enable track_progress for comments, fix mcp config (#558)

* enable track_progress for comments

* refactor: pass mode explicitly to prepareMcpConfig

Update prepareMcpConfig to receive the mode parameter from its callers
instead of detecting agent mode by checking context.inputs.prompt.
This makes mode determination explicit and controlled by the caller.

Also update all test cases to include the required mode parameter
and fix agent mode test expectations to match new behavior where
MCP config is only included when tools are explicitly allowed.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* fix test

---------

Co-authored-by: Claude <noreply@anthropic.com>

test/install-mcp-server.test.ts

@@ -85,6 +85,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -106,6 +107,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContextWithSigning,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -129,6 +131,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: ["mcp__github__create_issue", "mcp__github__create_pr"],
       context: mockContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -149,6 +152,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: ["mcp__github_inline_comment__create_inline_comment"],
       context: mockPRContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -169,6 +173,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -189,6 +194,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContextWithSigning,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -208,6 +214,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContextWithSigning,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -225,6 +232,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockPRContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -244,6 +252,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);
@@ -261,6 +270,7 @@ describe("prepareMcpConfig", () => {
       baseBranch: "main",
       allowedTools: [],
       context: mockPRContext,
+      mode: "tag",
     });
 
     const parsed = JSON.parse(result);

test/modes/agent.test.ts

@@ -162,11 +162,11 @@ describe("Agent Mode", () => {
       githubToken: "test-token",
     });
 
-    // Verify claude_args includes MCP config and user args
+    // Verify claude_args includes user args (no MCP config in agent mode without allowed tools)
     const callArgs = setOutputSpy.mock.calls[0];
     expect(callArgs[0]).toBe("claude_args");
-    expect(callArgs[1]).toContain("--mcp-config");
-    expect(callArgs[1]).toContain("--model claude-sonnet-4 --max-turns 10");
+    expect(callArgs[1]).toBe("--model claude-sonnet-4 --max-turns 10");
+    expect(callArgs[1]).not.toContain("--mcp-config");
 
     // Verify return structure - should use "main" as fallback when no env vars set
     expect(result).toEqual({