fix: accumulate multiple --allowedTools flags for Agent SDK (#719)

* fix: merge allowedTools from claudeArgs when using Agent SDK

When USE_AGENT_SDK=true, the allowedTools from claudeArgs (which contains
tag mode's required tools like mcp__github_comment__update_claude_comment)
were being lost because parseClaudeArgsToExtraArgs converts args to a
Record<string, string>, and the SDK was using sdkOptions.allowedTools
(from direct options) instead of merging with extraArgs.allowedTools.

This fix:
- Extracts allowedTools/disallowedTools from extraArgs after parsing
- Merges them with any direct options.allowedTools/disallowedTools
- Removes them from extraArgs to prevent duplicate CLI flags
- Passes the merged list as sdkOptions.allowedTools

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

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

* fix: accumulate multiple --allowedTools flags in claudeArgs

When tag mode adds its --allowedTools (with MCP tools) and the user also
provides --allowedTools in their claude_args, the parseClaudeArgsToExtraArgs
function was only keeping the last value. This caused tag mode's required
tools like mcp__github_comment__update_claude_comment to be lost.

Now allowedTools and disallowedTools flags accumulate their values when
they appear multiple times in claudeArgs, so both tag mode's tools and
user's tools are preserved.

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

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

---------

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

base-action/src/parse-sdk-options.ts

@@ -11,9 +11,13 @@ export type ParsedSdkOptions = {
   hasJsonSchema: boolean;
 };
 
+// Flags that should accumulate multiple values instead of overwriting
+const ACCUMULATING_FLAGS = new Set(["allowedTools", "disallowedTools"]);
+
 /**
  * Parse claudeArgs string into extraArgs record for SDK pass-through
  * The SDK/CLI will handle --mcp-config, --json-schema, etc.
+ * For allowedTools and disallowedTools, multiple occurrences are accumulated (comma-joined).
  */
 function parseClaudeArgsToExtraArgs(
   claudeArgs?: string,
@@ -33,7 +37,12 @@ function parseClaudeArgsToExtraArgs(
 
       // Check if next arg is a value (not another flag)
       if (nextArg && !nextArg.startsWith("--")) {
-        result[flag] = nextArg;
+        // For accumulating flags, join multiple values with commas
+        if (ACCUMULATING_FLAGS.has(flag) && result[flag]) {
+          result[flag] = `${result[flag]},${nextArg}`;
+        } else {
+          result[flag] = nextArg;
+        }
         i++; // Skip the value
       } else {
         result[flag] = null; // Boolean flag
@@ -59,6 +68,33 @@ export function parseSdkOptions(options: ClaudeOptions): ParsedSdkOptions {
   // Detect if --json-schema is present (for hasJsonSchema flag)
   const hasJsonSchema = "json-schema" in extraArgs;
 
+  // Extract and merge allowedTools from both sources:
+  // 1. From extraArgs (parsed from claudeArgs - contains tag mode's tools)
+  // 2. From options.allowedTools (direct input - may be undefined)
+  // This prevents duplicate flags being overwritten when claudeArgs contains --allowedTools
+  const extraArgsAllowedTools = extraArgs["allowedTools"]
+    ? extraArgs["allowedTools"].split(",").map((t) => t.trim())
+    : [];
+  const directAllowedTools = options.allowedTools
+    ? options.allowedTools.split(",").map((t) => t.trim())
+    : [];
+  const mergedAllowedTools = [
+    ...new Set([...extraArgsAllowedTools, ...directAllowedTools]),
+  ];
+  delete extraArgs["allowedTools"];
+
+  // Same for disallowedTools
+  const extraArgsDisallowedTools = extraArgs["disallowedTools"]
+    ? extraArgs["disallowedTools"].split(",").map((t) => t.trim())
+    : [];
+  const directDisallowedTools = options.disallowedTools
+    ? options.disallowedTools.split(",").map((t) => t.trim())
+    : [];
+  const mergedDisallowedTools = [
+    ...new Set([...extraArgsDisallowedTools, ...directDisallowedTools]),
+  ];
+  delete extraArgs["disallowedTools"];
+
   // Build custom environment
   const env: Record<string, string | undefined> = { ...process.env };
   if (process.env.INPUT_ACTION_INPUTS_PRESENT) {
@@ -77,22 +113,21 @@ export function parseSdkOptions(options: ClaudeOptions): ParsedSdkOptions {
     };
   }
 
-  // Build SDK options - use direct options for explicit inputs, extraArgs for claudeArgs pass-through
+  // Build SDK options - use merged tools from both direct options and claudeArgs
   const sdkOptions: SdkOptions = {
     // Direct options from ClaudeOptions inputs
     model: options.model,
     maxTurns: options.maxTurns ? parseInt(options.maxTurns, 10) : undefined,
-    allowedTools: options.allowedTools
+    allowedTools:
-      ? options.allowedTools.split(",").map((t) => t.trim())
+      mergedAllowedTools.length > 0 ? mergedAllowedTools : undefined,
-      : undefined,
+    disallowedTools:
-    disallowedTools: options.disallowedTools
+      mergedDisallowedTools.length > 0 ? mergedDisallowedTools : undefined,
-      ? options.disallowedTools.split(",").map((t) => t.trim())
-      : undefined,
     systemPrompt,
     fallbackModel: options.fallbackModel,
     pathToClaudeCodeExecutable: options.pathToClaudeCodeExecutable,
 
     // Pass through claudeArgs as extraArgs - CLI handles --mcp-config, --json-schema, etc.
+    // Note: allowedTools and disallowedTools have been removed from extraArgs to prevent duplicates
     extraArgs,
     env,
   };

base-action/test/parse-sdk-options.test.ts

@@ -0,0 +1,163 @@
+#!/usr/bin/env bun
+
+import { describe, test, expect } from "bun:test";
+import { parseSdkOptions } from "../src/parse-sdk-options";
+import type { ClaudeOptions } from "../src/run-claude";
+
+describe("parseSdkOptions", () => {
+  describe("allowedTools merging", () => {
+    test("should extract allowedTools from claudeArgs", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--allowedTools "Edit,Read,Write"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual(["Edit", "Read", "Write"]);
+      expect(result.sdkOptions.extraArgs?.["allowedTools"]).toBeUndefined();
+    });
+
+    test("should extract allowedTools from claudeArgs with MCP tools", () => {
+      const options: ClaudeOptions = {
+        claudeArgs:
+          '--allowedTools "Edit,Read,mcp__github_comment__update_claude_comment"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual([
+        "Edit",
+        "Read",
+        "mcp__github_comment__update_claude_comment",
+      ]);
+    });
+
+    test("should accumulate multiple --allowedTools flags from claudeArgs", () => {
+      // This simulates tag mode adding its tools, then user adding their own
+      const options: ClaudeOptions = {
+        claudeArgs:
+          '--allowedTools "Edit,Read,mcp__github_comment__update_claude_comment" --model "claude-3" --allowedTools "Bash(npm install),mcp__github__get_issue"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual([
+        "Edit",
+        "Read",
+        "mcp__github_comment__update_claude_comment",
+        "Bash(npm install)",
+        "mcp__github__get_issue",
+      ]);
+    });
+
+    test("should merge allowedTools from both claudeArgs and direct options", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--allowedTools "Edit,Read"',
+        allowedTools: "Write,Glob",
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual([
+        "Edit",
+        "Read",
+        "Write",
+        "Glob",
+      ]);
+    });
+
+    test("should deduplicate allowedTools when merging", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--allowedTools "Edit,Read"',
+        allowedTools: "Edit,Write",
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual(["Edit", "Read", "Write"]);
+    });
+
+    test("should use only direct options when claudeArgs has no allowedTools", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--model "claude-3-5-sonnet"',
+        allowedTools: "Edit,Read",
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toEqual(["Edit", "Read"]);
+    });
+
+    test("should return undefined allowedTools when neither source has it", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--model "claude-3-5-sonnet"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.allowedTools).toBeUndefined();
+    });
+
+    test("should remove allowedTools from extraArgs after extraction", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--allowedTools "Edit,Read" --model "claude-3-5-sonnet"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.extraArgs?.["allowedTools"]).toBeUndefined();
+      expect(result.sdkOptions.extraArgs?.["model"]).toBe("claude-3-5-sonnet");
+    });
+  });
+
+  describe("disallowedTools merging", () => {
+    test("should extract disallowedTools from claudeArgs", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--disallowedTools "Bash,Write"',
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.disallowedTools).toEqual(["Bash", "Write"]);
+      expect(result.sdkOptions.extraArgs?.["disallowedTools"]).toBeUndefined();
+    });
+
+    test("should merge disallowedTools from both sources", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: '--disallowedTools "Bash"',
+        disallowedTools: "Write",
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.disallowedTools).toEqual(["Bash", "Write"]);
+    });
+  });
+
+  describe("other extraArgs passthrough", () => {
+    test("should pass through mcp-config in extraArgs", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: `--mcp-config '{"mcpServers":{}}' --allowedTools "Edit"`,
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.extraArgs?.["mcp-config"]).toBe(
+        '{"mcpServers":{}}',
+      );
+    });
+
+    test("should pass through json-schema in extraArgs", () => {
+      const options: ClaudeOptions = {
+        claudeArgs: `--json-schema '{"type":"object"}'`,
+      };
+
+      const result = parseSdkOptions(options);
+
+      expect(result.sdkOptions.extraArgs?.["json-schema"]).toBe(
+        '{"type":"object"}',
+      );
+      expect(result.hasJsonSchema).toBe(true);
+    });
+  });
+});