Summary

The parseAllowedTools() function in src/modes/agent/parse-tools.ts only extracts tools from the first --allowed-tools flag, ignoring any subsequent flags. This causes GitHub MCP servers (like github_inline_comment) to not initialize when users specify multiple --allowed-tools flags in their claude_args.

Reproduction

1. Configure a workflow with multiple --allowed-tools flags:

claude_args: |
  --allowed-tools 'mcp__context7__*'
  --allowed-tools 'Read,Glob,Grep,LS'
  --allowed-tools 'mcp__github_inline_comment__create_inline_comment'

2. Trigger Claude via a PR comment

3. Observe that:

   • mcp__github_inline_comment__create_inline_comment appears in final allowedTools array ✅
   • But github_inline_comment MCP server is NOT initialized ❌

Root Cause

In src/modes/agent/parse-tools.ts:

export function parseAllowedTools(claudeArgs: string): string[] {
  const patterns = [
    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/,
    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/,
    /--(?:allowedTools|allowed-tools)\s+([^\s]+)/,
  ];

  for (const pattern of patterns) {
    const match = claudeArgs.match(pattern);  // ← Only finds FIRST match
    if (match && match[1]) {
      return match[1].split(",")...;  // ← Returns immediately
    }
  }
  return [];
}

The regex patterns don't use the /g flag, and .match() only returns the first match. The function returns immediately after finding one match.

Impact

In Tag Mode, this parsed list is filtered for mcp__github_* tools to determine which MCP servers to start:

const userAllowedMCPTools = parseAllowedTools(userClaudeArgs).filter(
  (tool) => tool.startsWith("mcp__github_"),
);

If the first --allowed-tools flag doesn't contain mcp__github_* tools, no GitHub MCP servers get initialized from user config.

Suggested Fix

Use matchAll() with /g flag to find ALL occurrences:

export function parseAllowedTools(claudeArgs: string): string[] {
  const patterns = [
    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/g,
    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/g,
    /--(?:allowedTools|allowed-tools)\s+([^\s]+)/g,
  ];

  const tools: string[] = [];
  for (const pattern of patterns) {
    for (const match of claudeArgs.matchAll(pattern)) {
      if (match[1] && !match[1].startsWith("--")) {
        tools.push(...match[1].split(",").map((t) => t.trim()));
      }
    }
  }
  return [...new Set(tools)]; // Deduplicate
}

Workaround

Put mcp__github_* tools in the first --allowed-tools flag:

claude_args: |
  --allowed-tools 'mcp__github_inline_comment__create_inline_comment'  # Must be first!
  --allowed-tools 'mcp__context7__*'
  --allowed-tools 'Read,Glob,Grep,LS'

Environment

• claude-code-action version: v1.0.28 (c9ec2b0)
• Event type: issue_comment on PR