fix: parse ALL --allowed-tools flags, not just the first one (#801)

The parseAllowedTools() function previously used .match() which only
returns the first match. This caused tools specified in subsequent
--allowed-tools flags to be ignored during MCP server initialization.

Changes:
- Add /g flag to regex patterns for global matching
- Use matchAll() to find all occurrences
- Deduplicate tools while preserving order
- Make unquoted pattern not match quoted values

Fixes #800

 #vibe

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

src/modes/agent/parse-tools.ts

@@ -1,22 +1,33 @@
 export function parseAllowedTools(claudeArgs: string): string[] {
   // Match --allowedTools or --allowed-tools followed by the value
   // Handle both quoted and unquoted values
+  // Use /g flag to find ALL occurrences, not just the first one
   const patterns = [
-    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/, // Double quoted
-    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/, // Single quoted
-    /--(?:allowedTools|allowed-tools)\s+([^\s]+)/, // Unquoted
+    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/g, // Double quoted
+    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/g, // Single quoted
+    /--(?:allowedTools|allowed-tools)\s+([^'"\s][^\s]*)/g, // Unquoted (must not start with quote)
   ];
 
+  const tools: string[] = [];
+  const seen = new Set<string>();
+
   for (const pattern of patterns) {
-    const match = claudeArgs.match(pattern);
-    if (match && match[1]) {
-      // Don't return if the value starts with -- (another flag)
-      if (match[1].startsWith("--")) {
-        return [];
+    for (const match of claudeArgs.matchAll(pattern)) {
+      if (match[1]) {
+        // Don't add if the value starts with -- (another flag)
+        if (match[1].startsWith("--")) {
+          continue;
+        }
+        for (const tool of match[1].split(",")) {
+          const trimmed = tool.trim();
+          if (trimmed && !seen.has(trimmed)) {
+            seen.add(trimmed);
+            tools.push(trimmed);
+          }
+        }
       }
-      return match[1].split(",").map((t) => t.trim());
     }
   }
 
-  return [];
+  return tools;
 }