See [AGENTS.md]({baseDir}/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. Sensitive files are automatically excluded: `.env*`, `credentials.json`, `secrets.*`, private keys (`.pem`, `.key`), and auth tokens (`.npmrc`, `.pypirc`, `.netrc`). Binary files are rejected by MIME type filtering. Build directories (`node_modules`, `__pycache__`, `.git`, `dist`, `build`) are skipped. 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](https://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](https://docs.astral.sh/uv/) installed (see [uv install docs](https://docs.astral.sh/uv/getting-started/installation/))

## Quick Start

## 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

| 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 |
| `--no-cache` | Skip research cache and force a fresh run |

The `start` subcommand is the default, so `research.py "question"` and `research.py start "question"` are equivalent.

**Important**: When `--output` or `--output-dir` is used, the command blocks until research completes (2-10+ minutes). Do not background it with `&`. Use non-blocking mode (omit `--output`) to get an ID immediately, then poll with `status` and save with `report`.

### Check Status

Returns the current status (`in_progress`, `completed`, `failed`) and outputs if available.

### Save Report

| 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:

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:

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

| Flag | Description |
|------|-------------|
| `--output-dir DIR` | Save response and metadata to a directory |

### Delete a Store

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.

| 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