diff --git a/pyproject.toml b/pyproject.toml
index 680d8599..667214c7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -61,8 +61,6 @@ explicit = true
 
 [project.scripts]
 serena = "serena.cli:top_level"
-serena-mcp-server = "serena.cli:start_mcp_server"
-index-project = "serena.cli:index_project"        # deprecated
 
 [project.license]
 text = "MIT"
diff --git a/scripts/mcp_server.py b/scripts/mcp_server.py
index 74d2ae52..9b5c3f5a 100644
--- a/scripts/mcp_server.py
+++ b/scripts/mcp_server.py
@@ -1,4 +1,4 @@
-from serena.cli import start_mcp_server
+from serena.cli import top_level
 
 if __name__ == "__main__":
-    start_mcp_server()
+    top_level.start_mcp_server()
diff --git a/src/serena/cli.py b/src/serena/cli.py
index 7ad3fb2d..666815ee 100644
--- a/src/serena/cli.py
+++ b/src/serena/cli.py
@@ -1109,23 +1109,16 @@ class PromptCommands(AutoRegisteringGroup):
         click.echo(f"Deleted override file '{prompt_yaml_name}'.")
 
 
-# Expose groups so we can reference them in pyproject.toml
-mode = ModeCommands()
-context = ContextCommands()
-project = ProjectCommands()
-config = SerenaConfigCommands()
-tools = ToolCommands()
-prompts = PromptCommands()
+_mode = ModeCommands()
+_context = ContextCommands()
+_project = ProjectCommands()
+_config = SerenaConfigCommands()
+_tools = ToolCommands()
+_prompts = PromptCommands()
 
-# Expose toplevel commands for the same reason
+# Expose so we can use this as an entrypoint
 top_level = TopLevelCommands()
-start_mcp_server = top_level.start_mcp_server
 
 # needed for the help script to work - register all subcommands to the top-level group
-for subgroup in (mode, context, project, config, tools, prompts):
+for subgroup in (_mode, _context, _project, _config, _tools, _prompts):
     top_level.add_command(subgroup)
-
-
-def get_help() -> str:
-    """Retrieve the help text for the top-level Serena CLI."""
-    return top_level.get_help(click.Context(top_level, info_name="serena"))