diff --git a/tools/RunScript.hx b/tools/RunScript.hx
index 03a9912b36..8b6060829e 100644
--- a/tools/RunScript.hx
+++ b/tools/RunScript.hx
@@ -127,19 +127,9 @@ class RunScript
 	{
 		var args = Sys.args();
 
-		var limeDirectory = Haxelib.getPath(new Haxelib("lime"), true);
-		var toolsDirectory = Path.combine(limeDirectory, "tools");
-
-		if (!FileSystem.exists(toolsDirectory))
-		{
-			limeDirectory = Path.combine(limeDirectory, "..");
-			toolsDirectory = Path.combine(limeDirectory, "tools");
-		}
-
-		if (args.length > 2 && args[0] == "rebuild" && args[1] == "tools")
+		if (args.length > 0)
 		{
 			var lastArgument = new Path(args[args.length - 1]).toString();
-			var cacheDirectory = Sys.getCwd();
 
 			if (((StringTools.endsWith(lastArgument, "/") && lastArgument != "/") || StringTools.endsWith(lastArgument, "\\"))
 				&& !StringTools.endsWith(lastArgument, ":\\"))
@@ -149,10 +139,25 @@ class RunScript
 
 			if (FileSystem.exists(lastArgument) && FileSystem.isDirectory(lastArgument))
 			{
-				Sys.setCwd(lastArgument);
+				Haxelib.workingDirectory = lastArgument;
 			}
+		}
+
+		var limeDirectory = Haxelib.getPath(new Haxelib("lime"), true);
+		var toolsDirectory = Path.combine(limeDirectory, "tools");
+
+		if (!FileSystem.exists(toolsDirectory))
+		{
+			limeDirectory = Path.combine(limeDirectory, "..");
+			toolsDirectory = Path.combine(limeDirectory, "tools");
+		}
+
+		if (args.length > 2 && args[0] == "rebuild" && args[1] == "tools")
+		{
+			var cacheDirectory = Sys.getCwd();
+			// used for Path.tryFullPath when setting overrides
+			Sys.setCwd(Haxelib.workingDirectory);
 
-			Haxelib.workingDirectory = Sys.getCwd();
 			var rebuildBinaries = true;
 
 			for (arg in args)
@@ -210,7 +215,7 @@ class RunScript
 				"-D", "lime",
 				"-cp", toolsDirectory,
 				"-cp", Path.combine(toolsDirectory, "platforms"),
-				"-cp", "src",
+				"-cp", Path.combine(limeDirectory, "src"),
 				"-lib", "format",
 				"-lib", "hxp",
 				"--run", "CommandLineTools"].concat(args);