diff --git a/scripts/fabric_sync.py b/scripts/fabric_sync.py
index fb0c02e..0a26ff1 100755
--- a/scripts/fabric_sync.py
+++ b/scripts/fabric_sync.py
@@ -111,11 +111,11 @@ def run_ai_scrutiny_review(scrutiny_report: dict, config: dict, tool_name: str,
     if not cmdforge_exe:
         return None
 
-    # Run the tool
+    # Run the tool (use -- to separate cmdforge args from tool args)
     try:
         result = subprocess.run(
             [
-                cmdforge_exe, "run", "scrutiny-ai-review",
+                cmdforge_exe, "run", "scrutiny-ai-review", "--",
                 "--warnings", json.dumps(warnings),
                 "--tool-config", json.dumps(tool_config),
             ],
diff --git a/src/cmdforge/cli/__init__.py b/src/cmdforge/cli/__init__.py
index 07ff350..7e0721d 100644
--- a/src/cmdforge/cli/__init__.py
+++ b/src/cmdforge/cli/__init__.py
@@ -67,7 +67,7 @@ def main():
     p_run.add_argument("--dry-run", action="store_true", help="Show what would happen without executing")
     p_run.add_argument("--show-prompt", action="store_true", help="Show prompts in addition to output")
     p_run.add_argument("-v", "--verbose", action="store_true", help="Show debug information")
-    p_run.add_argument("tool_args", nargs="*", help="Additional tool-specific arguments")
+    p_run.add_argument("tool_args", nargs=argparse.REMAINDER, help="Additional tool-specific arguments (use -- to separate)")
     p_run.set_defaults(func=cmd_run)
 
     # 'ui' command (explicit)
diff --git a/src/cmdforge/cli/tool_commands.py b/src/cmdforge/cli/tool_commands.py
index 6e94f8b..d313b79 100644
--- a/src/cmdforge/cli/tool_commands.py
+++ b/src/cmdforge/cli/tool_commands.py
@@ -202,26 +202,48 @@ def cmd_run(args):
 
     # Collect custom args from remaining arguments
     custom_args = {}
+
+    # Build a map from flag names to variable names for proper argument mapping
+    flag_to_var = {}
+    for tool_arg in tool.arguments:
+        # Handle both --flag and -f style flags
+        flag = tool_arg.flag
+        if flag.startswith('--'):
+            flag_key = flag[2:].replace('-', '_')
+        elif flag.startswith('-'):
+            flag_key = flag[1:].replace('-', '_')
+        else:
+            flag_key = flag.replace('-', '_')
+        flag_to_var[flag_key] = tool_arg.variable
+
     if args.tool_args:
+        # Remove leading '--' separator if present (used to separate cmdforge args from tool args)
+        tool_args = list(args.tool_args)
+        if tool_args and tool_args[0] == '--':
+            tool_args = tool_args[1:]
+
         # Parse tool-specific arguments
         i = 0
-        while i < len(args.tool_args):
-            arg = args.tool_args[i]
+        while i < len(tool_args):
+            arg = tool_args[i]
             if arg.startswith('--'):
-                key = arg[2:].replace('-', '_')
-                if i + 1 < len(args.tool_args) and not args.tool_args[i + 1].startswith('--'):
-                    custom_args[key] = args.tool_args[i + 1]
+                flag_key = arg[2:].replace('-', '_')
+                # Map flag name to variable name (use flag_key as fallback for unknown flags)
+                var_name = flag_to_var.get(flag_key, flag_key)
+                if i + 1 < len(tool_args) and not tool_args[i + 1].startswith('--'):
+                    custom_args[var_name] = tool_args[i + 1]
                     i += 2
                 else:
-                    custom_args[key] = True
+                    custom_args[var_name] = True
                     i += 1
             elif arg.startswith('-'):
-                key = arg[1:].replace('-', '_')
-                if i + 1 < len(args.tool_args) and not args.tool_args[i + 1].startswith('-'):
-                    custom_args[key] = args.tool_args[i + 1]
+                flag_key = arg[1:].replace('-', '_')
+                var_name = flag_to_var.get(flag_key, flag_key)
+                if i + 1 < len(tool_args) and not tool_args[i + 1].startswith('-'):
+                    custom_args[var_name] = tool_args[i + 1]
                     i += 2
                 else:
-                    custom_args[key] = True
+                    custom_args[var_name] = True
                     i += 1
             else:
                 i += 1
diff --git a/src/cmdforge/registry/app.py b/src/cmdforge/registry/app.py
index be9fc87..ce07a4d 100644
--- a/src/cmdforge/registry/app.py
+++ b/src/cmdforge/registry/app.py
@@ -251,11 +251,11 @@ def run_ai_scrutiny_review(scrutiny_report: dict, config: dict, tool_name: str,
     if not cmdforge_exe:
         return None
 
-    # Run the tool
+    # Run the tool (use -- to separate cmdforge args from tool args)
     try:
         result = subprocess.run(
             [
-                cmdforge_exe, "run", "scrutiny-ai-review",
+                cmdforge_exe, "run", "scrutiny-ai-review", "--",
                 "--warnings", json.dumps(warnings),
                 "--tool-config", json.dumps(tool_config),
             ],