ddg-deep-research 0.2.0__tar.gz

ddg_deep_research-0.2.0/.gitignore

@@ -0,0 +1,20 @@
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+build/
+.venv/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# IDE
+.vscode/
+.idea/
+
+# Logs
+*.log
+# Research outputs
+outputs/

ddg_deep_research-0.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 crftsmnd
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ddg_deep_research-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ddg-deep-research
+Version: 0.2.0
+Summary: 5-stage deep research pipeline using DuckDuckGo MCP — free, no API key, no rate limits
+Project-URL: Homepage, https://github.com/crftsmnd/ddg-deep-research
+Project-URL: Repository, https://github.com/crftsmnd/ddg-deep-research
+Project-URL: Bug Tracker, https://github.com/crftsmnd/ddg-deep-research/issues
+Author: crftsmnd
+License: MIT
+License-File: LICENSE
+Keywords: agent,deep-research,duckduckgo,llm,mcp,research,web-search
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Internet :: WWW/HTTP :: Indexing/Search
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Requires-Dist: mcp>=1.0
+Description-Content-Type: text/markdown
+
+# 🧠 ddg-deep-research
+
+**5-stage deep research pipeline** using DuckDuckGo MCP — **free, no API key, no rate limits**.
+
+```
+pip install ddg-deep-research
+ddg-deep-research search "your query"
+```
+
+## Why this exists
+
+Every other deep research agent requires OpenAI / Anthropic / Google API keys — or runs expensive local models. This one uses **DuckDuckGo MCP** for both search and content extraction. Completely free. Zero API keys. Zero rate limits.
+
+## Pipeline
+
+```
+Stage 1: Decompose  ──→ 3-6 sub-questions + search strategy
+Stage 2: Gather     ──→ DuckDuckGo MCP search (parallel, unlimited)
+Stage 3: Deep Read  ──→ DuckDuckGo MCP fetch_content + browser_use
+Stage 4: Verify     ──→ Cross-reference claims, flag contradictions
+Stage 5: Synthesize ──→ Cited brief.md + .provenance.md sidecar
+```
+
+## Quick Start
+
+```bash
+# Search the web (free, no API key!)
+ddg-deep-research search "latest advances in AI reasoning"
+
+# Fetch a webpage
+ddg-deep-research fetch "https://example.com/article"
+```
+
+### Full Pipeline
+
+```bash
+# Stage 1: Break question into sub-questions (template)
+ddg-deep-research decompose --question "How is RAG evolving?" --output plan.json
+
+# Stage 2: Search
+ddg-deep-research ddg_search --query "RAG architectures 2026" --output results.json
+
+# Stage 3: Fetch content
+ddg-deep-research ddg_fetch --url "https://..." --output-dir extracted/
+
+# Stage 4: Merge results
+ddg-deep-research merge --input-dir raw/ --output merged.json
+
+# Stage 5: Clean & verify
+ddg-deep-research clean --input extracted/ --output cleaned/
+ddg-deep-research verify --input cleaned/cleaned.json --output verified.json
+
+# Stage 6: Generate final brief
+ddg-deep-research synthesize --verified verified.json --question "..." --output-dir outputs/ --today $(date +%Y-%m-%d)
+```
+
+### Parallel DAG Execution
+
+```bash
+ddg-deep-research dag --plan workflow.json --verbose
+```
+
+Input JSON:
+```json
+{
+  "tasks": [
+    {"id": "search_1", "depends_on": [], "command": "ddg_search --query ..."},
+    {"id": "fetch_1", "depends_on": ["search_1"], "command": "ddg_fetch --url ..."},
+    {"id": "synthesize", "depends_on": ["search_1", "fetch_1"], "command": "synthesize ..."}
+  ]
+}
+```
+
+## Python API
+
+```python
+import asyncio
+from ddg_deep_research.ddg_mcp import search_web, fetch_content
+
+async def main():
+    results = await search_web("your query", max_results=10)
+    for r in results:
+        print(f"{r['title']}: {r['url']}")
+
+    content = await fetch_content("https://example.com")
+    print(content[:500])
+
+asyncio.run(main())
+```
+
+## Requirements
+
+- Python 3.10+
+- `uv` installed (for duckduckgo-mcp-server): `curl -LsSf https://astral.sh/uv/install.sh | sh`
+- No API keys. No subscriptions. Nothing.
+
+## How it works
+
+This package wraps [duckduckgo-mcp-server](https://github.com/nicholasgriffintn/duckduckgo-mcp-server) via Python's MCP stdio transport. All search and content extraction goes through DuckDuckGo's free anonymous API. The 5-stage pipeline is modeled after production research agents but without the API costs.
+
+## Comparison
+
+| Feature | OpenAI Deep Research | LangChain Deep Research | **ddg-deep-research** |
+|---|---|---|---|
+| API key needed | ✅ $200/mo | ✅ OpenAI key | **❌ Free** |
+| Search engine | Bing/Browser | Custom | **DuckDuckGo** |
+| Content extraction | Built-in | Built-in | **DuckDuckGo MCP** |
+| Provenance tracking | ✅ | ✅ | **✅ .provenance.md** |
+| DAG orchestration | ❌ | ❌ | **✅ Built-in** |
+| Open source | ❌ | ✅ | **✅ MIT** |
+| `pip install` | ❌ | ❌ | **✅ pip install** |
+
+## License
+
+MIT

ddg_deep_research-0.2.0/README.md

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+# 🧠 ddg-deep-research
+
+**5-stage deep research pipeline** using DuckDuckGo MCP — **free, no API key, no rate limits**.
+
+```
+pip install ddg-deep-research
+ddg-deep-research search "your query"
+```
+
+## Why this exists
+
+Every other deep research agent requires OpenAI / Anthropic / Google API keys — or runs expensive local models. This one uses **DuckDuckGo MCP** for both search and content extraction. Completely free. Zero API keys. Zero rate limits.
+
+## Pipeline
+
+```
+Stage 1: Decompose  ──→ 3-6 sub-questions + search strategy
+Stage 2: Gather     ──→ DuckDuckGo MCP search (parallel, unlimited)
+Stage 3: Deep Read  ──→ DuckDuckGo MCP fetch_content + browser_use
+Stage 4: Verify     ──→ Cross-reference claims, flag contradictions
+Stage 5: Synthesize ──→ Cited brief.md + .provenance.md sidecar
+```
+
+## Quick Start
+
+```bash
+# Search the web (free, no API key!)
+ddg-deep-research search "latest advances in AI reasoning"
+
+# Fetch a webpage
+ddg-deep-research fetch "https://example.com/article"
+```
+
+### Full Pipeline
+
+```bash
+# Stage 1: Break question into sub-questions (template)
+ddg-deep-research decompose --question "How is RAG evolving?" --output plan.json
+
+# Stage 2: Search
+ddg-deep-research ddg_search --query "RAG architectures 2026" --output results.json
+
+# Stage 3: Fetch content
+ddg-deep-research ddg_fetch --url "https://..." --output-dir extracted/
+
+# Stage 4: Merge results
+ddg-deep-research merge --input-dir raw/ --output merged.json
+
+# Stage 5: Clean & verify
+ddg-deep-research clean --input extracted/ --output cleaned/
+ddg-deep-research verify --input cleaned/cleaned.json --output verified.json
+
+# Stage 6: Generate final brief
+ddg-deep-research synthesize --verified verified.json --question "..." --output-dir outputs/ --today $(date +%Y-%m-%d)
+```
+
+### Parallel DAG Execution
+
+```bash
+ddg-deep-research dag --plan workflow.json --verbose
+```
+
+Input JSON:
+```json
+{
+  "tasks": [
+    {"id": "search_1", "depends_on": [], "command": "ddg_search --query ..."},
+    {"id": "fetch_1", "depends_on": ["search_1"], "command": "ddg_fetch --url ..."},
+    {"id": "synthesize", "depends_on": ["search_1", "fetch_1"], "command": "synthesize ..."}
+  ]
+}
+```
+
+## Python API
+
+```python
+import asyncio
+from ddg_deep_research.ddg_mcp import search_web, fetch_content
+
+async def main():
+    results = await search_web("your query", max_results=10)
+    for r in results:
+        print(f"{r['title']}: {r['url']}")
+
+    content = await fetch_content("https://example.com")
+    print(content[:500])
+
+asyncio.run(main())
+```
+
+## Requirements
+
+- Python 3.10+
+- `uv` installed (for duckduckgo-mcp-server): `curl -LsSf https://astral.sh/uv/install.sh | sh`
+- No API keys. No subscriptions. Nothing.
+
+## How it works
+
+This package wraps [duckduckgo-mcp-server](https://github.com/nicholasgriffintn/duckduckgo-mcp-server) via Python's MCP stdio transport. All search and content extraction goes through DuckDuckGo's free anonymous API. The 5-stage pipeline is modeled after production research agents but without the API costs.
+
+## Comparison
+
+| Feature | OpenAI Deep Research | LangChain Deep Research | **ddg-deep-research** |
+|---|---|---|---|
+| API key needed | ✅ $200/mo | ✅ OpenAI key | **❌ Free** |
+| Search engine | Bing/Browser | Custom | **DuckDuckGo** |
+| Content extraction | Built-in | Built-in | **DuckDuckGo MCP** |
+| Provenance tracking | ✅ | ✅ | **✅ .provenance.md** |
+| DAG orchestration | ❌ | ❌ | **✅ Built-in** |
+| Open source | ❌ | ✅ | **✅ MIT** |
+| `pip install` | ❌ | ❌ | **✅ pip install** |
+
+## License
+
+MIT

ddg_deep_research-0.2.0/pyproject.toml

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+[project]
+name = "ddg-deep-research"
+version = "0.2.0"
+description = "5-stage deep research pipeline using DuckDuckGo MCP — free, no API key, no rate limits"
+readme = "README.md"
+license = {text = "MIT"}
+requires-python = ">=3.10"
+authors = [
+    {name = "crftsmnd"},
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Topic :: Internet :: WWW/HTTP :: Indexing/Search",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+]
+keywords = ["deep-research", "duckduckgo", "research", "agent", "mcp", "web-search", "llm"]
+dependencies = [
+    "mcp>=1.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/crftsmnd/ddg-deep-research"
+Repository = "https://github.com/crftsmnd/ddg-deep-research"
+"Bug Tracker" = "https://github.com/crftsmnd/ddg-deep-research/issues"
+
+[project.scripts]
+ddg-deep-research = "ddg_deep_research.research_pipeline:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ddg_deep_research"]
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/ddg_deep_research/*.py",
+    "README.md",
+    "LICENSE",
+    "pyproject.toml",
+]

ddg_deep_research-0.2.0/src/ddg_deep_research/__init__.py

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+"""
+ddg-deep-research — 5-stage deep research pipeline using DuckDuckGo MCP (free, no API key).
+
+Zero API keys required. Zero rate limits. Zero paywalls.
+"""
+
+__version__ = "0.2.0"
+__license__ = "MIT"

ddg_deep_research-0.2.0/src/ddg_deep_research/ddg_mcp.py

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+#!/usr/bin/env python3
+"""
+DuckDuckGo MCP Bridge — free, no-API-key search & content extraction.
+
+Connects to duckduckgo-mcp-server via stdio MCP transport and exposes
+two commands: search (web search) and fetch (page content extraction).
+
+Usage:
+  uv run ddg_mcp.py search "query" [--max-results 10] [--region us-en]
+  uv run ddg_mcp.py fetch <url> [--max-length 8000]
+"""
+
+import asyncio
+import json
+import re
+import sys
+
+from mcp import ClientSession, StdioServerParameters
+from mcp.client.stdio import stdio_client
+
+# ── Regex to parse "N. Title\n   URL: ...\n   Summary: ..." format ────────
+RESULT_BLOCK_RE = re.compile(
+    r"^\d+\.\s+(?P<title>.+?)\n\s+URL:\s+(?P<url>\S+?)\s*\n\s+Summary:\s+(?P<snippet>.*?)$",
+    re.MULTILINE,
+)
+
+
+def parse_search_results(text: str) -> list[dict]:
+    """Parse the human-readable search result text into structured JSON."""
+    results = []
+    for match in RESULT_BLOCK_RE.finditer(text):
+        results.append(
+            {
+                "title": match.group("title").strip(),
+                "url": match.group("url").rstrip("/"),
+                "snippet": match.group("snippet").strip(),
+                "source": "duckduckgo",
+            }
+        )
+    return results
+
+
+async def search_web(
+    query: str, max_results: int = 10, region: str = "wt-wt"
+) -> list[dict]:
+    """Search using DuckDuckGo MCP and return structured results."""
+    server_params = StdioServerParameters(
+        command="uvx",
+        args=["duckduckgo-mcp-server"],
+    )
+    async with stdio_client(server_params) as (read, write):
+        async with ClientSession(read, write) as session:
+            await session.initialize()
+            result = await session.call_tool(
+                "search",
+                {"query": query, "max_results": max_results, "region": region},
+            )
+            # result.content is list[TextContent|...]
+            text = ""
+            for item in result.content:
+                if hasattr(item, "text"):
+                    text += item.text
+            return parse_search_results(text)
+
+
+async def fetch_content(url: str, max_length: int = 8000) -> str:
+    """Fetch and extract clean text from a webpage."""
+    server_params = StdioServerParameters(
+        command="uvx",
+        args=["duckduckgo-mcp-server"],
+    )
+    async with stdio_client(server_params) as (read, write):
+        async with ClientSession(read, write) as session:
+            await session.initialize()
+            result = await session.call_tool(
+                "fetch_content",
+                {"url": url, "max_length": max_length},
+            )
+            text = ""
+            for item in result.content:
+                if hasattr(item, "text"):
+                    text += item.text
+            return text
+
+
+# ── CLI ──────────────────────────────────────────────────────────────────
+
+
+def main():
+    if len(sys.argv) < 2:
+        print(__doc__, file=sys.stderr)
+        sys.exit(1)
+
+    cmd = sys.argv[1]
+
+    if cmd == "search":
+        if len(sys.argv) < 3:
+            print("Usage: ddg_mcp.py search <query> [--max-results N] [--region X]", file=sys.stderr)
+            sys.exit(1)
+        query = sys.argv[2]
+        max_results = 10
+        region = "wt-wt"
+        # Parse optional flags
+        args_iter = iter(sys.argv[3:])
+        for arg in args_iter:
+            if arg == "--max-results":
+                max_results = int(next(args_iter))
+            elif arg == "--region":
+                region = next(args_iter)
+        results = asyncio.run(search_web(query, max_results, region))
+        print(json.dumps(results, indent=2, ensure_ascii=False))
+
+    elif cmd == "fetch":
+        if len(sys.argv) < 3:
+            print("Usage: ddg_mcp.py fetch <url> [--max-length N]", file=sys.stderr)
+            sys.exit(1)
+        url = sys.argv[2]
+        max_length = 8000
+        args_iter = iter(sys.argv[3:])
+        for arg in args_iter:
+            if arg == "--max-length":
+                max_length = int(next(args_iter))
+        content = asyncio.run(fetch_content(url, max_length))
+        # Output has a leading prefix like "Content from https://...\n\n"
+        # Strip it for cleaner output
+        clean = re.sub(r"^Content from .+?\n\n", "", content, count=1)
+        print(clean)
+
+    else:
+        print(f"Unknown command: {cmd}", file=sys.stderr)
+        print(__doc__, file=sys.stderr)
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

ddg_deep_research-0.2.0/src/ddg_deep_research/research_pipeline.py

@@ -0,0 +1,431 @@
+#!/usr/bin/env python3
+"""
+Deep Research Pipeline — orchestration helpers for the 5-stage deep research workflow.
+
+Subcommands:
+  ddg_search   — search web via DuckDuckGo MCP (free, no API key)
+  ddg_fetch    — fetch page content via DuckDuckGo MCP
+  decompose    — break a research question into sub-questions + search strategy
+  merge        — merge & deduplicate search results from parallel subagents
+  clean        — normalize extracted text from browser_use calls
+  verify       — cross-reference claims across sources
+  synthesize   — generate cited brief.md + .provenance.md
+
+Usage: uv run research_pipeline.py <subcommand> [options]
+"""
+
+import argparse
+import asyncio
+import json
+import os
+import re
+import sys
+from datetime import datetime
+from pathlib import Path
+from urllib.parse import urlparse
+
+# ── Helpers ──────────────────────────────────────────────────────────────
+
+TOPIC_SLUG_RE = re.compile(r"[^a-z0-9-]+")
+
+
+def slugify(text: str) -> str:
+    return TOPIC_SLUG_RE.sub("-", text.lower()).strip("-")
+
+
+def ensure_dir(path: str) -> str:
+    Path(path).mkdir(parents=True, exist_ok=True)
+    return path
+
+
+def load_json(path: str):
+    with open(path) as f:
+        return json.load(f)
+
+
+def save_json(obj, path: str):
+    with open(path, "w") as f:
+        json.dump(obj, f, indent=2, ensure_ascii=False)
+
+
+def domain(url: str) -> str:
+    try:
+        return urlparse(url).netloc
+    except Exception:
+        return url
+
+
+# ── Subcommand: dag — Directed Acyclic Graph orchestration ────────────────
+
+def cmd_dag(args):
+    """
+    Execute sub-tasks with dependency graph support.
+    
+    Input: JSON file with:
+    {
+      "tasks": [
+        {"id": "search_1", "depends_on": [], "command": "ddg_search --query ... --output ..."},
+        {"id": "fetch_1", "depends_on": ["search_1"], "command": "ddg_fetch ..."},
+        {"id": "synthesize", "depends_on": ["search_1", "fetch_1"], "command": "synthesize ..."}
+      ]
+    }
+    
+    Output: Executes tasks in dependency order, parallelizing independent tasks.
+    """
+    import subprocess
+
+    plan = load_json(args.plan)
+    tasks = {t["id"]: t for t in plan["tasks"]}
+    completed = set()
+    results = {}
+    max_iterations = 100
+    iteration = 0
+
+    while len(completed) < len(tasks) and iteration < max_iterations:
+        iteration += 1
+        ready = [
+            t for t in plan["tasks"]
+            if t["id"] not in completed
+            and all(dep in completed for dep in t.get("depends_on", []))
+        ]
+
+        if not ready:
+            blocked = [t["id"] for t in plan["tasks"] if t["id"] not in completed]
+            raise RuntimeError(f"Dependency cycle detected or unsatisfied: {blocked}")
+
+        # Execute ready tasks in parallel
+        for task in ready:
+            cmd_parts = task["command"].split()
+            wrapped_cmd = ["uv", "run", "python3", __file__] + cmd_parts
+            try:
+                result = subprocess.run(wrapped_cmd, capture_output=True, text=True, timeout=args.task_timeout)
+                results[task["id"]] = {
+                    "status": "success" if result.returncode == 0 else "error",
+                    "stdout": result.stdout[-500:],
+                    "stderr": result.stderr[-500:],
+                }
+            except subprocess.TimeoutExpired:
+                results[task["id"]] = {"status": "timeout", "stdout": "", "stderr": "Timed out after {args.task_timeout}s"}
+            completed.add(task["id"])
+
+        if args.verbose:
+            print(f"[DAG] Iteration {iteration}: completed {len(completed)}/{len(tasks)} tasks")
+
+    # Save execution report
+    output = {
+        "plan_file": args.plan,
+        "tasks_total": len(tasks),
+        "tasks_completed": len(completed),
+        "results": results,
+    }
+    if args.output:
+        save_json(output, args.output)
+        print(f"DAG execution report → {args.output}")
+    else:
+        print(json.dumps(output, indent=2, ensure_ascii=False))
+
+
+# ── Subcommand: ddg_search ────────────────────────────────────────────────
+
+def cmd_ddg_search(args):
+    """Search using DuckDuckGo MCP (free, no API key)."""
+    from ddg_deep_research.ddg_mcp import search_web
+
+    results = asyncio.run(search_web(args.query, args.max_results, args.region))
+    save_json(results, args.output)
+    print(f"DuckDuckGo search returned {len(results)} results → {args.output}")
+
+
+# ── Subcommand: ddg_fetch ─────────────────────────────────────────────────
+
+def cmd_ddg_fetch(args):
+    """Fetch webpage content using DuckDuckGo MCP."""
+    from ddg_deep_research.ddg_mcp import fetch_content
+
+    content = asyncio.run(fetch_content(args.url, args.max_length))
+    out_dir = ensure_dir(args.output_dir)
+    slug = slugify(args.url.replace("https://", "").replace("http://", "").replace("/", "-"))
+    out_path = os.path.join(out_dir, f"{slug}.txt")
+    with open(out_path, "w") as f:
+        f.write(content)
+    print(f"Fetched {len(content)} chars → {out_path}")
+
+
+# ── Subcommand: decompose ─────────────────────────────────────────────────
+
+def cmd_decompose(args):
+    """Generate a research plan with sub-questions and search strategies."""
+    output_dir = Path(args.output).parent
+    ensure_dir(str(output_dir))
+
+    # This is called by the agent AFTER the agent has decomposed the question.
+    # The agent writes the plan, and this script just saves it in a standard format.
+    plan = {
+        "original_question": args.question,
+        "generated_at": datetime.now().isoformat(),
+        "slug": slugify(args.question),
+        "status": "plan_ready",
+        "sub_questions": [],
+        "notes": (
+            "The agent should populate sub_questions with 3-6 items. "
+            "Each item: {question, engine, priority, max_results, search_strategy}"
+        ),
+    }
+    save_json(plan, args.output)
+    print(f"Plan template saved to {args.output}")
+    print(f"Agent must now populate the sub_questions array and re-run.")
+
+
+# ── Subcommand: merge ────────────────────────────────────────────────────
+
+def cmd_merge(args):
+    """Merge and deduplicate search results from multiple subagent outputs."""
+    input_dir = Path(args.input_dir)
+    results = []
+    seen_urls = set()
+
+    for fpath in sorted(input_dir.glob("*.json")):
+        data = load_json(str(fpath))
+        items = data if isinstance(data, list) else data.get("results", data.get("items", []))
+        for item in items:
+            url = item.get("url", "") or item.get("link", "") or item.get("href", "")
+            if not url:
+                continue
+            norm_url = url.rstrip("/").lower()
+            if norm_url in seen_urls:
+                continue
+            seen_urls.add(norm_url)
+            results.append({
+                "title": item.get("title", "") or item.get("name", ""),
+                "url": url,
+                "snippet": item.get("snippet", "") or item.get("description", "") or "",
+                "source": item.get("source", fpath.stem),
+                "domain": domain(url),
+                "sub_question": item.get("sub_question", ""),
+            })
+
+    output = {
+        "total_urls": len(results),
+        "deduped_count": len(results),
+        "results": sorted(results, key=lambda r: r["url"]),
+        "generated_at": datetime.now().isoformat(),
+    }
+    save_json(output, args.output)
+    print(f"Merged {len(results)} unique results → {args.output}")
+
+
+# ── Subcommand: clean ────────────────────────────────────────────────────
+
+def cmd_clean(args):
+    """Normalize extracted text files into structured JSON records."""
+    input_dir = Path(args.input_dir)
+    ensure_dir(args.output)
+
+    records = []
+    for fpath in sorted(input_dir.rglob("*")):
+        if fpath.is_dir():
+            continue
+        text = fpath.read_text(encoding="utf-8", errors="replace")
+        # Strip excessive whitespace
+        lines = [l.strip() for l in text.split("\n")]
+        text = "\n".join(l for l in lines if l)
+        records.append({
+            "source_file": fpath.name,
+            "url": fpath.stem,  # Agent should write files named by URL-slug
+            "length_chars": len(text),
+            "length_words": len(text.split()),
+            "content": text,
+            "cleaned_at": datetime.now().isoformat(),
+        })
+
+    outpath = os.path.join(args.output, "cleaned.json")
+    save_json(records, outpath)
+    print(f"Cleaned {len(records)} extracts → {outpath}")
+
+
+# ── Subcommand: verify ───────────────────────────────────────────────────
+
+def cmd_verify(args):
+    """Cross-reference claims across cleaned extracts (structure for agent use)."""
+    cleaned_data = load_json(args.input)
+    # This prepares a verification skeleton — the agent (LLM) does the actual
+    # claim extraction and cross-referencing, then writes back.
+    sources = []
+    for rec in cleaned_data:
+        sources.append({
+            "url": rec.get("url", "unknown"),
+            "length_chars": rec.get("length_chars", 0),
+            "verified": False,
+            "claims_extracted": 0,
+        })
+
+    output = {
+        "total_sources": len(sources),
+        "sources": sources,
+        "verified_at": datetime.now().isoformat(),
+        "status": "ready_for_agent_verification",
+        "note": "Agent should read each source, extract claims, and annotate verified_at/confidence per claim.",
+    }
+    save_json(output, args.output)
+    print(f"Verification skeleton ({len(sources)} sources) → {args.output}")
+
+
+# ── Subcommand: synthesize ───────────────────────────────────────────────
+
+def cmd_synthesize(args):
+    """Generate the final brief.md + .provenance.md files."""
+    verified = load_json(args.verified)
+    output_dir = ensure_dir(args.output_dir)
+
+    slug = slugify(args.question)
+
+    # ── .provenance.md ───────────────────────────────────────────────────
+    prov_lines = [
+        f"# Provenance: {args.question}",
+        "",
+        f"**Research date:** {args.today}",
+        f"**Slug:** {slug}",
+        f"**Sources consulted:** {len(verified.get('sources', []))}",
+        "",
+        "## Sources",
+        "",
+    ]
+    for i, src in enumerate(verified.get("sources", []), 1):
+        prov_lines.append(f"{i}. **{src.get('url', 'unknown')}**")
+        prov_lines.append(f"   - Length: {src.get('length_chars', 0)} chars")
+        prov_lines.append(f"   - Claims extracted: {src.get('claims_extracted', 0)}")
+        if src.get("verified"):
+            prov_lines.append(f"   - ✓ Verified at: {src.get('verified_at', 'N/A')}")
+        else:
+            prov_lines.append(f"   - ○ Not yet verified")
+        prov_lines.append("")
+
+    prov_lines.extend([
+        "",
+        "## Methodology",
+        "",
+        "- **Stage 1 (Decompose):** Research question broken into focused sub-questions",
+        "- **Stage 2 (Gather):** Parallel search via DuckDuckGo MCP (free, no API key)",
+        "- **Stage 3 (Read):** Top URLs extracted via DuckDuckGo MCP fetch_content + browser_use",
+        "- **Stage 4 (Verify):** Claims cross-referenced across independent sources",
+        "- **Stage 5 (Synthesize):** This brief generated with full provenance tracking",
+        "",
+        f"*Generated by Omnibot Deep Research pipeline on {args.today}*",
+    ])
+
+    provenance_path = os.path.join(output_dir, ".provenance.md")
+    with open(provenance_path, "w") as f:
+        f.write("\n".join(prov_lines))
+    print(f"Provenance sidecar → {provenance_path}")
+
+    # ── brief.md ─────────────────────────────────────────────────────────
+    brief_lines = [
+        f"# Research Brief: {args.question}",
+        "",
+        f"**Date:** {args.today}  **Sources:** {len(verified.get('sources', []))}",
+        "",
+        "## Executive Summary",
+        "",
+        "*Agent: populate executive summary from verified claims here.*",
+        "",
+        "## Key Findings",
+        "",
+        "*Agent: organize findings by sub-question, each with [source: url] citations.*",
+        "",
+        "## Contradictions & Open Questions",
+        "",
+        "*Agent: list any conflicting claims across sources here.*",
+        "",
+        "## Gaps",
+        "",
+        "*Agent: note what wasn't found or needs more investigation.*",
+        "",
+        "## Follow-up Questions",
+        "",
+        "*Agent: suggest 2-3 questions the user could explore next.*",
+        "",
+        f"---",
+        f"*Generated by Omnibot Deep Research pipeline on {args.today}*",
+        f"*See [.provenance.md](.provenance.md) for full source list*",
+    ]
+
+    brief_path = os.path.join(output_dir, "brief.md")
+    with open(brief_path, "w") as f:
+        f.write("\n".join(brief_lines))
+    print(f"Cited brief → {brief_path}")
+
+    print(f"\nDone. Output in {output_dir}/")
+    print(f"  brief.md — the cited research brief (agent to fill findings)")
+    print(f"  .provenance.md — full source tracking")
+
+
+# ── CLI ──────────────────────────────────────────────────────────────────
+
+def main():
+    parser = argparse.ArgumentParser(description="Deep Research Pipeline")
+    sub = parser.add_subparsers(dest="command", required=True)
+
+    # decompose
+    p = sub.add_parser("decompose", help="Create research plan template")
+    p.add_argument("--question", required=True)
+    p.add_argument("--output", required=True)
+
+    # merge
+    p = sub.add_parser("merge", help="Merge & deduplicate search results")
+    p.add_argument("--input-dir", required=True)
+    p.add_argument("--output", required=True)
+
+    # clean
+    p = sub.add_parser("clean", help="Normalize extracted text")
+    p.add_argument("--input", required=True)
+    p.add_argument("--output", required=True)
+
+    # verify
+    p = sub.add_parser("verify", help="Prepare verification skeleton")
+    p.add_argument("--input", required=True)
+    p.add_argument("--output", required=True)
+
+    # synthesize
+    p = sub.add_parser("synthesize", help="Generate brief + provenance")
+    p.add_argument("--verified", required=True)
+    p.add_argument("--question", required=True)
+    p.add_argument("--output-dir", required=True)
+    p.add_argument("--today", default=datetime.now().strftime("%Y-%m-%d"))
+
+    # dag — Directed Acyclic Graph orchestration
+    p = sub.add_parser("dag", help="Execute sub-tasks with dependency graph")
+    p.add_argument("--plan", required=True, help="JSON file with tasks + dependencies")
+    p.add_argument("--output", default=None, help="Output execution report path")
+    p.add_argument("--task-timeout", type=int, default=120, help="Per-task timeout in seconds")
+    p.add_argument("--verbose", action="store_true", help="Print progress")
+
+    # ddg_search — DuckDuckGo MCP (free, no API key)
+    p = sub.add_parser("ddg_search", help="Search via DuckDuckGo MCP (free)")
+    p.add_argument("--query", required=True)
+    p.add_argument("--max-results", type=int, default=10)
+    p.add_argument("--region", default="wt-wt")
+    p.add_argument("--output", required=True)
+
+    # ddg_fetch — fetch page content via DuckDuckGo MCP
+    p = sub.add_parser("ddg_fetch", help="Fetch page content via DuckDuckGo MCP")
+    p.add_argument("--url", required=True)
+    p.add_argument("--max-length", type=int, default=8000)
+    p.add_argument("--output-dir", required=True)
+
+    args = parser.parse_args()
+
+    commands = {
+        "decompose": cmd_decompose,
+        "merge": cmd_merge,
+        "clean": cmd_clean,
+        "verify": cmd_verify,
+        "synthesize": cmd_synthesize,
+        "ddg_search": cmd_ddg_search,
+        "ddg_fetch": cmd_ddg_fetch,
+        "dag": cmd_dag,
+    }
+    commands[args.command](args)
+
+
+if __name__ == "__main__":
+    main()