diff --git a/src/Core/RemoteRefExtensions.cs b/src/Core/RemoteRefExtensions.cs
index bdda884..39097ae 100644
--- a/src/Core/RemoteRefExtensions.cs
+++ b/src/Core/RemoteRefExtensions.cs
@@ -1,6 +1,4 @@
-using System.Runtime.InteropServices;
-
-namespace Devlooped;
+namespace Devlooped;
 
 public static class RemoteRefExtensions
 {
@@ -11,13 +9,12 @@ public static class RemoteRefExtensions
         public string EnsureTempPath() => Directory.CreateUserDirectory(location.TempPath);
     }
 
-    /// <summary>Obtains the temporary directory root, e.g., <c>/tmp/dotnet/runfile/</c>.</summary>
+    /// <summary>Obtains the temporary directory root, e.g., <c>~/.local/share/dotnet/runfile/</c>.</summary>
     static string GetTempRoot()
     {
-        // We want a location where permissions are expected to be restricted to the current user.
-        string directory = RuntimeInformation.IsOSPlatform(OSPlatform.Windows)
-            ? Path.GetTempPath()
-            : Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData);
+        // We use LocalApplicationData (not the system temp folder) on all platforms so that
+        // dnx's built-in cleanup of %TEMP% doesn't prune our cached repo downloads mid-run.
+        string directory = Environment.GetFolderPath(Environment.SpecialFolder.LocalApplicationData);
 
         return Directory.CreateUserDirectory(Path.Join(directory, "dotnet", "runfile"));
     }
diff --git a/src/Core/RemoteRunner.cs b/src/Core/RemoteRunner.cs
index 089ff48..4fea6aa 100644
--- a/src/Core/RemoteRunner.cs
+++ b/src/Core/RemoteRunner.cs
@@ -108,8 +108,11 @@ await AnsiConsole.Status().StartAsync($":open_file_folder: {location} :backhand_
 
         if (updated)
         {
-            // Clean since otherwise we sometimes get stale build outputs? :/
-            Process.Start(DotnetMuxer.Path.FullName, ["clean", "-v:q", program]).WaitForExit();
+            var objDir = Path.Combine(location.TempPath, "obj");
+            // Only clean when there are existing build artifacts; skip on freshly extracted
+            // directories (no obj/) since dotnet clean on a new dir can corrupt the lock file.
+            if (Directory.Exists(objDir))
+                Process.Start(DotnetMuxer.Path.FullName, ["clean", "-v:q", program]).WaitForExit();
         }
 
         string[] runargs = aot