docs: update README with non-interactive mode, new MCP tools, and agent tool list

[vitali87]

Document the new --ask-agent non-interactive CLI flag, add the four newly exposed MCP tools (shell_command, document_analyzer, semantic_search, get_function_source) to the tools list, and expand the agent tools section with analyze_document, semantic_search_functions, and get_function_source_by_id.

Dependency graph

Merge in this order:

pr-1: chore: update .gitignore with popular vibe-coding agent directories
pr-2: fix(llm): add retries to RAG orchestrator to handle output validation issues
├── pr-4: feat(mcp/tools): add shell_command, document_analyzer, semantic_search, and ask_agent tools to MCP registry
│   └── pr-5: feat(mcp/client): add MCP client CLI for querying the code graph via MCP server
│       └── pr-7: docs: update README with non-interactive mode, new MCP tools, and agent tool list  <-- this PR
└── pr-6: feat(main): add non-interactive --ask-agent mode to the CLI
    └── pr-7: docs: update README with non-interactive mode, new MCP tools, and agent tool list  <-- this PR
pr-3: feat(mcp/server): improve MCP server logging and suppress output during tool execution
└── pr-4: feat(mcp/tools): add shell_command, document_analyzer, semantic_search, and ask_agent tools to MCP registry
    └── pr-5: feat(mcp/client): add MCP client CLI for querying the code graph via MCP server
        └── pr-7: docs: update README with non-interactive mode, new MCP tools, and agent tool list  <-- this PR

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request updates the project's README.md to reflect recent feature additions, including a new non-interactive CLI mode and several new tools for the MCP and agent functionalities. The changes aim to provide comprehensive and up-to-date documentation for users interacting with the codebase RAG system.

Highlights

• Non-interactive CLI mode: The README now includes instructions and an example for using the new --ask-agent flag for single, non-interactive queries.
• New MCP Tools: Four new MCP tools (shell_command, document_analyzer, semantic_search, get_function_source) have been added to the documented list of available tools.
• Expanded Agent Tools: The agent tools section has been updated to include analyze_document, semantic_search_functions, and get_function_source_by_id, providing more detail on their functionality.

Changelog

• README.md
  • Added a section detailing the non-interactive mode for the RAG CLI, including an example.
  • Updated the list of available MCP tools to include shell_command, document_analyzer, semantic_search, and get_function_source.
  • Expanded the agent tools section with descriptions for analyze_document, semantic_search_functions, and get_function_source_by_id.

Activity

• The pull request was created to update documentation.
• No human comments or reviews have been recorded yet.

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[gemini-code-assist]

Code Review

The pull request updates the README to document new features. The documentation for the new agent tools seems correct based on the provided code. However, there are a couple of inconsistencies with the code in this branch for other documented features. Specifically, the --ask-agent CLI flag and the new MCP tools are documented but do not appear to be implemented in the provided code context. This could be because the features are in other PRs, but it makes the documentation incorrect for the current state of this branch. I've left specific comments on these sections.

[gemini-code-assist]

The documentation introduces the --ask-agent flag for non-interactive mode. However, based on the provided codebase_rag/main.py file, the start command does not have this option defined. This makes the documentation inconsistent with the current state of the code in this branch. Please ensure the feature is included in this PR or that this documentation is merged only after the corresponding feature PR.

[gemini-code-assist]

This change adds several new tools to the MCP server's available tools list. However, in the provided codebase_rag/mcp/tools.py file, these tools (shell_command, document_analyzer, semantic_search, get_function_source) are not registered in the MCPToolsRegistry. This makes the documentation inconsistent with the code in this branch.

Additionally, there seems to be a naming inconsistency. The agent tools for similar functionalities are named execute_shell_command, analyze_document, semantic_search_functions, and get_function_source_by_id. It would be good to ensure the MCP tool names are consistent or that the difference is intentional and clear.

Please ensure the tool registration is part of this PR or that this documentation is merged after the feature is implemented and the names are confirmed.

[greptile-apps]

Greptile Summary

This PR updates the README with documentation for three new features:

• Non-interactive mode: Documents the --ask-agent CLI flag for single-query execution (useful for scripting)
• MCP tools: Adds 4 new tools to the MCP tools list (shell_command, document_analyzer, semantic_search, get_function_source)
• Agent tools: Adds 3 new tools to the agent tools section (analyze_document, semantic_search_functions, get_function_source_by_id)

The documentation is clear, well-structured, and accurate. Agent tool names were verified against the actual implementation in codebase_rag/tools/. The --ask-agent flag and MCP tools will be added in dependent PRs #6 and #4 respectively, as shown in the dependency graph.

Confidence Score: 5/5

• This PR is safe to merge with no risk - documentation-only changes that are accurate and well-written
• Documentation is clear, accurate, and follows consistent formatting. Agent tool names verified against actual implementation. Depends on PRs Chore/cleanup #4 and Add embeddings? #6 for features being documented, but this is intentional per the dependency graph.
• No files require special attention

Important Files Changed

Filename	Overview
README.md	Documentation updates for non-interactive CLI mode and new MCP/agent tools - clear, accurate, and well-structured

_{Last reviewed commit: b269054}