fix: only load GitHub MCP server when its tools are allowed (#124)

* fix: only load GitHub MCP server when its tools are allowed

- Add allowedTools parameter to prepareMcpConfig
- Check for mcp__github__ and mcp__github_file_ops__ tool prefixes
- Only include MCP servers when their tools are in allowed_tools
- Maintain backward compatibility when allowed_tools is not specified
- Update tests to reflect the new conditional loading behavior

This optimizes resource usage by not loading unnecessary MCP servers
when their tools are not allowed in the configuration.

Co-authored-by: ashwin-ant <ashwin-ant@users.noreply.github.com>

* fix: always load github_file_ops server regardless of allowed_tools

- Only apply conditional loading to the github MCP server
- Always load github_file_ops server as it contains essential tools
- Update tests to reflect this behavior

Co-authored-by: ashwin-ant <ashwin-ant@users.noreply.github.com>

* refactor: move allowedTools/disallowedTools parsing to parseGitHubContext

- Change allowedTools and disallowedTools from string to string[] in ParsedGitHubContext type
- Parse comma-separated environment variables into arrays in parseGitHubContext function
- Update create-prompt and install-mcp-server to use pre-parsed arrays
- Update all affected test files to use array syntax
- Eliminate duplicate parsing logic across the codebase

* style: apply prettier formatting

---------

Co-authored-by: claude[bot] <209825114+claude[bot]@users.noreply.github.com>
Co-authored-by: ashwin-ant <ashwin-ant@users.noreply.github.com>

src/create-prompt/index.ts

@@ -35,38 +35,35 @@ const BASE_ALLOWED_TOOLS = [
 ];
 const DISALLOWED_TOOLS = ["WebSearch", "WebFetch"];
 
-export function buildAllowedToolsString(customAllowedTools?: string): string {
+export function buildAllowedToolsString(customAllowedTools?: string[]): string {
   let baseTools = [...BASE_ALLOWED_TOOLS];
 
   let allAllowedTools = baseTools.join(",");
-  if (customAllowedTools) {
+  if (customAllowedTools && customAllowedTools.length > 0) {
-    allAllowedTools = `${allAllowedTools},${customAllowedTools}`;
+    allAllowedTools = `${allAllowedTools},${customAllowedTools.join(",")}`;
   }
   return allAllowedTools;
 }
 
 export function buildDisallowedToolsString(
-  customDisallowedTools?: string,
+  customDisallowedTools?: string[],
-  allowedTools?: string,
+  allowedTools?: string[],
 ): string {
   let disallowedTools = [...DISALLOWED_TOOLS];
 
   // If user has explicitly allowed some hardcoded disallowed tools, remove them from disallowed list
-  if (allowedTools) {
+  if (allowedTools && allowedTools.length > 0) {
-    const allowedToolsArray = allowedTools
-      .split(",")
-      .map((tool) => tool.trim());
     disallowedTools = disallowedTools.filter(
-      (tool) => !allowedToolsArray.includes(tool),
+      (tool) => !allowedTools.includes(tool),
     );
   }
 
   let allDisallowedTools = disallowedTools.join(",");
-  if (customDisallowedTools) {
+  if (customDisallowedTools && customDisallowedTools.length > 0) {
     if (allDisallowedTools) {
-      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools}`;
+      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools.join(",")}`;
     } else {
-      allDisallowedTools = customDisallowedTools;
+      allDisallowedTools = customDisallowedTools.join(",");
     }
   }
   return allDisallowedTools;
@@ -120,8 +117,10 @@ export function prepareContext(
     triggerPhrase,
     ...(triggerUsername && { triggerUsername }),
     ...(customInstructions && { customInstructions }),
-    ...(allowedTools && { allowedTools }),
+    ...(allowedTools.length > 0 && { allowedTools: allowedTools.join(",") }),
-    ...(disallowedTools && { disallowedTools }),
+    ...(disallowedTools.length > 0 && {
+      disallowedTools: disallowedTools.join(","),
+    }),
     ...(directPrompt && { directPrompt }),
     ...(claudeBranch && { claudeBranch }),
   };
@@ -636,11 +635,11 @@ export async function createPrompt(
 
     // Set allowed tools
     const allAllowedTools = buildAllowedToolsString(
-      preparedContext.allowedTools,
+      context.inputs.allowedTools,
     );
     const allDisallowedTools = buildDisallowedToolsString(
-      preparedContext.disallowedTools,
+      context.inputs.disallowedTools,
-      preparedContext.allowedTools,
+      context.inputs.allowedTools,
     );
 
     core.exportVariable("ALLOWED_TOOLS", allAllowedTools);

src/entrypoints/prepare.ts

@@ -92,6 +92,7 @@ async function run() {
       branch: branchInfo.currentBranch,
       additionalMcpConfig,
       claudeCommentId: commentId.toString(),
+      allowedTools: context.inputs.allowedTools,
     });
     core.setOutput("mcp_config", mcpConfig);
   } catch (error) {

src/github/context.ts

@@ -28,8 +28,8 @@ export type ParsedGitHubContext = {
   inputs: {
     triggerPhrase: string;
     assigneeTrigger: string;
-    allowedTools: string;
+    allowedTools: string[];
-    disallowedTools: string;
+    disallowedTools: string[];
     customInstructions: string;
     directPrompt: string;
     baseBranch?: string;
@@ -52,8 +52,14 @@ export function parseGitHubContext(): ParsedGitHubContext {
     inputs: {
       triggerPhrase: process.env.TRIGGER_PHRASE ?? "@claude",
       assigneeTrigger: process.env.ASSIGNEE_TRIGGER ?? "",
-      allowedTools: process.env.ALLOWED_TOOLS ?? "",
+      allowedTools: (process.env.ALLOWED_TOOLS ?? "")
-      disallowedTools: process.env.DISALLOWED_TOOLS ?? "",
+        .split(",")
+        .map((tool) => tool.trim())
+        .filter((tool) => tool.length > 0),
+      disallowedTools: (process.env.DISALLOWED_TOOLS ?? "")
+        .split(",")
+        .map((tool) => tool.trim())
+        .filter((tool) => tool.length > 0),
       customInstructions: process.env.CUSTOM_INSTRUCTIONS ?? "",
       directPrompt: process.env.DIRECT_PROMPT ?? "",
       baseBranch: process.env.BASE_BRANCH,

src/mcp/install-mcp-server.ts

@@ -7,6 +7,7 @@ type PrepareConfigParams = {
   branch: string;
   additionalMcpConfig?: string;
   claudeCommentId?: string;
+  allowedTools: string[];
 };
 
 export async function prepareMcpConfig(
@@ -19,24 +20,17 @@ export async function prepareMcpConfig(
     branch,
     additionalMcpConfig,
     claudeCommentId,
+    allowedTools,
   } = params;
   try {
-    const baseMcpConfig = {
+    const allowedToolsList = allowedTools || [];
+
+    const hasGitHubMcpTools = allowedToolsList.some((tool) =>
+      tool.startsWith("mcp__github__"),
+    );
+
+    const baseMcpConfig: { mcpServers: Record<string, unknown> } = {
       mcpServers: {
-        github: {
-          command: "docker",
-          args: [
-            "run",
-            "-i",
-            "--rm",
-            "-e",
-            "GITHUB_PERSONAL_ACCESS_TOKEN",
-            "ghcr.io/github/github-mcp-server:sha-e9f748f", // https://github.com/github/github-mcp-server/releases/tag/v0.4.0
-          ],
-          env: {
-            GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,
-          },
-        },
         github_file_ops: {
           command: "bun",
           args: [
@@ -57,6 +51,23 @@ export async function prepareMcpConfig(
       },
     };
 
+    if (hasGitHubMcpTools) {
+      baseMcpConfig.mcpServers.github = {
+        command: "docker",
+        args: [
+          "run",
+          "-i",
+          "--rm",
+          "-e",
+          "GITHUB_PERSONAL_ACCESS_TOKEN",
+          "ghcr.io/github/github-mcp-server:sha-e9f748f", // https://github.com/github/github-mcp-server/releases/tag/v0.4.0
+        ],
+        env: {
+          GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,
+        },
+      };
+    }
+
     // Merge with additional MCP config if provided
     if (additionalMcpConfig && additionalMcpConfig.trim()) {
       try {

test/create-prompt.test.ts

@@ -652,7 +652,7 @@ describe("buildAllowedToolsString", () => {
   });
 
   test("should append custom tools when provided", () => {
-    const customTools = "Tool1,Tool2,Tool3";
+    const customTools = ["Tool1", "Tool2", "Tool3"];
     const result = buildAllowedToolsString(customTools);
 
     // Base tools should be present
@@ -683,7 +683,7 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should append custom disallowed tools when provided", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
     const result = buildDisallowedToolsString(customDisallowedTools);
 
     // Base disallowed tools should be present
@@ -701,8 +701,8 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should remove hardcoded disallowed tools if they are in allowed tools", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
-    const allowedTools = "WebSearch,SomeOtherTool";
+    const allowedTools = ["WebSearch", "SomeOtherTool"];
     const result = buildDisallowedToolsString(
       customDisallowedTools,
       allowedTools,
@@ -720,7 +720,7 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should remove all hardcoded disallowed tools if they are all in allowed tools", () => {
-    const allowedTools = "WebSearch,WebFetch,SomeOtherTool";
+    const allowedTools = ["WebSearch", "WebFetch", "SomeOtherTool"];
     const result = buildDisallowedToolsString(undefined, allowedTools);
 
     // Both hardcoded disallowed tools should be removed
@@ -732,8 +732,8 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should handle custom disallowed tools when all hardcoded tools are overridden", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
-    const allowedTools = "WebSearch,WebFetch";
+    const allowedTools = ["WebSearch", "WebFetch"];
     const result = buildDisallowedToolsString(
       customDisallowedTools,
       allowedTools,

test/install-mcp-server.test.ts

@@ -24,21 +24,19 @@ describe("prepareMcpConfig", () => {
     processExitSpy.mockRestore();
   });
 
-  test("should return base config when no additional config is provided", async () => {
+  test("should return base config when no additional config is provided and no allowed_tools", async () => {
     const result = await prepareMcpConfig({
       githubToken: "test-token",
       owner: "test-owner",
       repo: "test-repo",
       branch: "test-branch",
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
-    expect(parsed.mcpServers.github.env.GITHUB_PERSONAL_ACCESS_TOKEN).toBe(
-      "test-token",
-    );
     expect(parsed.mcpServers.github_file_ops.env.GITHUB_TOKEN).toBe(
       "test-token",
     );
@@ -49,6 +47,60 @@ describe("prepareMcpConfig", () => {
     );
   });
 
+  test("should include github MCP server when mcp__github__ tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.github.env.GITHUB_PERSONAL_ACCESS_TOKEN).toBe(
+      "test-token",
+    );
+  });
+
+  test("should not include github MCP server when only file_ops tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [
+        "mcp__github_file_ops__commit_files",
+        "mcp__github_file_ops__update_claude_comment",
+      ],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should include file_ops server even when no GitHub tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: ["Edit", "Read", "Write"],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
   test("should return base config when additional config is empty string", async () => {
     const result = await prepareMcpConfig({
       githubToken: "test-token",
@@ -56,11 +108,12 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: "",
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
     expect(consoleWarningSpy).not.toHaveBeenCalled();
   });
@@ -72,11 +125,12 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: "   \n\t  ",
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
     expect(consoleWarningSpy).not.toHaveBeenCalled();
   });
@@ -100,6 +154,10 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
     });
 
     const parsed = JSON.parse(result);
@@ -133,6 +191,10 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
     });
 
     const parsed = JSON.parse(result);
@@ -169,12 +231,13 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(parsed.customProperty).toBe("custom-value");
     expect(parsed.anotherProperty).toEqual({ nested: "value" });
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.custom_server).toBeDefined();
   });
 
@@ -187,13 +250,14 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: invalidJson,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(consoleWarningSpy).toHaveBeenCalledWith(
       expect.stringContaining("Failed to parse additional MCP config:"),
     );
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
   });
 
@@ -206,6 +270,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: nonObjectJson,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
@@ -215,7 +280,7 @@ describe("prepareMcpConfig", () => {
     expect(consoleWarningSpy).toHaveBeenCalledWith(
       expect.stringContaining("MCP config must be a valid JSON object"),
     );
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
   });
 
@@ -228,6 +293,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: nullJson,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
@@ -237,7 +303,7 @@ describe("prepareMcpConfig", () => {
     expect(consoleWarningSpy).toHaveBeenCalledWith(
       expect.stringContaining("MCP config must be a valid JSON object"),
     );
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
   });
 
@@ -250,6 +316,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: arrayJson,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
@@ -258,7 +325,7 @@ describe("prepareMcpConfig", () => {
     expect(consoleInfoSpy).toHaveBeenCalledWith(
       "Merging additional MCP server configuration with built-in servers",
     );
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
     // The array will be spread into the config (0: 1, 1: 2, 2: 3)
     expect(parsed[0]).toBe(1);
@@ -295,12 +362,13 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers.server1).toBeDefined();
     expect(parsed.mcpServers.server2).toBeDefined();
-    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
     expect(parsed.mcpServers.github_file_ops.command).toBe("overridden");
     expect(parsed.mcpServers.github_file_ops.env.CUSTOM).toBe("value");
     expect(parsed.otherConfig.nested.deeply).toBe("value");
@@ -315,6 +383,7 @@ describe("prepareMcpConfig", () => {
       owner: "test-owner",
       repo: "test-repo",
       branch: "test-branch",
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);
@@ -334,6 +403,7 @@ describe("prepareMcpConfig", () => {
       owner: "test-owner",
       repo: "test-repo",
       branch: "test-branch",
+      allowedTools: [],
     });
 
     const parsed = JSON.parse(result);

test/mockContext.ts

@@ -11,8 +11,8 @@ const defaultInputs = {
   triggerPhrase: "/claude",
   assigneeTrigger: "",
   anthropicModel: "claude-3-7-sonnet-20250219",
-  allowedTools: "",
+  allowedTools: [] as string[],
-  disallowedTools: "",
+  disallowedTools: [] as string[],
   customInstructions: "",
   directPrompt: "",
   useBedrock: false,

test/permissions.test.ts

@@ -62,8 +62,8 @@ describe("checkWritePermissions", () => {
     inputs: {
       triggerPhrase: "@claude",
       assigneeTrigger: "",
-      allowedTools: "",
+      allowedTools: [],
-      disallowedTools: "",
+      disallowedTools: [],
       customInstructions: "",
       directPrompt: "",
     },

test/prepare-context.test.ts

@@ -242,7 +242,7 @@ describe("parseEnvVarsWithContext", () => {
         ...mockPullRequestCommentContext,
         inputs: {
           ...mockPullRequestCommentContext.inputs,
-          allowedTools: "Tool1,Tool2",
+          allowedTools: ["Tool1", "Tool2"],
         },
       });
       const result = prepareContext(contextWithAllowedTools, "12345");

test/trigger-validation.test.ts

@@ -30,8 +30,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "/claude",
           assigneeTrigger: "",
           directPrompt: "Fix the bug in the login form",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -56,8 +56,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "/claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -228,8 +228,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -255,8 +255,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -282,8 +282,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });