refactor CLI command modules and synchronize docs

src/vlm/commands/plan.py

@@ -81,6 +81,15 @@ def plan_cmd(ctx: CLIContext, input: Path, output: Path, analysis: Optional[Path
         click.echo(f"  ⚠️  Conflicts detected: {conflicts}")
         click.echo("     Review the plan file for details on conflicting operations.")
 
+    # Check for directory warnings
+    directory_warning = execution_plan.metadata.get("directory_warning", False)
+    if directory_warning:
+        emptied_dirs = execution_plan.metadata.get("emptied_directories", [])
+        click.echo()
+        click.echo(f"  ⚠️  Directory preservation warning: {len(emptied_dirs)} directories will be emptied")
+        click.echo("     These directories will be preserved but may be empty after execution.")
+        click.echo("     Review the plan file for details on preserved directories.")
+
     click.echo()
     click.echo(f"Saving execution plan to: {output}")
     output.parent.mkdir(parents=True, exist_ok=True)