Fix MCP toolset prerequisites check

[feiskyer]

There are high chances of empty MCP tools when using remote MCP server.

This PR ensures MCP servers reload their tools even when previously failed by including MCP toolsets in prerequisites check regardless of status.

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All committers have signed the CLA.

[coderabbitai]

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Walkthrough

The cache collection logic in holmes/core/toolset_manager.py now collects enabled toolsets whose status is ENABLED or whose type is MCP, so MCP-typed toolsets are reloaded from cache even when their cached status is not ENABLED. An inline comment documents this behavior.

Changes

Cohort / File(s)	Summary
Toolset cache handling holmes/core/toolset_manager.py	Broadened condition when collecting enabled toolsets from cache: include toolsets that are enabled and either have status == ENABLED or type == MCP; added inline comment noting MCP prerequisite reload behavior.

Sequence Diagram(s)

sequenceDiagram
    autonumber
    actor Caller
    participant TM as ToolsetManager
    participant Cache
    participant TS as Toolset

    Caller->>TM: load_toolsets()
    TM->>Cache: get_cached_toolsets()
    Cache-->>TM: cached_toolsets

    loop per cached toolset t
        TM->>TM: is_enabled(t)?
        alt t.status == ENABLED or t.type == MCP
            note right of TM #E7F6E7: collect t into enabled_toolsets_from_cache
            TM->>TS: reload prerequisites / init_config as needed
            TS-->>TM: ready
        else
            TM->>TM: skip t
        end
    end

    TM-->>Caller: enabled_toolsets_from_cache

Loading

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Run prerequisite for each cache toolset #909 — Adjusts the same conditional in holmes/core/toolset_manager.py for cache collection, closely related to this MCP-inclusive change.
• fix(toolset): fix toolset config is not initialized when check prerequisites is not called #535 — Modifies load_toolset_with_status in toolset_manager.py around cached toolset prerequisite checks and init behavior.
• MCP toolset validation fixes #556 — Alters MCP-specific handling in toolset_manager.py (type preservation and YAML validation), related to MCP logic.

Suggested reviewers

• nherment
• aantn
• mainred

Pre-merge checks and finishing touches

✅ Passed checks (3 passed)

Check name	Status	Explanation
Title Check	✅ Passed	The title accurately and concisely summarizes the primary change by indicating that the PR fixes the prerequisites check specifically for MCP toolsets, and it avoids unnecessary detail or noise.
Description Check	✅ Passed	The description clearly explains the underlying issue with empty MCP tools when using a remote MCP server and how the PR modifies the prerequisites check to ensure MCP toolsets are reloaded even after failures, directly matching the changes in the code.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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[mainred]

Currently refresh toolsets happens when the first the user runs holmesgpt or specify refresh-toolsets, and mcp server is reachable, its status will be cached.
I think your case is mcp server is not reachable the first time we run hollmesgpt?

[feiskyer]

per my local test, the mcp endpoint is always reachable, but holmes failed to fetch its tool list. That's why I have this PR.
And holmes should retry here as well when last refresh has failed.