHON_BIN=python3
fi
export PYTHON_BIN

Step 1: Resolve the source

1. If /init passed a canonical_ingest_path, enter INIT MODE and consume that path verbatim. Do not rescan raw/. See references/init-mode.md.
2. If the source is an arXiv URL, extract the arXiv ID, use "$PYTHON_BIN" tools/fetch_s2.py paper <arxiv-id> to recover the title when possible, then run "$PYTHON_BIN" tools/init_discovery.py download --raw-root raw --arxiv-id <arxiv-id> --title "<title-or-arxiv-id>". Continue from the returned canonical_ingest_path. The helper tries arXiv source first and falls back to PDF; do not call fetch_arxiv.py for a single paper because it is RSS-only.
3. If the source is a local .tex, use it directly.
4. If the source is a local .pdf, run the preprocessing pipeline in references/pdf-preprocessing.md to produce a prepared .tex under raw/tmp/ before continuing.

Raw persistence rule: never copy or duplicate a file already under raw/discovered/, raw/tmp/, or raw/papers/ into a different raw subtree.

Step 2: Paper identity and enrichment

1. Generate the paper slug:

   "$PYTHON_BIN" tools/research_wiki.py slug "<paper-title>"
   

2. Stop-if-exists: if wiki/papers/{slug}.md already exists and the arXiv ID or title matches, report and exit. If they differ, resolve the collision per references/error-handling.md.

3. When an arXiv ID is available, query Semantic Scholar:

   "$PYTHON_BIN" tools/fetch_s2.py paper <arxiv-id>
   

   Use the result for venue, year, s2_id, citation count, and the evidence behind the importance score (1-5).

4. Optional DeepXiv enrichment, when available. Skip silently if it fails:

   "$PYTHON_BIN" tools/fetch_deepxiv.py brief <arxiv-id>
   "$PYTHON_BIN" tools/fetch_deepxiv.py head <arxiv-id>
   "$PYTHON_BIN" tools/fetch_deepxiv.py social <arxiv-id>
   

   brief seeds the Key-idea section; head sanity-checks your tex parsing against the section structure; social is an auxiliary importance signal.

Step 3: Write the paper page

Open docs/runtime-page-templates.en.md for the paper template. Fill every required frontmatter field; leave cited_by empty for now (step 5 backfills it).

Before writing, run a shape check on the frontmatter you are about to emit — no more than this:

• every required key is present and non-empty
• importance ∈ {1,2,3,4,5}; status on claims ∈ the documented set; maturity on concepts ∈ the documented set; claim confidence ∈ [0,1]
• YAML parses

The shape check is intentionally narrow. Backlink symmetry, dangling-node detection, and cross-entity consistency are /check's job, not this skill's.

Body sections to populate: Problem, Key idea, Method, Results, Limitations, Open questions, My take, Related.

Step 4: Concepts, claims, people

Follow references/dedup-policy.md. In short:

1. For each candidate concept or claim, call the matching find-similar-* tool first.
2. Prefer merging into the top result. Create a new page only when the tool returns no acceptable candidate and the paper's importance justifies it.
3. For each entity you write or edit, write the reverse link in the same turn. The obligation matrix lives in references/cross-references.md.
4. Create a wiki/people/{slug}.md only for papers with importance ≥ 4. Otherwise append to existing author pages only.

Step 5: Paper-to-paper edges and cited_by

Skip this whole step in INIT MODE — the parent /init handles it at fan-in.

"$PYTHON_BIN" tools/fetch_s2.py references <arxiv-id>
"$PYTHON_BIN" tools/fetch_s2.py citations <arxiv-id>

• For each reference whose arXiv ID or title resolves to an existing wiki/papers/{slug}.md, add a bibliographic cites row to graph/citations.jsonl.
• Add a semantic paper-to-paper edge in graph/edges.jsonl only when the source text gives a clear cue. Edge-type selection is in references/cross-references.md. If no semantic relation cleanly fits, keep only the cites row.
• For each citation already in the wiki, append the citer's slug to this paper's cited_by.
• Surface unmatched high-citation references in the final report so the user can decide whether to follow up with another /ingest.

Step 6: Topics and index

1. Match the paper's domain and tags against existing wiki/topics/*.md. For each match:
   • importance ≥ 4 → append to the topic's ## Seminal works
   • importance < 4 → append under ## SOTA tracker or ## Recent work by year
   • if the paper directly addresses a listed open problem, annotate that line on the topic page
2. Do not create new topic pages from /ingest — topic creation belongs to /init and /edit.
3. Append new or edited page entries to wiki/index.md under their category headings. See docs/runtime-support-files.en.md for the exact format.

Step 7: Log and rebuild

"$PYTHON_BIN" tools/research_wiki.py log wiki/ "ingest | added papers/<slug> | updated: <list>"

Unless in INIT MODE:

"$PYTHON_BIN" tools/research_wiki.py rebuild-context-brief wiki/
"$PYTHON_BIN" tools/research_wiki.py rebuild-open-questions wiki/

Step 8: Report

Emit one compact summary covering: pages created, pages updated, graph edges added, contradictions surfaced (if any), and high-citation references not yet in the wiki (suggested follow-up ingests). Close with:

Wiki: +1 paper, +{N} claims, +{M} concepts, +{K} edges

Step 9: Optional discovery (only if --discover is set)

Skip this step unless the user explicitly passed --discover. Also skip it in INIT MODE — /init's parent process decides whether to run discovery at fan-in, not individual subagents.

When active, invoke /discover with the just-ingested paper as the single anchor:

"$PYTHON_BIN" tools/discover.py from-anchors \
  --id <arxiv-id-of-this-paper> \
  --wiki-root wiki \
  --limit 10 \
  --output-checkpoint .checkpoints/ \
  --markdown

Append the markdown output to the report under a heading like "Related papers you may want to ingest next". Do not auto-ingest anything from the shortlist — the user picks. If discovery fails (S2 outage, all channels empty), note the failure in one line and continue — a failed /discover must not fail an otherwise successful /ingest.

Constraints

• raw/papers/, raw/notes/, raw/web/ are user-owned and read-only. Direct local /ingest may add prepared sidecars under raw/tmp/; direct arXiv ingests may write fetched source artifacts under raw/discovered/. INIT MODE treats all of raw/ as read-only.
• wiki/graph/ is tool-owned. Edit only through tools/research_wiki.py.
• Slugs always come from tools/research_wiki.py slug. Never hand-craft.
• Every forward link writes its reverse link in the same turn — the wiki's bidirectional-link invariant. The only exception is links to wiki/foundations/, which are terminal.
• In INIT MODE, do not write reverse links into pages that already exist (created by a sibling worktree or scaffold). Record the relationship via tools/research_wiki.py add-edge only; the parent /init backfills reverse links during fan-in.
• Source priority: .tex > .pdf > vision API fallback. Never ingest from a PDF when a usable .tex is available.
• Ingest is conservative about new entities:
  • importance < 4: at most 1 new concept and 1 new claim per paper
  • importance ≥ 4: at most 3 new concepts and 2 new claims per paper
  • Any further candidates must be merged into their nearest find-similar-* result, or left out for /check to flag. Rationale and matching rules: references/dedup-policy.md.
• /ingest runs a shape check on its own output (required keys, enum ranges, YAML parses) and stops there. Backlink symmetry, dangling nodes, and full semantic audits belong to /check. Do not re-implement them here.
• Assume another /ingest may run concurrently in a sibling worktree. All shared-file writes (graph/edges.jsonl, graph/citations.jsonl, index.md, log.md) must go through tools/research_wiki.py or use append-only semantics. See references/init-mode.md.
• In INIT MODE, skip fetch_s2.py citations, fetch_s2.py references, and the rebuild-* commands — the parent /init runs them once after fan-in.

Error Handling

See references/error-handling.md. Highlights: source parse failures cascade tex → PDF → vision API → user handoff; S2 outages default importance to 3 and skip citation backfill; DeepXiv outages skip enrichment silently; slug collisions append a numeric suffix.

Dependencies

Tools (via Bash)

• "$PYTHON_BIN" tools/research_wiki.py slug "<title>"
• "$PYTHON_BIN" tools/research_wiki.py find-similar-concept wiki/ "<title>" --aliases "<a,b,c>"
• "$PYTHON_BIN" tools/research_wiki.py find-similar-claim wiki/ "<title>" --tags "<a,b,c>"
• "$PYTHON_BIN" tools/research_wiki.py add-edge wiki/ --from <id> --to <id> --type <type> --evidence "<text>" [--confidence high|medium|low]
  • --confidence high|medium|low is required for paper-paper and paper-concept semantic edges.
• "$PYTHON_BIN" tools/research_wiki.py add-citation wiki/ --from papers/<citing> --to papers/<cited> --source semantic_scholar
• "$PYTHON_BIN" tools/research_wiki.py log wiki/ "<message>"
• "$PYTHON_BIN" tools/research_wiki.py rebuild-context-brief wiki/
• "$PYTHON_BIN" tools/research_wiki.py rebuild-open-questions wiki/
• "$PYTHON_BIN" tools/prepare_paper_source.py --raw-root raw --source <local-path> [--title "<recovered-title>"] [--arxiv-id "<recovered-arxiv-id>"]
• "$PYTHON_BIN" tools/init_discovery.py download --raw-root raw --arxiv-id <id> --title "<title-or-id>" — single-paper arXiv source/PDF download into raw/discovered/
• "$PYTHON_BIN" tools/fetch_s2.py paper|citations|references <arxiv-id>
• "$PYTHON_BIN" tools/fetch_deepxiv.py brief|head|social <arxiv-id>
• "$PYTHON_BIN" tools/discover.py from-anchors --id <arxiv-id> --wiki-root wiki --limit 10 --output-checkpoint .checkpoints/ --markdown — only when --discover is set

Shared References

• .claude/skills/shared-references/citation-verification.md

Skills

• /init — calls /ingest in parallel subagents via INIT MODE
• /check — audits wiki state after /ingest completes; owns every semantic check /ingest intentionally does not perform
• /discover — optional follow-up when --discover is set; produces a shortlist of related papers the user may want to ingest next

External APIs

• Semantic Scholar (via tools/fetch_s2.py)
• DeepXiv (via tools/fetch_deepxiv.py, optional; graceful fallback)
• arXiv (source download)