Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add commands/ccam80/deep-zotero/installgit clone --depth 1 https://github.com/ccam80/deep-zoteroWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/commands/ccam80/deep-zotero/install)<a href="https://agentmods.dev/commands/ccam80/deep-zotero/install"><img src="https://agentmods.dev/badge/commands/ccam80/deep-zotero/install.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00021 | $0.01108 |
| Opus 5 | $0.00010 | $0.00554 |
| Sonnet 5 | $0.00004 | $0.00222 |
| Haiku 4.5 | $0.00002 | $0.00111 |
Grade B, and why
install scanned grade B with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
- Debian/Ubuntu: `sudo apt install tesseract-ocr`. How it starts
The opening of the file, as written. The whole thing — 87 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Set up deep-zotero (agent runbook)
You are an AI coding agent setting up an installed deep-zotero plugin.
Work through the steps in order and verify each before moving on. The user should only have to paste API keys and confirm system changes.
1. Preconditions
Confirm:
uvis onPATH(uv --version). If missing, point the user at https://docs.astral.sh/uv/ and stop.- The plugin is installed and its tools are visible. If not,
/plugin install deep-zoteroand restart Claude Code. - Zotero 8 with PDFs in
storage/. On Zotero 7 every citation key comes back empty.
Locate the Zotero data directory, which contains zotero.sqlite and storage/. The default is ~/Zotero. Confirm the path exists.
2. API keys
Ask the user for the keys they have:
- Gemini (embeddings, required by default) — https://aistudio.google.com/app/apikey
- Anthropic (vision table extraction) — https://console.anthropic.com/ . Without it, text and figures still index but no tables are extracted.
Do not echo the full keys back in your messages.
3. Environment variables
The server reads its whole configuration from the environment Claude Code starts from.
| Variable | Value |
|---|---|
DEEP_ZOTERO_DATA_DIR |
the Zotero data directory from step 1 |
DEEP_ZOTERO_CHROMA_PATH |
where the index should live, e.g. ~/.local/share/deep-zotero/chroma |
GEMINI_API_KEY |
from step 2 |
ANTHROPIC_API_KEY |
from step 2, omit if the user opted out of vision |
Set them for the user's account, then have them restart Claude Code — a newly set persistent variable only reaches new processes.
Windows (PowerShell), per variable:
[Environment]::SetEnvironmentVariable("DEEP_ZOTERO_DATA_DIR", "C:\Users\you\Zotero", "User")
macOS/Linux: add export lines to ~/.zshrc or ~/.bashrc.
To supply settings beyond these four, point DEEP_ZOTERO_CONFIG at a JSON config file. It takes precedence over the environment wherever both supply a setting.
4. Tesseract-OCR (only if the user has scanned PDFs)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago First seen · 87 lines · 21 tokens per session scan B 4143ab8a5416
install is a command published in the GitHub repository ccam80/deep-zotero (9 stars, last pushed 1mo ago), licensed MIT. It adds 21 tokens to every session and 1,108 once invoked, about $0.0001 per session on Opus 5. A static security scan graded it B with 1 finding (asks for root). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other commands, from other repositories
git
Git operations with intelligent commit messages and workflow optimization.
checklist
Generate a custom checklist for the current feature based on user requirements.
clarify
Identify underspecified areas in the current feature spec by asking up to 5 highly targeted clarification questions and encoding answers back into the spec.
specify
Create or update the feature specification from a natural language feature description.
analyze
Perform a non-destructive cross-artifact consistency and quality analysis across spec.md, plan.md, and tasks.md after task generation.
converge
Assess the current codebase against the feature's spec, plan, and tasks, then append any remaining unbuilt work as new tasks to tasks.md so implement can complete it.