Activating the skill & daily workflow

Activating the research workflow skill

The skill is a markdown file that tells Claude Code how to behave during research sessions. One-time installation:

# Create the skills folder in your vault
mkdir -p ~/Documents/ResearchVault/.claude/skills

# Copy the skill file to the vault
cp research-workflow-skill-v1.16.md ~/Documents/ResearchVault/.claude/skills/

Then add the following line to your CLAUDE.md (at the bottom):

## Active skills
- Read and follow `.claude/skills/research-workflow-skill-v1.16.md` during every research session.

From that point on, the skill is active as soon as you open Claude Code in your vault. You can start the workflow by typing: /research or simply "start research workflow".

Daily workflow after installation

Once everything is set up, the daily workflow is straightforward. The feedreader runs automatically — no action required.

Browse the filtered feed at http://localhost:8765/filtered.html (or in NetNewsWire via http://localhost:8765/filtered.xml). Items are sorted by relevance score. Send interesting ones to Zotero _inbox via the browser extension or iOS app.
Start Zotero (so the local API is active)
Open Terminal in your vault: cd ~/Documents/ResearchVault && claude
Activate the skill: type /research or "start research workflow"
Claude Code asks an intake question and guides you interactively from there

You do not need to know exactly what you are looking for — the skill is designed to help you with that.

Full session flow

Browse the filtered feed and forward interesting items to Zotero _inbox
Start Zotero
Open Terminal, navigate to your vault, and start Claude Code:
```
cd ~/Documents/ResearchVault
claude
```
Activate the research workflow:
```
/research
```
or just type: start research workflow
Optionally, run index-score.py first to prioritize your review:
```
~/.local/share/uv/tools/zotero-mcp-server/bin/python3 .claude/index-score.py
```
This ranks all _inbox items by semantic similarity to your existing library (using the ChromaDB embeddings from zotero-mcp), so you know which items to focus on.
Claude Code retrieves all items from your Zotero _inbox and presents each one with a short summary and relevance assessment — the summary is generated locally by Qwen3.5:9b. You respond Go or No-go per item.
For each Go: Claude Code writes a structured literature note using the safe pipeline below.
For each No-go: Claude Code removes the item from _inbox (after your confirmation).
At the end of the session, Claude Code shows a summary: X approved, Y removed. If new papers were added, update the semantic search database:
```
zotero-mcp update-db            # quick (metadata only)
zotero-mcp update-db --fulltext # recommended (includes full text)
```
Or use the alias: update-zotero (equivalent to --fulltext). Check database status with zotero-mcp db-status.

Helper scripts

The workflow uses three helper scripts in .claude/. They keep source content out of Claude Code's context and handle Zotero write operations.

`fetch-fulltext.py` — retrieve and save attachment text

Fetches the full text of a Zotero attachment and saves it to a local file. Only prints status; never prints content.

~/.local/share/uv/tools/zotero-mcp-server/bin/python3 .claude/fetch-fulltext.py ITEMKEY inbox/bron.txt
# Output: Saved: inbox/bron.txt (12,345 chars, type: application/pdf)

`ollama-generate.py` — generate text via Ollama REST API

Calls Ollama's REST API directly (no CLI, no ANSI codes). Prepends /no_think to suppress Qwen3.5:9b's reasoning step. Prints only status lines.

~/.local/share/uv/tools/zotero-mcp-server/bin/python3 .claude/ollama-generate.py \
  --input  inbox/bron.txt \
  --output literature/notitie.md \
  --prompt "Write a literature note in Dutch..."
# Output: Input: inbox/bron.txt (12,345 chars) | Written: literature/notitie.md (3,200 chars)

`zotero-remove-from-inbox.py` — remove processed item from `_inbox`

Removes the item from the _inbox collection in Zotero via the web API. Requires ZOTERO_API_KEY in the environment or .env file (see step 4d).

~/.local/share/uv/tools/zotero-mcp-server/bin/python3 .claude/zotero-remove-from-inbox.py ITEMKEY
# Output: Item ITEMKEY removed from _inbox.

Local Research Workflow