An Opus 5 + Obsidian Research System

The CLAUDE.md That Runs The System

RESEARCH SYSTEM PROTOCOL

This vault is a research system. Structure:
/raw - source material exactly as ingested, never edited
/wiki - processed, linked knowledge organized by topic
/questions - open questions not yet resolved
/digests - weekly summaries, timestamped

When a new source is dropped into /raw:
1. Extract the specific, genuinely new claims and findings, not a
   summary of the whole document.
2. Check /wiki for existing notes on the same topic. Extend an
   existing note rather than creating a duplicate if the topic
   already has one.
3. Link every new claim to related existing notes using [[wikilinks]].
4. If a claim contradicts something already in /wiki, do not silently
   overwrite it. Flag the contradiction explicitly in both notes.
5. If a source raises a genuine open question you cannot resolve
   from other material already in the vault, add it to /questions
   rather than guessing at an answer.

When asked to synthesize or generate a digest:
Pull from /wiki, not directly from /raw. The wiki is the processed,
trustworthy layer. Raw sources may contain claims that were later
found to be wrong or superseded, which is why step 4 above exists.

Before reporting any extraction as complete, confirm you actually
checked /wiki for existing related notes rather than assuming this
is entirely new material.

The Ingestion Pipeline

Ingest the new files in /raw that have not been processed yet.
For each one, extract genuinely new claims, check /wiki for related
existing notes, extend or create notes as appropriate, and flag any
contradictions with what is already recorded. Add unresolved
questions to /questions rather than guessing.

The Weekly Digest, Automated

Generate this week's research digest. Pull from /wiki, focused
specifically on what was added or updated in the last 7 days, not
the entire vault's history.

Structure:
1. The 3 to 5 most significant new findings this week, with links
   to the full notes in /wiki.
2. Any contradictions flagged this week between new material and
   existing notes, since these deserve your direct attention.
3. Open questions added to /questions this week that remain
   unresolved.
4. One line noting any topic that received unusually heavy activity
   this week, since a topic accumulating many related notes quickly
   is often worth deeper, deliberate attention rather than passive
   accumulation.

Save the result to /digests with this week's date. Keep the whole
digest under 500 words. This is a pointer to the full notes, not a
replacement for reading them.

Querying Across Everything, Not Just What You Remember

Based on everything in /wiki, what have I learned about [specific
topic]? Cite the specific notes each claim comes from. If sources
in the vault disagree with each other on this topic, say so
explicitly rather than picking one and presenting it as consensus.

Scaling To Multiple Research Topics

MULTI-TOPIC SCOPE
This vault covers multiple research areas, each in its own top-level
folder under /wiki: /wiki/topic-a, /wiki/topic-b, etc.
When ingesting a new source, first determine which topic it belongs
to. If it genuinely spans two topics, note the cross-topic connection
explicitly rather than filing it ambiguously in one folder without
explanation.
Digests should be generated per topic, not as one combined summary,
unless explicitly asked to synthesize across topics.