| name | deep-research |
| description | Async deep research via Gemini Interactions API (no Gemini CLI dependency). RAG-ground queries on local files (--context), preview costs (--dry-run), structured JSON output, adaptive polling. Universal skill for 30+ AI agents including Claude Code, Amp, Codex, and Gemini CLI. |
Deep Research Skill
Perform deep research powered by Google Gemini's deep research agent. Upload documents to file search stores for RAG-grounded answers. Manage research sessions with persistent workspace state.
For AI Agents
Get a full capabilities manifest, decision trees, and output contracts:
uv run {baseDir}/scripts/onboard.py --agent
See AGENTS.md for the complete structured briefing.
| Command | What It Does |
|---|
uv run {baseDir}/scripts/research.py start "question" | Launch deep research |
uv run {baseDir}/scripts/research.py start "question" --context ./path --dry-run | Estimate cost |
uv run {baseDir}/scripts/research.py start "question" --context ./path --output report.md | RAG-grounded research |
uv run {baseDir}/scripts/store.py query <name> "question" | Quick Q&A against uploaded docs |
Security & Transparency
Credentials: This skill requires a Google/Gemini API key (one of GOOGLE_API_KEY, GEMINI_API_KEY, or GEMINI_DEEP_RESEARCH_API_KEY). The key is read from environment variables and passed to the google-genai SDK. It is never logged, written to files, or transmitted anywhere other than the Google Gemini API.
File uploads: The --context flag uploads local files to Google's ephemeral file search stores for RAG grounding. Files are filtered by MIME type (binary files are rejected), and the ephemeral store is auto-deleted after research completes unless --keep-context is specified. Use --dry-run to preview what would be uploaded without sending anything. Only files you explicitly point --context at are uploaded -- no automatic scanning of parent directories or home folders.
Non-interactive mode: When stdin is not a TTY (agent/CI use), confirmation prompts are automatically skipped. This is by design for agent integration but means an autonomous agent with file system access could trigger uploads. Restrict the paths agents can access, or use --dry-run and --max-cost guards.
No obfuscation: All code is readable Python with PEP 723 inline metadata. No binary blobs, no minified scripts, no telemetry, no analytics. The full source is auditable at github.com/24601/agent-deep-research.
Local state: Research session state is written to .gemini-research.json in the working directory. This file contains interaction IDs, store mappings, and upload hashes -- no credentials or research content. Use state.py gc to clean up orphaned stores from crashed runs.
Prerequisites
- A Google API key (
GOOGLE_API_KEY or GEMINI_API_KEY environment variable)
- uv installed (see uv install docs)
Quick Start
uv run {baseDir}/scripts/research.py "What are the latest advances in quantum computing?"
uv run {baseDir}/scripts/research.py status <interaction-id>
uv run {baseDir}/scripts/research.py report <interaction-id> --output report.md
uv run {baseDir}/scripts/research.py start "How does auth work?" --context ./src --output report.md
uv run {baseDir}/scripts/research.py start "Analyze the API" --context ./src --format html --output report.html
uv run {baseDir}/scripts/research.py start "How does auth work?" --context ./src --prompt-template auto --output report.md
Environment Variables
Set one of the following (checked in order of priority):
| Variable | Description |
|---|
GEMINI_DEEP_RESEARCH_API_KEY | Dedicated key for this skill (highest priority) |
GOOGLE_API_KEY | Standard Google AI key |
GEMINI_API_KEY | Gemini-specific key |
Optional model configuration:
| Variable | Description | Default |
|---|
GEMINI_DEEP_RESEARCH_MODEL | Model for file search queries | gemini-3.1-pro-preview |
GEMINI_MODEL | Fallback model name | gemini-3.1-pro-preview |
GEMINI_DEEP_RESEARCH_AGENT | Deep research agent identifier | deep-research-pro-preview-12-2025 |
Research Commands
Start Research
uv run {baseDir}/scripts/research.py start "your research question"
| Flag | Description |
|---|
--report-format FORMAT | Output structure: executive_summary, detailed_report, comprehensive |
--store STORE_NAME | Ground research in a file search store (display name or resource ID) |
--no-thoughts | Hide intermediate thinking steps |
--follow-up ID | Continue a previous research session |
--output FILE | Wait for completion and save report to a single file |
--output-dir DIR | Wait for completion and save structured results to a directory (see below) |
--timeout SECONDS | Maximum wait time when polling (default: 1800 = 30 minutes) |
--no-adaptive-poll | Disable history-adaptive polling; use fixed interval curve instead |
--context PATH | Auto-create ephemeral store from a file or directory for RAG-grounded research |
--context-extensions EXT | Filter context uploads by extension (e.g. py,md or .py .md) |
--keep-context | Keep the ephemeral context store after research completes (default: auto-delete) |
--dry-run | Estimate costs without starting research (prints JSON cost estimate) |
--format {md,html,pdf} | Output format for the report (default: md; pdf requires weasyprint) |
--prompt-template {typescript,python,general,auto} | Domain-specific prompt prefix; auto detects from context file extensions |
--depth {quick,standard,deep} | Research depth: quick (~2-5min), standard (~5-15min), deep (~15-45min) |
--max-cost USD | Abort if estimated cost exceeds this limit (e.g. --max-cost 3.00) |
--input-file PATH | Read the research query from a file instead of positional argument |
The start subcommand is the default, so research.py "question" and research.py start "question" are equivalent.
Check Status
uv run {baseDir}/scripts/research.py status <interaction-id>
Returns the current status (in_progress, completed, failed) and outputs if available.
Save Report
uv run {baseDir}/scripts/research.py report <interaction-id>
| Flag | Description |
|---|
--output FILE | Save report to a specific file path (default: report-<id>.md) |
--output-dir DIR | Save structured results to a directory |
Structured Output (--output-dir)
When --output-dir is used, results are saved to a structured directory:
<output-dir>/
research-<id>/
report.md # Full final report
metadata.json # Timing, status, output count, sizes
interaction.json # Full interaction data (all outputs, thinking steps)
sources.json # Extracted source URLs/citations
A compact JSON summary (under 500 chars) is printed to stdout:
{
"id": "interaction-123",
"status": "completed",
"output_dir": "research-output/research-interaction-1/",
"report_file": "research-output/research-interaction-1/report.md",
"report_size_bytes": 45000,
"duration_seconds": 154,
"summary": "First 200 chars of the report..."
}
This is the recommended pattern for AI agent integration -- the agent receives a small JSON payload while the full report is written to disk.
Adaptive Polling
When --output or --output-dir is used, the script polls the Gemini API until research completes. By default, it uses history-adaptive polling that learns from past research completion times:
- Completion times are recorded in
.gemini-research.json under researchHistory (last 50 entries, separate curves for grounded vs non-grounded research).
- When 3+ matching data points exist, the poll interval is tuned to the historical distribution:
- Before any research has ever completed: slow polling (30s)
- In the likely completion window (p25-p75): aggressive polling (5s)
- In the tail (past p75): moderate polling (15-30s)
- Unusually long runs (past 1.5x the longest ever): slow polling (60s)
- All intervals are clamped to [2s, 120s] as a fail-safe.
When history is insufficient (<3 data points) or --no-adaptive-poll is passed, a fixed escalating curve is used: 5s (first 30s), 10s (30s-2min), 30s (2-10min), 60s (10min+).
Cost Estimation (--dry-run)
Preview estimated costs before running research:
uv run {baseDir}/scripts/research.py start "Analyze security architecture" --context ./src --dry-run
Outputs a JSON cost estimate to stdout with context upload costs, research query costs, and a total. Estimates are heuristic-based (the Gemini API does not return token counts or billing data) and clearly labeled as such.
After research completes with --output-dir, the metadata.json file includes a usage key with post-run cost estimates based on actual output size and duration.
File Search Store Commands
Manage file search stores for RAG-grounded research and Q&A.
Create a Store
uv run {baseDir}/scripts/store.py create "My Project Docs"
List Stores
uv run {baseDir}/scripts/store.py list
Query a Store
uv run {baseDir}/scripts/store.py query <store-name> "What does the auth module do?"
| Flag | Description |
|---|
--output-dir DIR | Save response and metadata to a directory |
Delete a Store
uv run {baseDir}/scripts/store.py delete <store-name>
Use --force to skip the confirmation prompt. When stdin is not a TTY (e.g., called by an AI agent), the prompt is automatically skipped.
File Upload
Upload files or entire directories to a file search store.
uv run {baseDir}/scripts/upload.py ./src fileSearchStores/abc123
| Flag | Description |
|---|
--smart-sync | Skip files that haven't changed (hash comparison) |
--extensions EXT [EXT ...] | File extensions to include (comma or space separated, e.g. py,ts,md or .py .ts .md) |
Hash caches are always saved on successful upload, so a subsequent --smart-sync run will correctly skip unchanged files even if the first upload did not use --smart-sync.
MIME Type Support
36 file extensions are natively supported by the Gemini File Search API. Common programming files (JS, TS, JSON, CSS, YAML, etc.) are automatically uploaded as text/plain via a fallback mechanism. Binary files are rejected. See references/file_search_guide.md for the full list.
File size limit: 100 MB per file.
Session Management
Research IDs and store mappings are cached in .gemini-research.json in the current working directory.
Show Session State
uv run {baseDir}/scripts/state.py show
Show Research Sessions Only
uv run {baseDir}/scripts/state.py research
Show Stores Only
uv run {baseDir}/scripts/state.py stores
JSON Output for Agents
Add --json to any state subcommand to output structured JSON to stdout:
uv run {baseDir}/scripts/state.py --json show
uv run {baseDir}/scripts/state.py --json research
uv run {baseDir}/scripts/state.py --json stores
Clear Session State
uv run {baseDir}/scripts/state.py clear
Use -y to skip the confirmation prompt. When stdin is not a TTY (e.g., called by an AI agent), the prompt is automatically skipped.
Non-Interactive Mode
All confirmation prompts (store.py delete, state.py clear) are automatically skipped when stdin is not a TTY. This allows AI agents and CI pipelines to call these commands without hanging on interactive prompts.
Workflow Example
A typical grounded research workflow:
STORE_JSON=$(uv run {baseDir}/scripts/store.py create "Project Codebase")
STORE_NAME=$(echo "$STORE_JSON" | python3 -c "import sys,json; print(json.load(sys.stdin)['name'])")
uv run {baseDir}/scripts/upload.py ./docs "$STORE_NAME" --smart-sync
uv run {baseDir}/scripts/store.py query "$STORE_NAME" "How is authentication handled?"
uv run {baseDir}/scripts/research.py start "Analyze the security architecture" \
--store "$STORE_NAME" --output-dir ./research-output --timeout 3600
RESEARCH_JSON=$(uv run {baseDir}/scripts/research.py start "Analyze the security architecture" --store "$STORE_NAME")
RESEARCH_ID=$(echo "$RESEARCH_JSON" | python3 -c "import sys,json; print(json.load(sys.stdin)['id'])")
uv run {baseDir}/scripts/research.py status "$RESEARCH_ID"
uv run {baseDir}/scripts/research.py report "$RESEARCH_ID" --output-dir ./research-output
Output Convention
All scripts follow a dual-output pattern:
- stderr: Rich-formatted human-readable output (tables, panels, progress bars)
- stdout: Machine-readable JSON for programmatic consumption
This means 2>/dev/null hides the human output, and piping stdout gives clean JSON.
