integrative-deep-research

---

name: integrative-deep-research description: Use when the user wants a deterministic NotebookLM-backed deep research run with one human clarification step and a self-contained HTML report. The driver runs agy scoping, NotebookLM fast research, one askq/chat question, NotebookLM deep research on the same notebook, fixed topic-anchored query angles, and local report rendering. Triggers: "integrative deep research", "interactive deep research", "NotebookLM deep research with one question", "deep research HTML report". version: 0.1.0 license: MIT metadata: tags: [deep-research, notebooklm, antigravity, deterministic, token-efficient, report, mermaid, human-in-the-loop] related_skills: [interactive-deep-research, askq, deep-research-scorecard]

Integrative Deep Research

integrative-deep-research is the pipeline driver. It keeps the agent's work small and deterministic: fire fixed CLI steps, relay exactly one question to the human, and let NotebookLM do the expensive research reasoning.

CLI: idr on PATH, or:

python3 ~/.claude/skills/integrative-deep-research/scripts/idr.py

Install the full v0.1.0 source bundle from the repository root:

git clone https://github.com/Martin-Hausleitner/interactive-deep-research.git
cd interactive-deep-research
git checkout v0.1.0
./install.sh

The installer copies packaged skills to ~/.claude/skills and links idr, askq, and scorecard into ~/.local/bin by default. Override with CLAUDE_SKILLS_DIR or BIN_DIR if needed. Use a tagged source checkout for reproducible installs; no package-manager distribution is published for v0.1.0.

Run artifacts live in:

~/.local/share/idr/runs/<run_id>/

Fixed Flow

flowchart TD
    A["idr plan TOPIC"] --> B["agy seed"]
    B --> C["NotebookLM fast pass<br/>--auto-import"]
    C --> D["status + import<br/>sources available"]
    D --> E["one question<br/>askq or chat relay"]
    E --> F["idr resume RUN --answer ..."]
    F --> G["NotebookLM deep pass<br/>same notebook, --force --auto-import"]
    G --> H["fixed query angles"]
    H --> I["report.html"]

1. agy scoping seed: write seed.md, optionally ask Antigravity for a short NotebookLM-ready brief.
2. NotebookLM fast pass: nlm research start --mode fast --auto-import.
3. Import stabilization: poll nlm research status, then run nlm research import.
4. One clarifying question: ask NotebookLM for the single most important question.
5. Human answer: relay in chat for agent sessions, or use askq in terminals.
6. NotebookLM deep pass: same notebook, user answer as context, --force --auto-import.
7. Fixed angles: overview, comparison table, recommendation.
8. Local HTML report: report.html, Mermaid-capable, 0 formatting tokens.

Commands

Phased mode, preferred inside coding/agent environments:

idr plan "<topic>"
idr resume <run_id> --answer "<human answer>"

Full interactive terminal loop:

idr run "<topic>"

Regenerate the report from existing run content:

idr report <run_id>

Offline smoke test:

IDR_MOCK=1 idr plan "test topic"
IDR_MOCK=1 idr resume <run_id> --answer "self-hosted only"

--mock is equivalent for plan and run.

Live proof mode:

IDR_REQUIRE_LIVE=1 idr plan "<small synthetic topic>"
IDR_REQUIRE_LIVE=1 idr resume <run_id> --answer "<synthetic answer>"

IDR_REQUIRE_LIVE=1 is for proof runs. It prevents silent degradation to mock text when NotebookLM startup, query, or deep research fails.

Output Contract

Command	stdout	Main files
idr plan	JSON {run_id, rundir, notebook_id, question}	state.json, seed.md, optional agy_brief.md
idr resume	JSON {run_id, report, notebook_id}	content/*.md, report.html, updated state.json
idr run	JSON {run_id, report, notebook_id}	same as plan + resume, with askq bridge
idr report	JSON {report}	regenerated report.html

Live verification should set IDR_REQUIRE_LIVE=1; this turns missing notebook IDs, failed nlm query, and failed deep passes into non-zero errors instead of falling back to mock text. Do not combine IDR_REQUIRE_LIVE=1 with IDR_MOCK=1.

Agent Guidance

• Do not ask clarifying questions before idr plan; the pipeline creates the one sanctioned question after source discovery.
• In non-interactive agent sessions, do not run a bare blocking askq. Relay the returned question to the user, then call idr resume.
• Keep the run_id; it is the stable handle for state, content, and the report.
• Use deep-research-scorecard after research when a comparison needs a decisive weighted winner.

Preflight

nlm doctor
agy --version
IDR_MOCK=1 idr plan "smoke test"

agy is optional. If it is unavailable or fails, the driver falls back to the original topic/brief. nlm needs an authenticated NotebookLM session for live runs.

Environment Contract

Variable	Effect
IDR_MOCK=1	Stub agy and NotebookLM; full plan/resume/report flow runs offline.
IDR_RUNS_DIR=/tmp/idr-runs	Override the run artifact directory. Use this in tests.
ASKQ_SCRIPT=/path/to/askq.py	Override the question bridge used by idr run.
ASKQ_ANSWER=...	Non-interactive answer inherited by askq when idr run calls it.
IDR_REQUIRE_LIVE=1	Fail closed on live NotebookLM failures instead of falling back to mock text.
IDR_LIVE_E2E=1	Used by pytest to enable the opt-in live NotebookLM E2E.
IDR_LIVE_TOPIC, IDR_LIVE_ANSWER	Override the synthetic live E2E topic/answer.

Privacy / No PII

Use synthetic or public topics for tests, CI, and examples. Do not put secrets, credentials, personal data, private customer material, account IDs, or internal hostnames into topics, human answers, NotebookLM notebooks, askq logs, run state, content files, or rendered reports. If a live run requires sensitive context, keep it outside the repository and do not commit the run directory.

For vulnerability reporting and responsible-use boundaries, follow the repository SECURITY.md.

Gotchas

• nlm query returns JSON; parse .value.answer.
• NotebookLM deep research needs --force in headless runs.
• fast --auto-import can return before sources are imported; poll and import.
• agy may print leading status lines; strip them before using the answer.
• Prefix fixed query prompts with Topic: <topic> so the notebook stays on-task.
• Use IDR_MOCK=1 for CI and smoke tests to avoid auth, network, and quota issues.

Failure Modes

Symptom	Cause	Fix
nlm missing/auth error	NotebookLM CLI unavailable or login expired	nlm login, then nlm doctor.
notebook_id is empty	Fast pass failed or CLI output changed	Use IDR_REQUIRE_LIVE=1 and inspect stderr.
Weak/canned question	Sources were not imported	Ensure status wait + explicit import ran.
Deep pass prompt/abort	Pending NotebookLM research	The driver uses --force; upgrade nlm if behavior changes.
Agent session blocks	idr run invoked interactive askq	Use idr plan/resume or ASKQ_ANSWER.
askq failed	ASKQ_SCRIPT missing/not executable	Install skills or set ASKQ_SCRIPT to the repo script.
Quota/429	NotebookLM quota/backoff	Wait or use IDR_MOCK=1.