diff --git a/src/mcp_agent/cli/__main__.py b/src/mcp_agent/cli/__main__.py
index 09adcb09e..1295f56b8 100644
--- a/src/mcp_agent/cli/__main__.py
+++ b/src/mcp_agent/cli/__main__.py
@@ -25,35 +25,35 @@
 }
 
 KNOWN = {
-    "go",
-    "check",
-    "chat",
-    "dev",
-    "invoke",
-    "serve",
+    # Curated top-level commands
     "init",
     "quickstart",
     "config",
-    "keys",
-    "models",
-    "server",
-    "build",
-    "logs",
     "doctor",
-    "configure",
+    "deploy",
+    "login",
+    "whoami",
+    "logout",
     "cloud",
+    # Umbrella group
+    "dev",
 }
 
 
 def main():
     if len(sys.argv) > 1:
         first = sys.argv[1]
-        if first not in KNOWN:
+        # Back-compat: allow `mcp-agent go ...`
+        if first == "go":
+            sys.argv.insert(1, "dev")
+        elif first not in KNOWN:
             for i, arg in enumerate(sys.argv[1:], 1):
                 if arg in GO_OPTIONS or any(
                     arg.startswith(opt + "=") for opt in GO_OPTIONS
                 ):
-                    sys.argv.insert(i, "go")
+                    # Route bare chat-like invocations to dev go (legacy behavior)
+                    sys.argv.insert(i, "dev")
+                    sys.argv.insert(i + 1, "go")
                     break
     app()
 
diff --git a/src/mcp_agent/cli/commands/chat.py b/src/mcp_agent/cli/commands/chat.py
index 25d533b68..44c8db725 100644
--- a/src/mcp_agent/cli/commands/chat.py
+++ b/src/mcp_agent/cli/commands/chat.py
@@ -16,10 +16,13 @@
     attach_stdio_servers,
     attach_url_servers,
     load_user_app,
+    detect_default_script,
+    select_servers_from_config,
 )
 from mcp_agent.cli.utils.url_parser import generate_server_configs, parse_server_urls
 from mcp_agent.workflows.factory import create_llm
 from mcp_agent.agents.agent import Agent
+from mcp_agent.config import get_settings
 
 
 app = typer.Typer(help="Ephemeral REPL for quick iteration")
@@ -99,7 +102,7 @@ def chat(
     npx: Optional[str] = typer.Option(None, "--npx"),
     uvx: Optional[str] = typer.Option(None, "--uvx"),
     stdio: Optional[str] = typer.Option(None, "--stdio"),
-    script: Optional[Path] = typer.Option(Path("agent.py"), "--script"),
+    script: Optional[Path] = typer.Option(None, "--script"),
     list_servers: bool = typer.Option(False, "--list-servers"),
     list_tools: bool = typer.Option(False, "--list-tools"),
     list_resources: bool = typer.Option(False, "--list-resources"),
@@ -107,6 +110,9 @@ def chat(
         None, "--server", help="Filter to a single server"
     ),
 ) -> None:
+    # Resolve script with auto-detection
+    script = detect_default_script(script)
+
     server_list = servers_csv.split(",") if servers_csv else None
 
     url_servers = None
@@ -140,12 +146,21 @@ def chat(
             else:
                 server_list.extend(list(stdio_servers.keys()))
 
+    # Smart defaults for servers
+    resolved_server_list = select_servers_from_config(
+        servers_csv, url_servers, stdio_servers
+    )
+
     # Listing mode (no generation)
     if list_servers or list_tools or list_resources:
         try:
 
             async def _list():
-                app_obj = load_user_app(script or Path("agent.py"))
+                # Disable progress display for cleaner listing output
+                settings = get_settings()
+                if settings.logger:
+                    settings.logger.progress_display = False
+                app_obj = load_user_app(script, settings_override=settings)
                 await app_obj.initialize()
                 attach_url_servers(app_obj, url_servers)
                 attach_stdio_servers(app_obj, stdio_servers)
@@ -163,7 +178,7 @@ async def _list():
                     agent = Agent(
                         name="chat-lister",
                         instruction="You list tools and resources",
-                        server_names=target_servers,
+                        server_names=resolved_server_list or target_servers,
                         context=app_obj.context,
                     )
                     async with agent:
@@ -203,7 +218,11 @@ async def _list():
         ):
 
             async def _parallel_repl():
-                app_obj = load_user_app(script or Path("agent.py"))
+                # Disable progress display for cleaner multi-model REPL
+                settings = get_settings()
+                if settings.logger:
+                    settings.logger.progress_display = False
+                app_obj = load_user_app(script, settings_override=settings)
                 await app_obj.initialize()
                 attach_url_servers(app_obj, url_servers)
                 attach_stdio_servers(app_obj, stdio_servers)
@@ -227,7 +246,7 @@ async def _parallel_repl():
                                 provider = prov_guess
                         llm = create_llm(
                             agent_name=m,
-                            server_names=server_list or [],
+                            server_names=resolved_server_list or [],
                             provider=(provider or "openai"),
                             model=m,
                             context=app_obj.context,
@@ -276,7 +295,9 @@ async def _parallel_repl():
                             ag = _Agent(
                                 name="chat-lister",
                                 instruction="list tools",
-                                server_names=[srv] if srv else (server_list or []),
+                                server_names=[srv]
+                                if srv
+                                else (resolved_server_list or []),
                                 context=app_obj.context,
                             )
                             async with ag:
@@ -294,7 +315,9 @@ async def _parallel_repl():
                             ag = _Agent(
                                 name="chat-lister",
                                 instruction="list resources",
-                                server_names=[srv] if srv else (server_list or []),
+                                server_names=[srv]
+                                if srv
+                                else (resolved_server_list or []),
                                 context=app_obj.context,
                             )
                             async with ag:
@@ -367,8 +390,8 @@ async def _gen(llm_instance):
             try:
                 out = asyncio.run(
                     _run_single_model(
-                        script=script or Path("agent.py"),
-                        servers=server_list,
+                        script=script,
+                        servers=resolved_server_list,
                         url_servers=url_servers,
                         stdio_servers=stdio_servers,
                         model=m,
@@ -392,9 +415,12 @@ async def _gen(llm_instance):
             and not models
             and not (list_servers or list_tools or list_resources)
         ):
-            # Interactive loop
+            # Interactive loop - disable progress display for cleaner REPL experience
             async def _repl():
-                app_obj = load_user_app(script or Path("agent.py"))
+                settings = get_settings()
+                if settings.logger:
+                    settings.logger.progress_display = False
+                app_obj = load_user_app(script, settings_override=settings)
                 await app_obj.initialize()
                 attach_url_servers(app_obj, url_servers)
                 attach_stdio_servers(app_obj, stdio_servers)
@@ -416,7 +442,7 @@ async def _repl():
                         provider = model_id.split(":", 1)[0]
                     llm = create_llm(
                         agent_name=(name or "chat"),
-                        server_names=server_list or [],
+                        server_names=resolved_server_list or [],
                         provider=(provider or "openai"),
                         model=model_id,
                         context=app_obj.context,
@@ -476,7 +502,7 @@ async def _repl():
                                 # Recreate LLM with new model
                                 llm_local = create_llm(
                                     agent_name=(name or "chat"),
-                                    server_names=server_list or [],
+                                    server_names=resolved_server_list or [],
                                     provider=(prov or "openai"),
                                     model=model_id,
                                     context=app_obj.context,
@@ -502,7 +528,9 @@ async def _repl():
                             ag = Agent(
                                 name="chat-lister",
                                 instruction="list tools",
-                                server_names=[srv] if srv else (server_list or []),
+                                server_names=[srv]
+                                if srv
+                                else (resolved_server_list or []),
                                 context=app_obj.context,
                             )
                             async with ag:
@@ -521,7 +549,9 @@ async def _repl():
                             ag = Agent(
                                 name="chat-lister",
                                 instruction="list resources",
-                                server_names=[srv] if srv else (server_list or []),
+                                server_names=[srv]
+                                if srv
+                                else (resolved_server_list or []),
                                 context=app_obj.context,
                             )
                             async with ag:
@@ -558,7 +588,7 @@ async def _repl():
                                 prompt_msgs = await ag.create_prompt(
                                     prompt_name=prompt_name,
                                     arguments=arguments,
-                                    server_names=server_list or [],
+                                    server_names=resolved_server_list or [],
                                 )
                                 # Generate with prompt messages
                                 out = await llm.generate_str(prompt_msgs)
@@ -698,8 +728,8 @@ async def _repl():
         else:
             out = asyncio.run(
                 _run_single_model(
-                    script=script or Path("agent.py"),
-                    servers=server_list,
+                    script=script,
+                    servers=resolved_server_list,
                     url_servers=url_servers,
                     stdio_servers=stdio_servers,
                     model=model,
diff --git a/src/mcp_agent/cli/commands/dev.py b/src/mcp_agent/cli/commands/dev.py
index d598893b5..89da14d16 100644
--- a/src/mcp_agent/cli/commands/dev.py
+++ b/src/mcp_agent/cli/commands/dev.py
@@ -15,6 +15,7 @@
 from rich.console import Console
 
 from mcp_agent.config import get_settings
+from mcp_agent.cli.core.utils import detect_default_script
 
 
 app = typer.Typer(help="Run app locally with diagnostics")
@@ -22,7 +23,7 @@
 
 
 @app.callback(invoke_without_command=True)
-def dev(script: Path = typer.Option(Path("agent.py"), "--script")) -> None:
+def dev(script: Path = typer.Option(None, "--script")) -> None:
     """Run the user's app script with optional live reload and preflight checks."""
 
     def _preflight_ok() -> bool:
@@ -49,6 +50,9 @@ def _run_script() -> subprocess.Popen:
             stdin=None,  # Inherit stdin
         )
 
+    # Resolve script path with auto-detection (main.py preferred)
+    script = detect_default_script(script)
+
     # Simple preflight
     _ = _preflight_ok()
 
diff --git a/src/mcp_agent/cli/commands/doctor.py b/src/mcp_agent/cli/commands/doctor.py
index c593c342b..88bfde75c 100644
--- a/src/mcp_agent/cli/commands/doctor.py
+++ b/src/mcp_agent/cli/commands/doctor.py
@@ -412,7 +412,7 @@ def doctor() -> None:
             "• Add API key: [cyan]mcp-agent keys set <provider> <key>[/cyan]\n"
             "• Add server: [cyan]mcp-agent server add recipe filesystem[/cyan]\n"
             "• Start chat: [cyan]mcp-agent chat --model anthropic.haiku[/cyan]\n"
-            "• Run agent: [cyan]mcp-agent dev --script agent.py[/cyan]",
+            "• Run agent: [cyan]mcp-agent dev start --script main.py[/cyan]",
             title="Getting Started",
             border_style="dim",
         )
diff --git a/src/mcp_agent/cli/commands/go.py b/src/mcp_agent/cli/commands/go.py
index 2b763daf7..01304ad0f 100644
--- a/src/mcp_agent/cli/commands/go.py
+++ b/src/mcp_agent/cli/commands/go.py
@@ -18,6 +18,8 @@
     attach_stdio_servers,
     attach_url_servers,
     load_user_app,
+    detect_default_script,
+    select_servers_from_config,
 )
 from mcp_agent.cli.utils.url_parser import generate_server_configs, parse_server_urls
 from mcp_agent.workflows.factory import create_llm
@@ -268,8 +270,11 @@ def go(
     npx: Optional[str] = typer.Option(None, "--npx"),
     uvx: Optional[str] = typer.Option(None, "--uvx"),
     stdio: Optional[str] = typer.Option(None, "--stdio"),
-    script: Optional[Path] = typer.Option(Path("agent.py"), "--script"),
+    script: Optional[Path] = typer.Option(None, "--script"),
 ) -> None:
+    # Resolve script with auto-detection
+    script = detect_default_script(script)
+
     # Parse server names from config if provided
     server_list = servers.split(",") if servers else None
 
@@ -302,6 +307,11 @@ def go(
         else:
             server_list.extend(list(stdio_servers.keys()))
 
+    # Smart defaults from config if still unspecified
+    resolved_server_list = select_servers_from_config(
+        ",".join(server_list) if server_list else None, url_servers, stdio_servers
+    )
+
     # Multi-model support if comma-separated
     if model and "," in model:
         models = [m.strip() for m in model.split(",") if m.strip()]
@@ -311,7 +321,7 @@ def go(
                 asyncio.run(
                     _run_agent(
                         app_script=script,
-                        server_list=server_list,
+                        server_list=resolved_server_list,
                         model=m,
                         message=message,
                         prompt_file=prompt_file,
@@ -331,7 +341,7 @@ def go(
         asyncio.run(
             _run_agent(
                 app_script=script,
-                server_list=server_list,
+                server_list=resolved_server_list,
                 model=model,
                 message=message,
                 prompt_file=prompt_file,
diff --git a/src/mcp_agent/cli/commands/init.py b/src/mcp_agent/cli/commands/init.py
index e0cce1d3f..a7bd07c7c 100644
--- a/src/mcp_agent/cli/commands/init.py
+++ b/src/mcp_agent/cli/commands/init.py
@@ -100,6 +100,7 @@ def init(
     console.print(f"Template: [cyan]{template}[/cyan] - {templates[template]}\n")
 
     files_created = []
+    entry_script_name: str | None = None
 
     # Always create config files
     config_path = dir / "mcp_agent.config.yaml"
@@ -122,15 +123,35 @@ def init(
 
     # Create template-specific files
     if template == "basic":
-        agent_path = dir / "agent.py"
+        # Determine entry script name and handle existing files
+        script_name = "main.py"
+        script_path = dir / script_name
         agent_content = _load_template("basic_agent.py")
-        if agent_content and _write(agent_path, agent_content, force):
-            files_created.append("agent.py")
-            # Make executable
-            try:
-                agent_path.chmod(agent_path.stat().st_mode | 0o111)
-            except Exception:
-                pass
+
+        if agent_content:
+            write_force_flag = force
+            if script_path.exists() and not force:
+                if Confirm.ask(f"{script_path} exists. Overwrite?", default=False):
+                    write_force_flag = True
+                else:
+                    # Ask for an alternate filename and ensure it ends with .py
+                    alt_name = Prompt.ask(
+                        "Enter a filename to save the agent", default="agent.py"
+                    )
+                    if not alt_name.endswith(".py"):
+                        alt_name += ".py"
+                    script_name = alt_name
+                    script_path = dir / script_name
+                    # keep write_force_flag as-is to allow overwrite prompt if needed
+
+            if _write(script_path, agent_content, write_force_flag):
+                files_created.append(script_name)
+                entry_script_name = script_name
+                # Make executable
+                try:
+                    script_path.chmod(script_path.stat().st_mode | 0o111)
+                except Exception:
+                    pass
 
     elif template == "server":
         server_path = dir / "server.py"
@@ -185,20 +206,29 @@ def init(
         console.print("2. Review and customize [cyan]mcp_agent.config.yaml[/cyan]")
 
         if template == "basic":
-            console.print("3. Run your agent: [cyan]python agent.py[/cyan]")
-            console.print("   Or use: [cyan]mcp-agent dev --script agent.py[/cyan]")
-            console.print("   Or chat: [cyan]mcp-agent chat[/cyan]")
+            run_file = entry_script_name or "main.py"
+            console.print(f"3. Run your agent: [cyan]uv run {run_file}[/cyan]")
+            console.print(
+                f"   Or use: [cyan]mcp-agent dev start --script {run_file}[/cyan]"
+            )
+            console.print(
+                f"   Or serve: [cyan]mcp-agent dev serve --script {run_file}[/cyan]"
+            )
+            console.print("   Or chat: [cyan]mcp-agent dev chat[/cyan]")
+            console.print(
+                "4. Edit config: [cyan]mcp-agent config edit[/cyan] (then rerun)"
+            )
         elif template == "server":
-            console.print("3. Run the server: [cyan]python server.py[/cyan]")
+            console.print("3. Run the server: [cyan]uv run server.py[/cyan]")
             console.print(
-                "   Or serve: [cyan]mcp-agent serve --script server.py[/cyan]"
+                "   Or serve: [cyan]mcp-agent dev serve --script server.py[/cyan]"
             )
         elif template == "token":
-            console.print("3. Run the example: [cyan]python token_example.py[/cyan]")
+            console.print("3. Run the example: [cyan]uv run token_example.py[/cyan]")
             console.print("   Watch token usage in real-time!")
         elif template == "factory":
             console.print("3. Customize agents in [cyan]agents.yaml[/cyan]")
-            console.print("4. Run the factory: [cyan]python factory.py[/cyan]")
+            console.print("4. Run the factory: [cyan]uv run factory.py[/cyan]")
         elif template == "minimal":
             console.print("3. Create your agent script")
             console.print("   See examples: [cyan]mcp-agent quickstart[/cyan]")
diff --git a/src/mcp_agent/cli/commands/invoke.py b/src/mcp_agent/cli/commands/invoke.py
index 38434f7ab..8864c423c 100644
--- a/src/mcp_agent/cli/commands/invoke.py
+++ b/src/mcp_agent/cli/commands/invoke.py
@@ -7,11 +7,16 @@
 import asyncio
 import json
 from typing import Optional
+from pathlib import Path
 
 import typer
 from rich.console import Console
 
-from mcp_agent.cli.core.utils import load_user_app
+from mcp_agent.cli.core.utils import (
+    load_user_app,
+    detect_default_script,
+    select_servers_from_config,
+)
 from mcp_agent.workflows.factory import create_llm
 
 
@@ -48,13 +53,13 @@ def invoke(
         raise typer.Exit(6)
 
     async def _run():
-        app_obj = load_user_app(Path(script) if script else Path("agent.py"))
+        script_path = detect_default_script(Path(script) if script else None)
+        app_obj = load_user_app(script_path)
         await app_obj.initialize()
         async with app_obj.run():
             if agent:
                 # Run via LLM
-                server_list = servers.split(",") if servers else []
-                server_list = [s.strip() for s in server_list if s.strip()]
+                server_list = select_servers_from_config(servers, None, None)
                 llm = create_llm(
                     agent_name=agent,
                     server_names=server_list,
@@ -105,8 +110,6 @@ async def _run():
                 val = result
             console.print(val, end="\n\n\n")
 
-    from pathlib import Path
-
     try:
         asyncio.run(_run())
     except KeyboardInterrupt:
diff --git a/src/mcp_agent/cli/commands/keys.py b/src/mcp_agent/cli/commands/keys.py
index 0acf9bc3b..ea4b0f13f 100644
--- a/src/mcp_agent/cli/commands/keys.py
+++ b/src/mcp_agent/cli/commands/keys.py
@@ -44,7 +44,7 @@
             "claude-3-opus-20240229",
             "claude-3-haiku-20240307",
         ],
-        "test_endpoint": "https://api.anthropic.com/v1/messages",
+        "test_endpoint": "https://api.anthropic.com/v1/models",
         "docs": "https://console.anthropic.com/settings/keys",
     },
     "google": {
diff --git a/src/mcp_agent/cli/commands/serve.py b/src/mcp_agent/cli/commands/serve.py
index fbc2de633..09137eae8 100644
--- a/src/mcp_agent/cli/commands/serve.py
+++ b/src/mcp_agent/cli/commands/serve.py
@@ -19,7 +19,7 @@
 from rich.progress import Progress, SpinnerColumn, TextColumn
 
 from mcp_agent.server.app_server import create_mcp_server_for_app
-from mcp_agent.cli.core.utils import load_user_app
+from mcp_agent.cli.core.utils import load_user_app, detect_default_script
 from mcp_agent.config import get_settings
 
 
@@ -118,9 +118,9 @@ def serve(
     Start an MCP server for your app.
 
     Examples:
-        mcp-agent serve --script agent.py
-        mcp-agent serve --transport http --port 8000
-        mcp-agent serve --reload --debug
+        mcp-agent dev serve --script agent.py
+        mcp-agent dev serve --transport http --port 8000
+        mcp-agent dev serve --reload --debug
     """
 
     if ctx.invoked_subcommand:
@@ -138,12 +138,14 @@ def serve(
     # Load configuration path is handled after loading app by overriding app settings
 
     async def _run():
-        # Load the app
-        script_path = Path(script) if script else Path("agent.py")
+        # Load the app (auto-detect main.py preferred)
+        script_path = detect_default_script(Path(script) if script else None)
 
         if not script_path.exists():
             console.print(f"[red]Script not found: {script_path}[/red]")
-            console.print("\n[dim]Create an agent.py file or specify --script[/dim]")
+            console.print(
+                "\n[dim]Create a main.py (preferred) or agent.py file, or specify --script[/dim]"
+            )
             raise typer.Exit(1)
 
         console.print("\n[bold cyan]🚀 MCP-Agent Server[/bold cyan]")
@@ -379,10 +381,13 @@ def test(
     timeout: float = typer.Option(5.0, "--timeout", "-t", help="Test timeout"),
 ) -> None:
     """Test if the server can be loaded and initialized."""
-    script_path = Path(script) if script else Path("agent.py")
+    script_path = detect_default_script(Path(script) if script else None)
 
     if not script_path.exists():
         console.print(f"[red]Script not found: {script_path}[/red]")
+        console.print(
+            "\n[dim]Create a main.py (preferred) or agent.py file, or specify --script[/dim]"
+        )
         raise typer.Exit(1)
 
     console.print(f"\n[bold]Testing server: {script_path}[/bold]\n")
@@ -463,7 +468,7 @@ async def _test():
             )
 
             console.print("\n[dim]Server is ready to run with:[/dim]")
-            console.print(f"  [cyan]mcp-agent serve --script {script_path}[/cyan]")
+            console.print(f"  [cyan]mcp-agent dev serve --script {script_path}[/cyan]")
 
         except Exception:
             console.print("\n[red bold]❌ Server test failed[/red bold]")
@@ -526,9 +531,11 @@ def generate(
     console.print("\n[bold]Next steps:[/bold]")
     console.print(f"1. Edit the server: [cyan]{output}[/cyan]")
     console.print(
-        f"2. Test the server: [cyan]mcp-agent serve test --script {output}[/cyan]"
+        f"2. Test the server: [cyan]mcp-agent dev serve test --script {output}[/cyan]"
+    )
+    console.print(
+        f"3. Run the server: [cyan]mcp-agent dev serve --script {output}[/cyan]"
     )
-    console.print(f"3. Run the server: [cyan]mcp-agent serve --script {output}[/cyan]")
     console.print(
-        f"4. Or serve via HTTP: [cyan]mcp-agent serve --script {output} --transport http --port 8000[/cyan]"
+        f"4. Or serve via HTTP: [cyan]mcp-agent dev serve --script {output} --transport http --port 8000[/cyan]"
     )
diff --git a/src/mcp_agent/cli/core/utils.py b/src/mcp_agent/cli/core/utils.py
index 3a6b570fe..2743feaa9 100644
--- a/src/mcp_agent/cli/core/utils.py
+++ b/src/mcp_agent/cli/core/utils.py
@@ -3,10 +3,10 @@
 import sys
 
 from pathlib import Path
-from typing import Any, Dict
+from typing import Any, Dict, List, Optional
 
 from mcp_agent.app import MCPApp
-from mcp_agent.config import MCPServerSettings, MCPSettings
+from mcp_agent.config import MCPServerSettings, MCPSettings, Settings, get_settings
 
 
 def run_async(coro):
@@ -27,13 +27,17 @@ def run_async(coro):
         raise
 
 
-def load_user_app(script_path: Path | None) -> MCPApp:
+def load_user_app(script_path: Path | None, settings_override: Optional[Settings] = None) -> MCPApp:
     """Import a user script and return an MCPApp instance.
 
     Resolution order within module globals:
       1) variable named 'app' that is MCPApp
       2) callable 'create_app' or 'get_app' that returns MCPApp
       3) first MCPApp instance found in globals
+    
+    Args:
+        script_path: Path to the Python script containing the MCPApp
+        settings_override: Optional settings to override the app's configuration
     """
     if script_path is None:
         raise FileNotFoundError("No script specified")
@@ -52,6 +56,8 @@ def load_user_app(script_path: Path | None) -> MCPApp:
     # 1) app variable
     app_obj = getattr(module, "app", None)
     if isinstance(app_obj, MCPApp):
+        if settings_override:
+            app_obj._config = settings_override
         return app_obj
 
     # 2) factory
@@ -60,11 +66,15 @@ def load_user_app(script_path: Path | None) -> MCPApp:
         if callable(fn):
             res = fn()
             if isinstance(res, MCPApp):
+                if settings_override:
+                    res._config = settings_override
                 return res
 
     # 3) scan globals
     for val in module.__dict__.values():
         if isinstance(val, MCPApp):
+            if settings_override:
+                val._config = settings_override
             return val
 
     raise RuntimeError(
@@ -81,6 +91,57 @@ def ensure_mcp_servers(app: MCPApp) -> None:
         cfg.mcp.servers = {}
 
 
+def detect_default_script(explicit: Optional[Path]) -> Path:
+    """Choose a default script path.
+
+    Preference order:
+      1) explicit value if provided
+      2) ./main.py
+      3) ./agent.py
+    Returns the first existing file; if none exist, returns the first preference path (main.py).
+    """
+    if explicit:
+        return explicit
+    cwd = Path.cwd()
+    main_candidate = cwd / "main.py"
+    agent_candidate = cwd / "agent.py"
+    if main_candidate.exists():
+        return main_candidate
+    if agent_candidate.exists():
+        return agent_candidate
+    # Fall back to main.py (even if missing) so callers can show a helpful message
+    return main_candidate
+
+
+def select_servers_from_config(
+    explicit_servers_csv: Optional[str],
+    url_servers: Optional[Dict[str, Dict[str, Any]]],
+    stdio_servers: Optional[Dict[str, Dict[str, Any]]],
+) -> List[str]:
+    """Resolve which servers should be active based on inputs and config.
+
+    - If explicit --servers provided, use those
+    - Else, if dynamic URL/stdio servers provided, use their names
+    - Else, use all servers from mcp_agent.config.yaml (if present)
+    """
+    if explicit_servers_csv:
+        items = [s.strip() for s in explicit_servers_csv.split(",") if s.strip()]
+        return items
+
+    names: List[str] = []
+    if url_servers:
+        names.extend(list(url_servers.keys()))
+    if stdio_servers:
+        names.extend(list(stdio_servers.keys()))
+    if names:
+        return names
+
+    settings = get_settings()
+    if settings.mcp and settings.mcp.servers:
+        return list(settings.mcp.servers.keys())
+    return []
+
+
 def attach_url_servers(app: MCPApp, servers: Dict[str, Dict[str, Any]] | None) -> None:
     """Attach URL-based servers (http/sse/streamable_http) to app config."""
     if not servers:
diff --git a/src/mcp_agent/cli/main.py b/src/mcp_agent/cli/main.py
index 5b6dd359a..599836d0c 100644
--- a/src/mcp_agent/cli/main.py
+++ b/src/mcp_agent/cli/main.py
@@ -10,6 +10,7 @@
 from __future__ import annotations
 
 import logging
+from pathlib import Path
 
 import typer
 from rich.console import Console
@@ -24,7 +25,7 @@
 
 
 # Local command groups (scaffolded)
-from mcp_agent.cli.cloud.commands import deploy_config, login, logout, whoami
+from mcp_agent.cli.cloud.commands import deploy_config, login
 from mcp_agent.cli.commands import (
     check as check_cmd,
     chat as chat_cmd,
@@ -65,6 +66,25 @@
     cls=HelpfulTyperGroup,
 )
 
+# Local development umbrella group
+dev_group = typer.Typer(
+    help="Local development: start app, chat, invoke, serve, servers, build, logs",
+    no_args_is_help=False,
+    cls=HelpfulTyperGroup,
+)
+
+
+@dev_group.callback(invoke_without_command=True)
+def _dev_group_entry(
+    ctx: typer.Context,
+    script: Path = typer.Option(None, "--script", help="Entry script"),
+):
+    """If no subcommand is provided, behave like 'dev start'."""
+    if ctx.invoked_subcommand:
+        return
+    # Delegate to the existing dev implementation
+    dev_cmd.dev(script=script)
+
 
 console = Console(stderr=False)
 err_console = Console(stderr=True)
@@ -123,43 +143,47 @@ def main(
         console.print("Run 'mcp-agent --help' to see all commands.")
 
 
-# Mount non-cloud command groups
+# Mount non-cloud command groups (top-level, curated)
 app.add_typer(init_cmd.app, name="init", help="Scaffold a new mcp-agent project")
 app.add_typer(quickstart_cmd.app, name="quickstart", help="Copy curated examples")
-app.add_typer(go_cmd.app, name="go", help="Quick interactive agent")
-app.add_typer(check_cmd.app, name="check", help="Check configuration and environment")
 app.add_typer(config_cmd.app, name="config", help="Manage and inspect configuration")
-app.add_typer(keys_cmd.app, name="keys", help="Manage provider API keys")
-app.add_typer(models_cmd.app, name="models", help="List and manage models")
+app.add_typer(doctor_cmd.app, name="doctor", help="Comprehensive diagnostics")
 
-app.add_typer(chat_cmd.app, name="chat", help="Ephemeral REPL for quick iteration")
-app.add_typer(dev_cmd.app, name="dev", help="Run app locally with live reload")
-app.add_typer(
+# Group local dev/runtime commands under `dev`
+dev_group.add_typer(dev_cmd.app, name="start", help="Run app locally with live reload")
+dev_group.add_typer(
+    chat_cmd.app, name="chat", help="Ephemeral REPL for quick iteration"
+)
+dev_group.add_typer(
     invoke_cmd.app, name="invoke", help="Invoke agent/workflow programmatically"
 )
-app.add_typer(serve_cmd.app, name="serve", help="Serve app as an MCP server")
-app.add_typer(server_cmd.app, name="server", help="Local server helpers")
-app.add_typer(
+dev_group.add_typer(serve_cmd.app, name="serve", help="Serve app as an MCP server")
+dev_group.add_typer(server_cmd.app, name="server", help="Local server helpers")
+dev_group.add_typer(
     build_cmd.app, name="build", help="Preflight and bundle prep for deployment"
 )
-app.add_typer(logs_cmd.app, name="logs", help="Tail local logs")
-app.add_typer(doctor_cmd.app, name="doctor", help="Comprehensive diagnostics")
-app.add_typer(configure_cmd.app, name="configure", help="Client integration helpers")
+dev_group.add_typer(logs_cmd.app, name="logs", help="Tail local logs")
+dev_group.add_typer(
+    check_cmd.app, name="check", help="Check configuration and environment"
+)
+dev_group.add_typer(go_cmd.app, name="go", help="Quick interactive agent")
+dev_group.add_typer(keys_cmd.app, name="keys", help="Manage provider API keys")
+dev_group.add_typer(models_cmd.app, name="models", help="List and manage models")
+dev_group.add_typer(configure_cmd.app, name="client", help="Client integration helpers")
+
+# Mount the dev umbrella group
+app.add_typer(dev_group, name="dev", help="Local development and runtime")
 
 # Mount cloud commands
 app.add_typer(cloud_app, name="cloud", help="MCP Agent Cloud commands")
 
-# Register some key cloud commands directly as top-level commands
+# Register key cloud commands directly as top-level aliases
 app.command("deploy", help="Deploy an MCP agent (alias for 'cloud deploy')")(
     deploy_config
 )
 app.command(
     "login", help="Authenticate to MCP Agent Cloud API (alias for 'cloud login')"
 )(login)
-app.command(
-    "whoami", help="Print current identity and org(s) (alias for 'cloud whoami')"
-)(whoami)
-app.command("logout", help="Clear credentials (alias for 'cloud logout')")(logout)
 
 
 def run() -> None: