diff --git a/kt-kernel/python/cli/commands/doctor.py b/kt-kernel/python/cli/commands/doctor.py
index 681ece2c1..5b32a0cd7 100644
--- a/kt-kernel/python/cli/commands/doctor.py
+++ b/kt-kernel/python/cli/commands/doctor.py
@@ -4,6 +4,8 @@
 Diagnoses environment issues and provides recommendations.
 """
 
+import glob
+import os
 import platform
 import shutil
 from pathlib import Path
@@ -29,6 +31,67 @@
 )
 
 
+def _get_kt_kernel_info() -> dict:
+    """Get kt-kernel installation information."""
+    info = {
+        "installed": False,
+        "version": None,
+        "cpu_variant": None,
+        "install_path": None,
+        "available_variants": [],
+        "extension_file": None,
+    }
+
+    try:
+        import kt_kernel
+
+        info["installed"] = True
+        info["version"] = getattr(kt_kernel, "__version__", "unknown")
+        info["cpu_variant"] = getattr(kt_kernel, "__cpu_variant__", "unknown")
+
+        # Get installation path
+        info["install_path"] = os.path.dirname(kt_kernel.__file__)
+
+        # Find available .so files
+        kt_kernel_dir = info["install_path"]
+        so_files = glob.glob(os.path.join(kt_kernel_dir, "_kt_kernel_ext_*.so"))
+        so_files.extend(glob.glob(os.path.join(kt_kernel_dir, "kt_kernel_ext*.so")))
+
+        # Parse variant names from filenames
+        variants = set()
+        for so_file in so_files:
+            basename = os.path.basename(so_file)
+            if "_kt_kernel_ext_" in basename:
+                # Extract variant from _kt_kernel_ext_amx.cpython-311-x86_64-linux-gnu.so
+                parts = basename.split("_")
+                if len(parts) >= 4:
+                    variant = parts[3]  # "amx" from "_kt_kernel_ext_amx..."
+                    if variant.startswith("avx"):
+                        # Normalize avx variants
+                        if variant in ["avx512", "avx512_bf16", "avx512_vbmi", "avx512_vnni", "avx512_base"]:
+                            variants.add("avx512")
+                        else:
+                            variants.add(variant)
+                    else:
+                        variants.add(variant)
+            elif "kt_kernel_ext" in basename:
+                variants.add("default")
+
+        info["available_variants"] = sorted(list(variants))
+
+        # Get current extension file
+        if hasattr(kt_kernel, "kt_kernel_ext"):
+            ext_module = kt_kernel.kt_kernel_ext
+            info["extension_file"] = getattr(ext_module, "__file__", None)
+
+    except ImportError:
+        info["installed"] = False
+    except Exception as e:
+        info["error"] = str(e)
+
+    return info
+
+
 def doctor(
     verbose: bool = typer.Option(False, "--verbose", "-v", help="Show detailed diagnostics"),
 ) -> None:
@@ -157,6 +220,76 @@ def doctor(
         }
     )
 
+    # 6b. kt-kernel installation check
+    kt_info = _get_kt_kernel_info()
+
+    if kt_info["installed"]:
+        # Build display string for kt-kernel
+        variant = kt_info["cpu_variant"]
+        version = kt_info["version"]
+        available_variants = kt_info["available_variants"]
+
+        # Determine status based on CPU variant
+        if variant == "amx":
+            kt_status = "ok"
+            kt_hint = "AMX variant loaded - optimal performance"
+        elif variant.startswith("avx512"):
+            kt_status = "ok"
+            kt_hint = "AVX512 variant loaded - good performance"
+        elif variant == "avx2":
+            kt_status = "warning"
+            kt_hint = "AVX2 variant - consider upgrading CPU for AMX/AVX512"
+        else:
+            kt_status = "warning"
+            kt_hint = f"Unknown variant: {variant}"
+
+        kt_value = f"v{version} ({variant.upper()})"
+        if verbose and available_variants:
+            kt_value += f" [dim] - available: {', '.join(available_variants)}[/dim]"
+
+        checks.append(
+            {
+                "name": "kt-kernel",
+                "status": kt_status,
+                "value": kt_value,
+                "hint": kt_hint,
+            }
+        )
+
+        # Show extension file path in verbose mode
+        if verbose and kt_info.get("extension_file"):
+            ext_file = os.path.basename(kt_info["extension_file"])
+            checks.append(
+                {
+                    "name": "  └─ Extension",
+                    "status": "ok",
+                    "value": ext_file,
+                    "hint": None,
+                }
+            )
+
+        # Show installation path in verbose mode
+        if verbose and kt_info.get("install_path"):
+            checks.append(
+                {
+                    "name": "  └─ Path",
+                    "status": "ok",
+                    "value": kt_info["install_path"],
+                    "hint": None,
+                }
+            )
+    else:
+        error_msg = kt_info.get("error", "Not installed")
+        checks.append(
+            {
+                "name": "kt-kernel",
+                "status": "error",
+                "value": error_msg,
+                "hint": "kt-kernel is required - run: pip install kt-kernel",
+            }
+        )
+        issues_found = True
+
     # 7. System memory (with frequency if available)
     mem_info = detect_memory_info()
     if mem_info.frequency_mhz and mem_info.type:
@@ -204,7 +337,6 @@ def doctor(
     # 6. Required packages
     packages = [
         ("kt-kernel", ">=0.4.0", False),  # name, version_req, required
-        ("ktransformers", ">=0.4.0", False),
         ("sglang", ">=0.4.0", False),
         ("torch", ">=2.4.0", True),
         ("transformers", ">=4.45.0", True),
diff --git a/kt-kernel/python/cli/commands/run.py b/kt-kernel/python/cli/commands/run.py
index 7bcc08514..b2bb475cc 100644
--- a/kt-kernel/python/cli/commands/run.py
+++ b/kt-kernel/python/cli/commands/run.py
@@ -10,6 +10,7 @@
 from pathlib import Path
 from typing import Optional
 
+import click
 import typer
 
 from kt_kernel.cli.config.settings import get_settings
@@ -30,128 +31,163 @@
 from kt_kernel.cli.utils.model_registry import MODEL_COMPUTE_FUNCTIONS, ModelInfo, get_registry
 
 
+@click.command(
+    context_settings={"ignore_unknown_options": True, "allow_extra_args": True},
+    add_help_option=False,  # We'll handle help manually to avoid conflicts
+)
+@click.argument("model", required=False, default=None)
+@click.option("--host", "-H", default=None, help="Server host address")
+@click.option("--port", "-p", type=int, default=None, help="Server port")
+@click.option("--gpu-experts", type=int, default=None, help="Number of GPU experts per layer")
+@click.option("--cpu-threads", type=int, default=None, help="Number of CPU inference threads")
+@click.option("--numa-nodes", type=int, default=None, help="Number of NUMA nodes")
+@click.option(
+    "--tensor-parallel-size", "--tp", "tensor_parallel_size", type=int, default=None, help="Tensor parallel size"
+)
+@click.option("--model-path", type=click.Path(), default=None, help="Custom model path")
+@click.option("--weights-path", type=click.Path(), default=None, help="Custom quantized weights path")
+@click.option("--kt-method", default=None, help="KT quantization method")
+@click.option(
+    "--kt-gpu-prefill-threshold", "kt_gpu_prefill_threshold", type=int, default=None, help="GPU prefill token threshold"
+)
+@click.option("--attention-backend", default=None, help="Attention backend")
+@click.option("--max-total-tokens", "max_total_tokens", type=int, default=None, help="Maximum total tokens")
+@click.option("--max-running-requests", "max_running_requests", type=int, default=None, help="Maximum running requests")
+@click.option("--chunked-prefill-size", "chunked_prefill_size", type=int, default=None, help="Chunked prefill size")
+@click.option("--mem-fraction-static", "mem_fraction_static", type=float, default=None, help="Memory fraction static")
+@click.option("--watchdog-timeout", "watchdog_timeout", type=int, default=None, help="Watchdog timeout")
+@click.option("--served-model-name", "served_model_name", default=None, help="Served model name")
+@click.option(
+    "--disable-shared-experts-fusion",
+    "disable_shared_experts_fusion",
+    is_flag=True,
+    default=None,
+    help="Disable shared experts fusion",
+)
+@click.option(
+    "--enable-shared-experts-fusion",
+    "enable_shared_experts_fusion",
+    is_flag=True,
+    default=False,
+    help="Enable shared experts fusion",
+)
+@click.option("--quantize", "-q", is_flag=True, default=False, help="Quantize model")
+@click.option("--advanced", is_flag=True, default=False, help="Show advanced options")
+@click.option("--dry-run", "dry_run", is_flag=True, default=False, help="Show command without executing")
+@click.pass_context
 def run(
-    model: Optional[str] = typer.Argument(
-        None,
-        help="Model name or path (e.g., deepseek-v3, qwen3-30b). If not specified, shows interactive selection.",
-    ),
-    host: str = typer.Option(
-        None,
-        "--host",
-        "-H",
-        help="Server host address",
-    ),
-    port: int = typer.Option(
-        None,
-        "--port",
-        "-p",
-        help="Server port",
-    ),
-    # CPU/GPU configuration
-    gpu_experts: Optional[int] = typer.Option(
-        None,
-        "--gpu-experts",
-        help="Number of GPU experts per layer",
-    ),
-    cpu_threads: Optional[int] = typer.Option(
-        None,
-        "--cpu-threads",
-        help="Number of CPU inference threads (kt-cpuinfer, defaults to 80% of CPU cores)",
-    ),
-    numa_nodes: Optional[int] = typer.Option(
-        None,
-        "--numa-nodes",
-        help="Number of NUMA nodes",
-    ),
-    tensor_parallel_size: Optional[int] = typer.Option(
-        None,
-        "--tensor-parallel-size",
-        "--tp",
-        help="Tensor parallel size (number of GPUs)",
-    ),
-    # Model paths
-    model_path: Optional[Path] = typer.Option(
-        None,
-        "--model-path",
-        help="Custom model path",
-    ),
-    weights_path: Optional[Path] = typer.Option(
-        None,
-        "--weights-path",
-        help="Custom quantized weights path",
-    ),
-    # KT-kernel options
-    kt_method: Optional[str] = typer.Option(
-        None,
-        "--kt-method",
-        help="KT quantization method (AMXINT4, RAWFP8, etc.)",
-    ),
-    kt_gpu_prefill_token_threshold: Optional[int] = typer.Option(
-        None,
-        "--kt-gpu-prefill-threshold",
-        help="GPU prefill token threshold for kt-kernel",
-    ),
-    # SGLang options
-    attention_backend: Optional[str] = typer.Option(
-        None,
-        "--attention-backend",
-        help="Attention backend (triton, flashinfer)",
-    ),
-    max_total_tokens: Optional[int] = typer.Option(
-        None,
-        "--max-total-tokens",
-        help="Maximum total tokens",
-    ),
-    max_running_requests: Optional[int] = typer.Option(
-        None,
-        "--max-running-requests",
-        help="Maximum running requests",
-    ),
-    chunked_prefill_size: Optional[int] = typer.Option(
-        None,
-        "--chunked-prefill-size",
-        help="Chunked prefill size",
-    ),
-    mem_fraction_static: Optional[float] = typer.Option(
-        None,
-        "--mem-fraction-static",
-        help="Memory fraction for static allocation",
-    ),
-    watchdog_timeout: Optional[int] = typer.Option(
-        None,
-        "--watchdog-timeout",
-        help="Watchdog timeout in seconds",
-    ),
-    served_model_name: Optional[str] = typer.Option(
-        None,
-        "--served-model-name",
-        help="Custom model name for API responses",
-    ),
-    # Performance flags
-    disable_shared_experts_fusion: Optional[bool] = typer.Option(
-        None,
-        "--disable-shared-experts-fusion/--enable-shared-experts-fusion",
-        help="Disable/enable shared experts fusion",
-    ),
-    # Other options
-    quantize: bool = typer.Option(
-        False,
-        "--quantize",
-        "-q",
-        help="Quantize model if weights not found",
-    ),
-    advanced: bool = typer.Option(
-        False,
-        "--advanced",
-        help="Show advanced options",
-    ),
-    dry_run: bool = typer.Option(
-        False,
-        "--dry-run",
-        help="Show command without executing",
-    ),
+    ctx: click.Context,
+    model: Optional[str],
+    host: Optional[str],
+    port: Optional[int],
+    gpu_experts: Optional[int],
+    cpu_threads: Optional[int],
+    numa_nodes: Optional[int],
+    tensor_parallel_size: Optional[int],
+    model_path: Optional[str],
+    weights_path: Optional[str],
+    kt_method: Optional[str],
+    kt_gpu_prefill_threshold: Optional[int],
+    attention_backend: Optional[str],
+    max_total_tokens: Optional[int],
+    max_running_requests: Optional[int],
+    chunked_prefill_size: Optional[int],
+    mem_fraction_static: Optional[float],
+    watchdog_timeout: Optional[int],
+    served_model_name: Optional[str],
+    disable_shared_experts_fusion: Optional[bool],
+    enable_shared_experts_fusion: bool,
+    quantize: bool,
+    advanced: bool,
+    dry_run: bool,
 ) -> None:
-    """Start model inference server."""
+    """Start model inference server.
+
+    \b
+    Examples: kt run deepseek-v3 | kt run m2 --tensor-parallel-size 2 | kt run /path/to/model --gpu-experts 4
+
+    \b
+    Custom Options: Pass any SGLang server option directly (e.g., kt run m2 --fp8-gemm-backend triton).
+    Common: --fp8-gemm-backend, --tool-call-parser, --reasoning-parser, --dp-size, --enable-ma
+    For full list: python -m sglang.launch_server --help
+    """
+    # Handle --help manually since we disabled it
+    # Check sys.argv for --help or -h since ctx.args may not be set yet
+    if "--help" in sys.argv or "-h" in sys.argv:
+        click.echo(ctx.get_help())
+        return
+
+    # Handle disable/enable shared experts fusion flags
+    if enable_shared_experts_fusion:
+        disable_shared_experts_fusion = False
+    elif disable_shared_experts_fusion is None:
+        disable_shared_experts_fusion = None
+
+    # Convert Path objects from click
+    model_path_obj = Path(model_path) if model_path else None
+    weights_path_obj = Path(weights_path) if weights_path else None
+
+    # Get extra args that weren't parsed (unknown options)
+    # click stores these in ctx.args when ignore_unknown_options=True
+    extra_cli_args = list(ctx.args) if ctx.args else []
+
+    # Remove --help from extra args if present (already handled)
+    extra_cli_args = [arg for arg in extra_cli_args if arg not in ["--help", "-h"]]
+
+    # Call the actual run function implementation
+    _run_impl(
+        model=model,
+        host=host,
+        port=port,
+        gpu_experts=gpu_experts,
+        cpu_threads=cpu_threads,
+        numa_nodes=numa_nodes,
+        tensor_parallel_size=tensor_parallel_size,
+        model_path=model_path_obj,
+        weights_path=weights_path_obj,
+        kt_method=kt_method,
+        kt_gpu_prefill_threshold=kt_gpu_prefill_threshold,
+        attention_backend=attention_backend,
+        max_total_tokens=max_total_tokens,
+        max_running_requests=max_running_requests,
+        chunked_prefill_size=chunked_prefill_size,
+        mem_fraction_static=mem_fraction_static,
+        watchdog_timeout=watchdog_timeout,
+        served_model_name=served_model_name,
+        disable_shared_experts_fusion=disable_shared_experts_fusion,
+        quantize=quantize,
+        advanced=advanced,
+        dry_run=dry_run,
+        extra_cli_args=extra_cli_args,
+    )
+
+
+def _run_impl(
+    model: Optional[str],
+    host: Optional[str],
+    port: Optional[int],
+    gpu_experts: Optional[int],
+    cpu_threads: Optional[int],
+    numa_nodes: Optional[int],
+    tensor_parallel_size: Optional[int],
+    model_path: Optional[Path],
+    weights_path: Optional[Path],
+    kt_method: Optional[str],
+    kt_gpu_prefill_threshold: Optional[int],
+    attention_backend: Optional[str],
+    max_total_tokens: Optional[int],
+    max_running_requests: Optional[int],
+    chunked_prefill_size: Optional[int],
+    mem_fraction_static: Optional[float],
+    watchdog_timeout: Optional[int],
+    served_model_name: Optional[str],
+    disable_shared_experts_fusion: Optional[bool],
+    quantize: bool,
+    advanced: bool,
+    dry_run: bool,
+    extra_cli_args: list[str],
+) -> None:
+    """Actual implementation of run command."""
     # Check if SGLang is installed before proceeding
     from kt_kernel.cli.utils.sglang_checker import (
         check_sglang_installation,
@@ -387,7 +423,7 @@ def run(
     # KT-kernel options
     final_kt_method = kt_method or model_defaults.get("kt-method") or settings.get("inference.kt_method", "AMXINT4")
     final_kt_gpu_prefill_threshold = (
-        kt_gpu_prefill_token_threshold
+        kt_gpu_prefill_threshold
         or model_defaults.get("kt-gpu-prefill-token-threshold")
         or settings.get("inference.kt_gpu_prefill_token_threshold", 4096)
     )
@@ -456,6 +492,7 @@ def run(
         disable_shared_experts_fusion=final_disable_shared_experts_fusion,
         settings=settings,
         extra_model_params=extra_params,
+        extra_cli_args=extra_cli_args,
     )
 
     # Prepare environment variables
@@ -535,29 +572,51 @@ def run(
         raise typer.Exit(1)
 
 
-def _find_model_path(model_info: ModelInfo, settings) -> Optional[Path]:
-    """Find the model path on disk by searching all configured model paths."""
+def _find_model_path(model_info: ModelInfo, settings, max_depth: int = 3) -> Optional[Path]:
+    """Find the model path on disk by searching all configured model paths.
+
+    Args:
+        model_info: Model information to search for
+        settings: Settings instance
+        max_depth: Maximum depth to search within each model path (default: 3)
+
+    Returns:
+        Path to the model directory, or None if not found
+    """
     model_paths = settings.get_model_paths()
 
+    # Generate possible names to search for
+    possible_names = [
+        model_info.name,
+        model_info.name.lower(),
+        model_info.name.replace(" ", "-"),
+        model_info.hf_repo.split("/")[-1],
+        model_info.hf_repo.replace("/", "--"),
+    ]
+
+    # Add alias-based names
+    for alias in model_info.aliases:
+        possible_names.append(alias)
+        possible_names.append(alias.lower())
+
     # Search in all configured model directories
     for models_dir in model_paths:
-        # Check common path patterns
-        possible_paths = [
-            models_dir / model_info.name,
-            models_dir / model_info.name.lower(),
-            models_dir / model_info.name.replace(" ", "-"),
-            models_dir / model_info.hf_repo.split("/")[-1],
-            models_dir / model_info.hf_repo.replace("/", "--"),
-        ]
+        if not models_dir.exists():
+            continue
 
-        # Add alias-based paths
-        for alias in model_info.aliases:
-            possible_paths.append(models_dir / alias)
-            possible_paths.append(models_dir / alias.lower())
+        # Search recursively up to max_depth
+        for depth in range(max_depth):
+            for name in possible_names:
+                if depth == 0:
+                    # Direct children: models_dir / name
+                    search_paths = [models_dir / name]
+                else:
+                    # Nested: use rglob to find directories matching the name
+                    search_paths = list(models_dir.rglob(name))
 
-        for path in possible_paths:
-            if path.exists() and (path / "config.json").exists():
-                return path
+                for path in search_paths:
+                    if path.exists() and (path / "config.json").exists():
+                        return path
 
     return None
 
@@ -613,6 +672,7 @@ def _build_sglang_command(
     disable_shared_experts_fusion: bool,
     settings,
     extra_model_params: Optional[dict] = None,  # New parameter for additional params
+    extra_cli_args: Optional[list[str]] = None,  # Extra args from CLI to pass to sglang
 ) -> list[str]:
     """Build the SGLang launch command."""
     cmd = [
@@ -734,6 +794,10 @@ def _build_sglang_command(
     if extra_args:
         cmd.extend(extra_args)
 
+    # Add extra CLI args (user-provided options not defined in kt CLI)
+    if extra_cli_args:
+        cmd.extend(extra_cli_args)
+
     return cmd
 
 
diff --git a/kt-kernel/python/cli/main.py b/kt-kernel/python/cli/main.py
index 7be1dce4e..43449f9c4 100644
--- a/kt-kernel/python/cli/main.py
+++ b/kt-kernel/python/cli/main.py
@@ -68,7 +68,8 @@ def _update_help_texts() -> None:
 
 # Register commands
 app.command(name="version", help="Show version information")(version.version)
-app.command(name="run", help="Start model inference server")(run.run)
+# Run command is handled specially in main() to allow extra args
+# (not registered here to avoid typer's argument parsing)
 app.command(name="chat", help="Interactive chat with running model")(chat.chat)
 app.command(name="quant", help="Quantize model weights")(quant.quant)
 app.command(name="bench", help="Run full benchmark")(bench.bench)
@@ -429,6 +430,15 @@ def main():
     if should_check_first_run and args:
         check_first_run()
 
+    # Handle "run" command specially to pass through unknown options
+    if args and args[0] == "run":
+        # Get args after "run"
+        run_args = args[1:]
+        # Use click command directly with ignore_unknown_options
+        from kt_kernel.cli.commands import run as run_module
+
+        sys.exit(run_module.run.main(args=run_args, standalone_mode=False))
+
     app()
 
 
diff --git a/kt-kernel/python/cli/utils/model_registry.py b/kt-kernel/python/cli/utils/model_registry.py
index f62154b47..099cc6ef7 100644
--- a/kt-kernel/python/cli/utils/model_registry.py
+++ b/kt-kernel/python/cli/utils/model_registry.py
@@ -280,9 +280,12 @@ def list_all(self) -> list[ModelInfo]:
         """List all registered models."""
         return list(self._models.values())
 
-    def find_local_models(self) -> list[tuple[ModelInfo, Path]]:
+    def find_local_models(self, max_depth: int = 3) -> list[tuple[ModelInfo, Path]]:
         """Find models that are downloaded locally in any configured model path.
 
+        Args:
+            max_depth: Maximum depth to search within each model path (default: 3)
+
         Returns:
             List of (ModelInfo, path) tuples for local models
         """
@@ -297,18 +300,40 @@ def find_local_models(self) -> list[tuple[ModelInfo, Path]]:
                 if not models_dir.exists():
                     continue
 
-                # Check common path patterns
-                possible_paths = [
-                    models_dir / model.name,
-                    models_dir / model.name.lower(),
-                    models_dir / model.hf_repo.split("/")[-1],
-                    models_dir / model.hf_repo.replace("/", "--"),
+                # Generate possible names to search for
+                possible_names = [
+                    model.name,
+                    model.name.lower(),
+                    model.hf_repo.split("/")[-1],
+                    model.hf_repo.replace("/", "--"),
                 ]
 
-                for path in possible_paths:
-                    if path.exists() and (path / "config.json").exists():
-                        results.append((model, path))
-                        found = True
+                # Search recursively up to max_depth
+                for depth in range(max_depth):
+                    # Build glob pattern for current depth
+                    # depth=0: direct children, depth=1: grandchildren, etc.
+                    glob_pattern = "*" if depth > 0 else ""
+                    for _ in range(depth):
+                        glob_pattern = "*/" + glob_pattern if glob_pattern else "*"
+
+                    for name in possible_names:
+                        if depth == 0:
+                            # Direct children: models_dir / name
+                            search_paths = [models_dir / name]
+                        else:
+                            # Nested: use rglob to find directories matching the name
+                            search_paths = list(models_dir.rglob(name))
+
+                        for path in search_paths:
+                            if path.exists() and (path / "config.json").exists():
+                                results.append((model, path))
+                                found = True
+                                break
+
+                        if found:
+                            break
+
+                    if found:
                         break
 
                 if found: