Warn about common run-file pitfalls

src/Cli/dotnet/Commands/CliCommandStrings.resx

@@ -960,6 +960,22 @@ Tool '{1}' (version '{2}') was successfully installed. Entry is added to the man
   <data name="RunCommandExceptionNoProjects" xml:space="preserve">
     <value>Couldn't find a project to run. Ensure a project exists in {0}, or pass the path to the project using {1}.</value>
   </data>
+  <data name="RunCommandWarningFileArgumentPassedToProject" xml:space="preserve">
+    <value>Warning: '{0}' appears to be a file-based app but was passed as an argument to the project '{1}'. To run it as a file-based app, use 'dotnet run --file {0}'. To pass it as an application argument, use 'dotnet run -- {0}' to suppress this warning.</value>
+    <comment>{0} is the file path argument. {1} is the project file path.{Locked="dotnet run --file"}{Locked="dotnet run --"}</comment>
+  </data>
+  <data name="WarningFileArgumentPassedToMSBuild" xml:space="preserve">
+    <value>Warning: '{0}' appears to be a file-based app but was treated as an MSBuild argument. To treat it as a file-based app, use 'dotnet {1} {0}'.</value>
+    <comment>{0} is the file path argument. {1} is the command name (e.g. build, clean, publish).{Locked="dotnet"}</comment>
+  </data>
+  <data name="WarningCsFileArgumentPassedToMSBuild" xml:space="preserve">
+    <value>Warning: '{0}' looks like a file-based app but the file was not found, and it was treated as an MSBuild argument.</value>
+    <comment>{0} is the .cs file path argument.</comment>
+  </data>
+  <data name="RunCommandWarningCsFileArgumentPassedToProject" xml:space="preserve">
+    <value>Warning: '{0}' looks like a file-based app but the file was not found, and it was passed as an argument to the project '{1}'. To pass it as an application argument, use 'dotnet run -- {0}' to suppress this warning.</value>
+    <comment>{0} is the .cs file path argument. {1} is the project file path.{Locked="dotnet run --"}</comment>
+  </data>
   <data name="RunCommandExceptionUnableToRun" xml:space="preserve">
     <value>Unable to proceed with project '{0}'.
 Ensure you have a runnable project type.

src/Cli/dotnet/Commands/CommandFactory.cs

@@ -5,6 +5,7 @@
 using Microsoft.DotNet.Cli.CommandLine;
 using Microsoft.DotNet.Cli.Commands.Run;
 using Microsoft.DotNet.Cli.Utils;
+using Microsoft.DotNet.Cli.Utils.Extensions;
 using Microsoft.DotNet.ProjectTools;
 
 namespace Microsoft.DotNet.Cli.Commands;
@@ -39,6 +40,26 @@ internal static CommandBase CreateVirtualOrPhysicalCommand(
         }
         else
         {
+            // Warn if any argument looks like a file-based program entry point but we're falling back to MSBuild.
+            // This can happen when extra positional arguments prevent the single-arg file-based path from being taken,
+            // or when a .cs file doesn't exist (so IsValidEntryPointPath returns false).
+            foreach (var candidate in nonBinLogArgs)
+            {
+                if (VirtualProjectBuilder.IsValidEntryPointPath(candidate))
+                {
+                    Reporter.Error.WriteLine(
+                        string.Format(CliCommandStrings.WarningFileArgumentPassedToMSBuild, candidate, commandDefinition.Name).Yellow());
+                    break;
+                }
+
+                if (candidate.EndsWith(".cs", StringComparison.OrdinalIgnoreCase))
+                {
+                    Reporter.Error.WriteLine(
+                        string.Format(CliCommandStrings.WarningCsFileArgumentPassedToMSBuild, candidate).Yellow());
+                    break;
+                }
+            }
+
             var msbuildArgs = MSBuildArgs.AnalyzeMSBuildArguments([.. forwardedArgs, .. args], [.. optionsToUseWhenParsingMSBuildFlags]);
             msbuildArgs = transformer?.Invoke(msbuildArgs) ?? msbuildArgs;
             return createPhysicalCommand(msbuildArgs, msbuildPath);

src/Cli/dotnet/Commands/Run/RunCommand.cs

@@ -862,6 +862,41 @@ public static RunCommand FromParseResult(ParseResult parseResult)
             ref args,
             out string? entryPointFilePath);
 
+        // Warn if an argument looks like a file-based program entry point but we're falling back to project-based run.
+        // This helps users who accidentally run `dotnet run file.cs` in a directory containing a project file.
+        // Do not warn if --project or --file was explicitly specified.
+        // Only consider arguments that appear before '--' in the command line.
+        if (projectFilePath is not null && projectOption is null && fileOption is null && !readCodeFromStdin)
+        {
+            var argValuesBeforeDoubleDash = parseResult.Tokens
+                .TakeWhile(static t => t.Type != TokenType.DoubleDash)
+                .Where(static t => t.Type == TokenType.Argument)
+                .Select(static t => t.Value)
+                .ToHashSet();
+
+            foreach (var arg in args)
+            {
+                if (!argValuesBeforeDoubleDash.Contains(arg))
+                {
+                    continue;
+                }
+
+                if (VirtualProjectBuilder.IsValidEntryPointPath(arg))
+                {
+                    Reporter.Error.WriteLine(
+                        string.Format(CliCommandStrings.RunCommandWarningFileArgumentPassedToProject, arg, projectFilePath).Yellow());
+                    break;
+                }
+
+                if (arg.EndsWith(".cs", StringComparison.OrdinalIgnoreCase))
+                {
+                    Reporter.Error.WriteLine(
+                        string.Format(CliCommandStrings.RunCommandWarningCsFileArgumentPassedToProject, arg, projectFilePath).Yellow());
+                    break;
+                }
+            }
+        }
+
         bool noBuild = parseResult.HasOption(definition.NoBuildOption);
         string launchProfile = parseResult.GetValue(definition.LaunchProfileOption) ?? string.Empty;