Add MCP tool integration to customization guide

[PicoNVIDIA]

Summary

• Add docs/source/customization/mcp-tools.md documenting how to add external tools through MCP
• Add example config configs/config_web_frag_mcp.yml showing MCP tool integration with the deep researcher
• Add MCP link to the customization index page

Covers non-authenticated MCP tools via mcp_tool_wrapper and mcp_client. Notes that authenticated MCP (OAuth2 pass-through) and UI support for MCP tools are planned for future releases.

[greptile-apps]

Greptile Summary

This PR adds MCP (Model Context Protocol) tool integration to the AIQ Blueprint customization guide, introducing a new documentation page (mcp-tools.md), a working example config (configs/config_web_frag_mcp.yml), and an index entry. The changes are well-structured and the config correctly addresses issues from earlier review rounds (using max_tool_iterations and keeping paper_search_tool commented out). A few documentation accuracy issues remain:

• The Step 2 tutorial snippet in mcp-tools.md explicitly lists paper_search_tool in agent tool lists without any comment noting it is optional and requires SERPER_API_KEY — copy-pasting the snippet as-is will produce a runtime error for users who have not defined that function.
• The mcp_client section (line 106) claims all discovered tools become available via the function group name in agents' tools lists, but this may be inaccurate — individual tool names from the MCP server are typically what must be referenced, not the group name.
• The clarifier_agent is wired up with the MCP tool in the example config but is omitted from the Step 2 documentation snippet, creating an inconsistency between the guide and the reference config.

Confidence Score: 3/5

• The config changes are safe; the documentation has a few accuracy gaps that could mislead users into broken configurations.
• The config file correctly incorporates feedback from previous review rounds and is functionally sound. However, the documentation page contains a snippet that references paper_search_tool without qualification, a potentially inaccurate description of how mcp_client group names are used in agents' tool lists, and an omission of clarifier_agent from the step-by-step guide. These are documentation issues that could cause user-facing errors if followed literally.
• docs/source/customization/mcp-tools.md — Step 2 snippet and mcp_client section need accuracy review before publication.

Important Files Changed

Filename	Overview
configs/config_web_frag_mcp.yml	New example config extending config_web_frag.yml with an MCP tool via mcp_tool_wrapper; paper_search_tool is correctly kept commented out, and max_tool_iterations is correctly set on shallow_research_agent.
docs/source/customization/mcp-tools.md	New documentation for MCP tool integration; Step 2 snippet references paper_search_tool without noting its optional/gated nature, mcp_client group-name referencing description may be inaccurate, and clarifier_agent is missing from the Step 2 example.
docs/source/customization/index.md	Adds a link to the new mcp-tools.md page in the customization index; straightforward and correctly placed.

Sequence Diagram

sequenceDiagram
    participant User
    participant DeepResearcher as Deep Researcher Agent
    participant IntentClassifier as Intent Classifier
    participant MCPToolWrapper as mcp_tool_wrapper
    participant MCPServer as External MCP Server

    User->>DeepResearcher: Research query
    DeepResearcher->>IntentClassifier: Route query to appropriate tools
    IntentClassifier-->>DeepResearcher: Selected tools (incl. mcp_financial_data)
    DeepResearcher->>MCPToolWrapper: Invoke mcp_financial_data tool
    MCPToolWrapper->>MCPServer: HTTP/SSE request (get_financial_data)
    MCPServer-->>MCPToolWrapper: Tool response (financial data)
    MCPToolWrapper-->>DeepResearcher: Parsed tool result
    DeepResearcher-->>User: Research response with financial data

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Comments Outside Diff (3)

1. docs/source/customization/mcp-tools.md, line 48-71 (link)

   paper_search_tool referenced in Step 2 snippet without prerequisite note

   The Step 2 code block references paper_search_tool in both the intent_classifier and deep_research_agent tool lists — but paper_search_tool is commented out by default (it requires SERPER_API_KEY). If a reader copies this snippet as written, they will reference an undefined function and get a startup error.

   The actual example config (configs/config_web_frag_mcp.yml) correctly keeps paper_search_tool commented out in both agent tool lists. The tutorial snippet should match that pattern or at minimum add a comment noting the dependency:

     intent_classifier:
       _type: intent_classifier
       tools:
         - web_search_tool
         # - paper_search_tool  # Uncomment if SERPER_API_KEY is set and function is defined
         - knowledge_search
         - mcp_financial_data
   
     ...
   
     deep_research_agent:
       _type: deep_research_agent
       tools:
         # - paper_search_tool  # Uncomment if SERPER_API_KEY is set and function is defined
         - advanced_web_search_tool
         - knowledge_search
         - mcp_financial_data

2. docs/source/customization/mcp-tools.md, line 106 (link)

   Potentially inaccurate description of mcp_client tool referencing

   The sentence states: "All tools served by that MCP server become available using the function group name (financial_tools) in the agents' tools lists."

   This implies agents would write - financial_tools in their tools list to get access. However, with mcp_client, tools from the MCP server are typically registered under their individual tool names (as reported by the MCP server), not under the function group name. A user following this guidance literally may be surprised to find that - financial_tools does not resolve to a usable tool.

   If the group name IS the correct handle to use in tools lists for mcp_client, a concrete example showing exactly that usage would prevent confusion:

     shallow_research_agent:
       _type: shallow_research_agent
       tools:
         - web_search_tool
         - financial_tools   # references the entire mcp_client group

   If instead each discovered tool must be referenced by its original MCP server name, this section should clearly state that and show an example.

3. docs/source/customization/mcp-tools.md, line 43-45 (link)

   clarifier_agent absent from Step 2 snippet

   The example config (configs/config_web_frag_mcp.yml) also adds mcp_financial_data to the clarifier_agent tools list, but this agent is entirely omitted from the Step 2 tutorial snippet. A user following the guide to configure their own clarifier_agent may miss this and end up with an inconsistent setup where the clarifier cannot access the MCP tool while all other agents can.

   Consider adding the clarifier_agent block to the snippet for completeness.

_{Last reviewed commit: 0356dcd}

[AjayThorve]

LGTM

[AjayThorve]

LGTM

[AjayThorve]

@PicoNVIDIA nemotron-super needs to be set for the nemotron_llm_deep config, check other configs in the develop branch