Phase 3: processing to the vault

Phase 3 converts approved items into structured Obsidian notes. All generation runs locally via Qwen3.5:9b. Add --hd to any command to use Claude Sonnet 4.6 instead (after explicit confirmation).

Papers

Papers reach _inbox via the Zotero browser extension, the iOS app, or automatically via the feedreader (after calibration). After a Go decision in Phase 2:

verwerk recente papers

Claude Code:

  1. Retrieves metadata from Zotero MCP (title, authors, year, journal, citation key, tags) — no full text
  2. Calls the local subagent process_item.py with only the item key and metadata:
    • process_item.py fetches the full text locally, generates a structured note via Qwen3.5:9b, builds the YAML frontmatter, and writes the .md file to literature/
    • Claude Code receives only {"status": "ok", "path": "literature/..."} — no source content
  3. Adds [[internal links]] to related notes in the vault
  4. Removes the item from Zotero _inbox

The generated note contains:

  • YAML frontmatter (title, authors, year, journal, citation key, tags, status)
  • Core question and main argument
  • Key findings (3–5 points)
  • Methodological notes
  • Relevant quotes (original language)
  • Links to related notes

Notes are saved to literature/[citation-key].md.

Privacy: no paper content ever appears in Claude Code's context. process_item.py is a self-contained local subagent — it fetches, generates, and writes without returning any source text to the orchestration layer.

YouTube videos

Videos added via the iOS share sheet from the YouTube app arrive in Zotero _inbox as watch URLs. After a Go decision:

transcript [URL]

Claude Code:

  1. Checks whether a transcript is already cached from the feedreader (.claude/transcript_cache/{video_id}.json) — no re-fetch needed if so
  2. Falls back to yt-dlp if no cache exists
  3. Generates a structured note locally via Qwen3.5:9b:
    • Title, speaker, channel, date, URL
    • Summary (3–5 sentences)
    • Key points with timestamps
    • Relevant quotes with timestamps
  4. Adds frontmatter, [[internal links]], and #video tag
  5. Removes the raw transcript from inbox/ and the item from Zotero _inbox

Notes are saved to literature/[speaker-year-keyword].md.

Podcasts

Podcast episodes added from Overcast (via iOS share sheet) arrive in Zotero _inbox as overcast.fm URLs. After a Go decision:

podcast [URL]

Claude Code:

  1. Checks for a cached show notes file in .claude/transcript_cache/podcast_{episode_id}.json
  2. If no cache: downloads audio via yt-dlp, transcribes locally via whisper.cpp (automatic language detection)
  3. For long episodes (> 45 min): generates a layered summary first (main line → per segment), then the final note
  4. Generates a structured note locally via Qwen3.5:9b:
    • Title, speaker(s), programme/channel, date, URL
    • Summary (3–5 sentences)
    • Key points with timestamps
    • Relevant quotes with timestamps (original language)
  5. Adds frontmatter, [[internal links]], and #podcast tag
  6. Removes raw .mp3 and .txt files from inbox/ and the item from Zotero _inbox

Notes are saved to literature/[speaker-year-keyword].md.

RSS web articles

Non-academic articles from RSS feeds that you forward to _inbox can be processed in two ways:

Via Zotero (recommended for articles worth citing):

verwerk recente papers

The item is already in _inbox with metadata from the Zotero Connector. Processed as a standard literature note.

Direct to inbox/ (for news items, policy documents, quick reads):

inbox [URL]

Claude Code fetches the article and saves it as a Markdown file in inbox/. You can then ask Claude Code to convert it to a note in literature/.

Notes get #web or #beleid as appropriate.

After processing

After each session, check whether:

  • New notes are linked to related existing notes ([[double brackets]])
  • Relevant syntheses in syntheses/ need updating
  • Flashcards should be created for the new notes:
maak flashcards voor literature/[note].md

If new papers were added to Zotero, update the semantic search database:

update-zotero