diff --git a/src/main/java/com/dostalgia/UploadResource.java b/src/main/java/com/dostalgia/UploadResource.java
index f5755e0..d6bc4fe 100644
--- a/src/main/java/com/dostalgia/UploadResource.java
+++ b/src/main/java/com/dostalgia/UploadResource.java
@@ -62,6 +62,8 @@ public class UploadResource {
 
             Path extractDir = tmpDir.resolve("extracted");
             unzip(zipPath, extractDir);
+            // If the ZIP has a single root directory, flatten it
+            flattenSingleDir(extractDir);
 
             // Find main executable
             String mainExe = findMainExe(extractDir);
@@ -86,7 +88,7 @@ public class UploadResource {
                 // Write js-dos config
                 Path jsdos = gameDir.resolve(".jsdos");
                 Files.createDirectories(jsdos);
-                String relExe = extractDir.relativize(Path.of(mainExe)).toString().replace('/', '\\');
+                String relExe = extractDir.relativize(Path.of(mainExe)).toString();
                 Files.writeString(jsdos.resolve("dosbox.conf"), buildDosboxConf(relExe));
                 Files.write(jsdos.resolve("jsdos.json"), buildJsdosJson(relExe));
                 bundleFile = ".jsdos/dosbox.conf";
@@ -170,6 +172,40 @@ public class UploadResource {
         }
     }
 
+    /**
+     * If the extraction directory contains a single subdirectory, move
+     * its contents up (flatten). This handles ZIPs where all game files
+     * are inside a folder (e.g. "game/DOOM2.EXE" → "DOOM2.EXE").
+     */
+    private void flattenSingleDir(Path dir) throws IOException {
+        List<Path> entries;
+        try (var files = Files.list(dir)) {
+            entries = files.toList();
+        }
+        if (entries.size() != 1) return;
+        Path only = entries.get(0);
+        if (!Files.isDirectory(only)) return;
+
+        LOG.info("Flattening single root directory: " + only.getFileName());
+        // Walk in reverse order so directories are empty when we delete them
+        try (var walk = Files.walk(only)) {
+            var list = walk.sorted(Comparator.reverseOrder()).toList();
+            for (Path f : list) {
+                if (f.equals(only)) continue;
+                Path target = dir.resolve(only.relativize(f));
+                if (Files.isDirectory(f)) {
+                    Files.createDirectories(target);
+                    Files.delete(f);
+                } else {
+                    Files.createDirectories(target.getParent());
+                    Files.move(f, target, StandardCopyOption.REPLACE_EXISTING);
+                }
+            }
+        }
+        Files.delete(only);
+        LOG.info("Flattened " + only.getFileName());
+    }
+
     // ─── Executable Detection ────────────────────────────────────
 
     private String findMainExe(Path dir) throws IOException {
@@ -211,7 +247,7 @@ public class UploadResource {
             // Create .jsdos config
             Path jsdos = tmpBundle.resolve(".jsdos");
             Files.createDirectories(jsdos);
-            String relExe = extractDir.relativize(Path.of(mainExe)).toString().replace('/', '\\');
+            String relExe = extractDir.relativize(Path.of(mainExe)).toString();
             Files.writeString(jsdos.resolve("dosbox.conf"), buildDosboxConf(relExe));
             Files.write(jsdos.resolve("jsdos.json"), buildJsdosJson(relExe));
 
@@ -236,11 +272,10 @@ public class UploadResource {
     // ─── Configuration Helpers ───────────────────────────────────
 
     private byte[] buildJsdosJson(String relExe) {
-        String parts[] = splitPath(relExe);
-        String script = (parts[0].isEmpty() ? "" : "cd " + parts[0] + " && ") + parts[1];
+        // relExe is always just a filename after flattenSingleDir
         String json = "{"
             + "\"autoexec\":{"
-            + "\"options\":{\"script\":{\"value\":\"" + escapeJson(script) + "\"}}"
+            + "\"options\":{\"script\":{\"value\":\"" + escapeJson(relExe) + "\"}}"
             + "},"
             + "\"output\":{"
             + "\"options\":{\"autolock\":{\"value\":true}}}"
@@ -249,10 +284,7 @@ public class UploadResource {
     }
 
     private String buildDosboxConf(String relExe) {
-        String parts[] = splitPath(relExe);
-        String dir = parts[0];
-        String exe = parts[1];
-
+        // relExe is always just a filename after flattenSingleDir
         return "[sdl]\n"
             + "autolock=true\n"
             + "usescancodes=true\n"
@@ -282,21 +314,7 @@ public class UploadResource {
             + "mount c .\n"
             + "c:\n"
             + "cls\n"
-            + (dir.isEmpty() ? "" : "cd " + dir + "\n")
-            + exe + "\n";
-    }
-
-    /**
-     * Split a DOS path into directory and filename parts.
-     * Handles both backslash and forward-slash separators.
-     * Returns [dir, exe] where dir is empty for root-level files.
-     */
-    private String[] splitPath(String path) {
-        int idx = Math.max(path.lastIndexOf('/'), path.lastIndexOf('\\'));
-        if (idx >= 0) {
-            return new String[]{path.substring(0, idx), path.substring(idx + 1)};
-        }
-        return new String[]{"", path};
+            + relExe + "\n";
     }
 
     private String escapeJson(String s) {