Make stdio MCPs Editable

[grfwings]

Makes stdio MCP sources editable via the GUI.

I tried to match existing behavior so it should be pretty intuitive. After a STDIO MCP config is changed, we validate first with tool discovery (require successful tools/list), then if that succeeds run a transaction to remove policies scoped to the integration and update the integration config.

For legacy configs where there are no visible connections, connection org/default with template none and empty values will be created.

[greptile-apps]

Greptile Summary

This PR adds a full edit UI for stdio MCP sources, replacing the previous read-only view. When process-affecting fields change (command, args, env, cwd), the server runs a preflight tool-discovery check before committing the change in a transaction that also clears source-scoped policies, then does a best-effort tools refresh.

• New stdio-config.ts module centralises argument and env parsing/formatting with round-trip-safe serialisation for the edit form; EditMcpSource.tsx is upgraded from a read-only display to a fully editable StdioEdit component.
• Backend (plugin.ts) adds configureServer with preflight + transactional commit + best-effort refresh logic, plus a new refreshServerTools endpoint for retrying a stale tool cache.
• Semantic change to env: environment variables supplied via env on addServer are now stored as static plaintext config rather than being migrated into a credential connection, and the legacy reconcileStdioConnections migration path has been updated accordingly.

Confidence Score: 5/5

Safe to merge; both findings are edge-case UX gaps, not correctness or data-safety regressions.

The preflight → transaction → best-effort refresh pipeline is well-structured and thoroughly tested. Both findings are minor edge-case gaps that do not affect the primary edit flow.

packages/plugins/mcp/src/sdk/plugin.ts — the zero-connections branch of refreshStdioConnections; packages/plugins/mcp/src/react/EditMcpSource.tsx — the missing retry UI for toolsRefreshFailed.

Important Files Changed

Filename	Overview
packages/plugins/mcp/src/sdk/plugin.ts	Core configureServer logic added with preflight validation, policy removal, and best-effort tools refresh; zero-connections branch of refreshStdioConnections creates a connection but skips discoverTools.
packages/plugins/mcp/src/sdk/stdio-config.ts	New file providing parse/serialize helpers for stdio command args and env; round-trip correctness for single-quoted values is handled via canFormatStdioEnvValueBare identity check.
packages/plugins/mcp/src/react/EditMcpSource.tsx	StdioReadOnly replaced with a full StdioEdit form; refreshMcpServerTools atom is exported but no retry button is wired up in this component, leaving the 'retry' user message without a corresponding UI action.
packages/plugins/mcp/src/sdk/plugin.test.ts	Good new test coverage for configure + refresh flows, policy clearing, malformed config, missing secrets, and flaky-refresh retry scenarios.
packages/plugins/mcp/src/sdk/connection.ts	connectionFailure refactored to an options object and now emits the full command string in the error message for stdio connections.
packages/plugins/mcp/src/react/atoms.ts	refreshMcpServerTools atom added; not yet consumed by any component in this PR.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
    participant UI as StdioEdit (UI)
    participant API as configureServer API
    participant Plugin as mcpPlugin
    participant DB as Storage/Policies
    participant Proc as stdio subprocess

    UI->>API: POST /mcp/servers/:slug/config
    API->>Plugin: configureServer(slug, config)
    Plugin->>DB: get integration record
    DB-->>Plugin: current config

    alt process config unchanged
        Plugin->>DB: integrations.update(config)
        Plugin-->>API: toolsRefreshFailed false
    else process config changed
        Plugin->>Proc: preflightStdioConfig discoverTools
        Proc-->>Plugin: tools list OK or error
        alt preflight fails
            Plugin-->>API: error
            API-->>UI: 4xx
        else preflight OK
            Plugin->>DB: transaction removePolicies and update config
            DB-->>Plugin: committed
            Plugin->>Proc: refreshStdioConnections
            Proc-->>Plugin: OK or failure
            Plugin-->>API: toolsRefreshFailed true or false
            API-->>UI: 200
        end
    end

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sequenceDiagram
    participant UI as StdioEdit (UI)
    participant API as configureServer API
    participant Plugin as mcpPlugin
    participant DB as Storage/Policies
    participant Proc as stdio subprocess

    UI->>API: POST /mcp/servers/:slug/config
    API->>Plugin: configureServer(slug, config)
    Plugin->>DB: get integration record
    DB-->>Plugin: current config

    alt process config unchanged
        Plugin->>DB: integrations.update(config)
        Plugin-->>API: toolsRefreshFailed false
    else process config changed
        Plugin->>Proc: preflightStdioConfig discoverTools
        Proc-->>Plugin: tools list OK or error
        alt preflight fails
            Plugin-->>API: error
            API-->>UI: 4xx
        else preflight OK
            Plugin->>DB: transaction removePolicies and update config
            DB-->>Plugin: committed
            Plugin->>Proc: refreshStdioConnections
            Proc-->>Plugin: OK or failure
            Plugin-->>API: toolsRefreshFailed true or false
            API-->>UI: 200
        end
    end

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_{Reviews (5): Last reviewed commit: "Don't use lossy args.join for StdioEdit,..." | Re-trigger Greptile}