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/[author-year-keyword1-keyword2].md — Qwen selects 2–4 nouns from the title and TLDR.

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

YouTube items follow an eager transcript pipeline: when you mark a video ✅ in the feedreader, attach-transcript.py runs automatically and stores a cleaned transcript as an attachment in the Zotero item — mirroring how a PDF accompanies a paper. This makes Go/No-go decisions content-based.

If the transcript attachment is missing (e.g. for manually added items), run it explicitly:

~/.local/share/uv/tools/zotero-mcp-server/bin/python3 .claude/attach-transcript.py ITEMKEY

This script:

  1. Fetches the transcript via YouTubeTranscriptApi (or from .claude/transcript_cache/)
  2. Qwen3.5:9b generates a cleaned transcript and a 3–5 sentence abstract
  3. Uploads the cleaned transcript as a .txt attachment to Zotero; sets abstractNote

After a Go decision, generate the literature note the same way as papers:

verwerk recente papers

Claude Code calls process_item.py, which reads the transcript attachment from Zotero locally via fetch-fulltext.py. No transcript content reaches Claude Code.

The generated note contains:

  • YAML frontmatter (title, authors, year, tags, status, Zotero deep link)
  • TLDR
  • Key findings (3–5 points)
  • Methodological notes
  • (No "Relevant quotes" section — timestamps are unreliable without a verifiable source)
  • Links to related notes
  • Flashcards (max 3)

Notes are saved to literature/[author-year-keyword1-keyword2].md — Qwen selects 2–4 nouns from the title and TLDR.

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.

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