Implementated selective disable of tools to spare with the schema size

[kecsap]

Implements #1022

[github-actions]

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[greptile-apps]

Greptile Summary

This PR adds selective tool disabling to the MCP server: a disabledTools string array in config.mcp is normalized (prefix-stripped, lowercased) and used to filter the tool list returned by ListTools and to gate execution in CallTool. Both single- and multi-repo modes are handled, and the feature is covered by new unit tests.

Confidence Score: 4/5

Safe to merge — the feature is well-tested and the two P2 findings are non-blocking style/ordering nits.

Only P2 findings present: a guard ordering issue that can cause a misleading error message for disabled tools in multi-repo mode, and a type-vs-runtime alignment gap for the optional field. No correctness bugs in the happy path.

src/mcp/server.ts (guard ordering) and src/types.ts (optional field typing)

Important Files Changed

Filename	Overview
src/mcp/tool-registry.ts	Adds buildDisabledToolSet and normalizeToolName helpers; updates buildToolList to accept and apply a disabled-tools list with prefix-stripping support.
src/mcp/server.ts	Reads disabledTools from config, passes enabled tool set to both the list and call handlers; disabled-tool guard runs after validateMultiRepoAccess (ordering issue flagged).
src/types.ts	Adds disabledTools: string[] to CodegraphConfig.mcp; should be optional to match the defensive runtime handling in server.ts.
src/infrastructure/config.ts	Adds disabledTools: [] as string[] to the DEFAULTS object so the field is always present after config merge.
tests/unit/mcp.test.ts	Adds unit tests for disabled-tool filtering in both single- and multi-repo modes, and an integration-style test verifying both list and call handlers respect disabledTools.
tests/unit/config.test.ts	Adds a simple assertion that DEFAULTS.mcp.disabledTools is an empty array.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[startMCPServer] --> B[loadConfig]
    B --> C{config.mcp.disabledTools?}
    C -->|yes| D[buildDisabledToolSet\nnormalize + lowercase + strip prefix]
    C -->|no| E[empty disabled set]
    D --> F[buildToolList multiRepo disabledTools]
    E --> F
    F --> G[filter BASE_TOOLS via includeTool]
    G --> H{multiRepo?}
    H -->|yes| I[add REPO_PROP to each tool\nconditionally add LIST_REPOS_TOOL]
    H -->|no| J[return baseTools only]
    I --> K[enabledTools]
    J --> K
    K --> L[enabledToolNames = new Set of tool names]
    L --> M[ListTools handler returns enabledTools]
    L --> N[CallTool handler]
    N --> O[validateMultiRepoAccess]
    O --> P{enabledToolNames.has name?}
    P -->|no| Q[return Unknown tool error]
    P -->|yes| R[dispatch to TOOL_HANDLERS]

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_{Reviews (1): Last reviewed commit: "Implementated selective disable of tools..." | Re-trigger Greptile}

[greptile-apps]

validateMultiRepoAccess runs before disabled-tool guard

validateMultiRepoAccess is called on line 171 before the enabledToolNames check on line 173. In multi-repo mode, if a caller omits the required repo argument when invoking a disabled tool, the handler will throw a multi-repo access error instead of returning the expected "Unknown tool: <name>" response. Swapping the two checks keeps the disabled-tool path clean.

Suggested change

	validateMultiRepoAccess(multiRepo, name, args);
	if (!enabledToolNames.has(name)) {
	return { content: [{ type: 'text', text: `Unknown tool: ${name}` }], isError: true };
	}
	if (!enabledToolNames.has(name)) {
	return { content: [{ type: 'text', text: `Unknown tool: ${name}` }], isError: true };
	}
	validateMultiRepoAccess(multiRepo, name, args);

[greptile-apps]

disabledTools typed as required but treated optionally at runtime

disabledTools: string[] is non-optional in CodegraphConfig, yet server.ts guards it with config.mcp?.disabledTools ? … : undefined. Any user-supplied config that includes an mcp block without disabledTools (e.g., configs predating this PR) will satisfy the type only because deep-merge with DEFAULTS fills the gap — but if the merge is ever a shallow spread the field can be absent at runtime while TypeScript believes it is always present. Making it optional (disabledTools?: string[]) would align the type with the actual runtime handling and avoid surprising TypeScript errors for callers that construct a partial CodegraphConfig.

Suggested change

	mcp: {
	defaults: McpDefaults;
	disabledTools: string[];
	};
	mcp: {
	defaults: McpDefaults;
	disabledTools?: string[];
	};

[kecsap]

I have read the CLA Document and I hereby sign the CLA