docs: add AutoDL/Linux CLI deployment guide

[Jasper-Zhang-A]

Description

This PR adds an AutoDL/Linux CLI deployment guide and links it from the README so that cloud GPU users have an official, end-to-end checklist for running DeepCode’s CLI from source on a fresh Ubuntu instance.

Related Issues

• No explicit GitHub issue, but this addresses common friction points for new users on cloud GPU platforms (AutoDL-style environments) when:
  • Setting up Python venv + pip from source.
  • Installing Node + MCP servers (Brave Search, filesystem).
  • Wiring the configuration together for the CLI workflow.

Changes Made

• Added docs/autodl_cli_guide.md:

  • Step-by-step walkthrough for an AutoDL-like Ubuntu 22.04 environment:
    • Cloning HKUDS/DeepCode under /root.
    • Creating and activating a Python virtual environment.
    • Installing dependencies via requirements.txt.
    • Installing Node 20 via the official NodeSource repo.
    • Globally installing MCP servers:
      • @modelcontextprotocol/server-brave-search
      • @modelcontextprotocol/server-filesystem
    • Configuring mcp_agent.secrets.yaml with OpenAI/Anthropic/Brave keys (without committing secrets).
    • Running cli/main_cli.py in U/F/T modes.
  • Included an FAQ / common pitfalls section:
    • Brave path or API key issues.
    • venv activation problems.
    • npm global install permissions.
    • Non-JSON ResourceProcessor outputs and how the stricter JSON contract helps.

• Updated README.md:

  • Added a link in the CLI section pointing to docs/autodl_cli_guide.md, so:
    • The base config remains platform-agnostic.
    • Linux/AutoDL-specific overrides are documented in one place for users who need them.

Checklist

• Changes tested locally (guide followed on an AutoDL Ubuntu 22.04 instance)
• Code reviewed
• Documentation updated (this PR)
• Unit tests added (if applicable)

Additional Notes

Test environment for the new guide:

• OS: Ubuntu 22.04 (cloud GPU / AutoDL-style instance)
• Python: 3.10.x (virtualenv)
• Node: 20.x
• MCP: global Brave Search + filesystem servers installed via npm

Following the guide from a clean instance is sufficient to:

• Clone the repository,
• Set up Python and Node environments,
• Configure MCP servers and secrets,
• And run the CLI pipeline successfully in both URL and file modes.