Fixes quarkusio#1443 by moving manifest generation in a specific meth…

…od, invoked after copying all files

The goal of this method is to make sure the entries we write in manfiest do not exist already or, if they exist, are compatible with quarkus requirements.
This goal is reached for MAIN_CLASS attribute, but not totally for CLASSPATH

core/creator/src/main/java/io/quarkus/creator/phase/runnerjar/RunnerJarPhase.java

@@ -325,17 +325,11 @@ public void accept(Path path) {
             }
         });
 
-        final Manifest manifest = new Manifest();
-        manifest.getMainAttributes().put(Attributes.Name.MANIFEST_VERSION, "1.0");
-        manifest.getMainAttributes().put(Attributes.Name.CLASS_PATH, classPath.toString());
-        manifest.getMainAttributes().put(Attributes.Name.MAIN_CLASS, mainClass);
-        try (OutputStream os = Files.newOutputStream(runnerZipFs.getPath("META-INF", "MANIFEST.MF"))) {
-            manifest.write(os);
-        }
-
         copyFiles(augmentOutcome.getAppClassesDir(), runnerZipFs);
         copyFiles(augmentOutcome.getTransformedClassesDir(), runnerZipFs);
 
+        generateManifest(runnerZipFs, classPath.toString());
+
         for (Map.Entry<String, List<byte[]>> entry : services.entrySet()) {
             try (OutputStream os = Files.newOutputStream(runnerZipFs.getPath(entry.getKey()))) {
                 for (byte[] i : entry.getValue()) {
@@ -346,6 +340,54 @@ public void accept(Path path) {
         }
     }
 
+    /**
+     * Manifest generation is quite simple : we just have to push some attributes in manfest.
+     * However, it gets a little more complex is manifest preexists.
+     * So we first try to see if a manifest exists, and otherwise create a new one.
+     * 
+     * <b>BEWARE</b> this method should be invoked after file copy from target/classes and so on.
+     * Otherwise this manifest manipulation will be useless.
+     * 
+     * @see https://github.com/quarkusio/quarkus/issues/1443
+     * @param runnerZipFs
+     * @param classPath
+     * @throws IOException
+     */
+    private void generateManifest(FileSystem runnerZipFs, final String classPath) throws IOException {
+        final Path manifestPath = runnerZipFs.getPath("META-INF", "MANIFEST.MF");
+        final Manifest manifest = new Manifest();
+        if (Files.exists(manifestPath)) {
+            log.warn(
+                    "Seems like you have a pre-existing MANIFEST.MF. Since quarkus generates an executable JAR, some entries will be added.");
+            try (InputStream is = Files.newInputStream(manifestPath)) {
+                manifest.read(is);
+            }
+        }
+        Attributes attributes = manifest.getMainAttributes();
+        if (!attributes.containsKey(Attributes.Name.MANIFEST_VERSION)) {
+            attributes.put(Attributes.Name.MANIFEST_VERSION, "1.0");
+        }
+        if (attributes.containsKey(Attributes.Name.CLASS_PATH)) {
+            log.warn(
+                    "Your MANIFEST.MF defines a CLASSPATH. We don't yet support merge of CLASSPATHS. So your CLASSPATH will be overwritten by Quarkus one.");
+        }
+        attributes.put(Attributes.Name.CLASS_PATH, classPath.toString());
+        if (attributes.containsKey(Attributes.Name.MAIN_CLASS)) {
+            String existingMainClass = attributes.getValue(Attributes.Name.MAIN_CLASS);
+            if (!mainClass.equals(existingMainClass)) {
+                log.errorf("Your MANIFEST.MF defines as %s %s, while Quarkus is configured to use %s. "
+                        + "Your main class will be replaced by quarkus one. This behaviour configured by property mainClass of quarkus plugin.",
+                        Attributes.Name.MAIN_CLASS, existingMainClass, mainClass);
+                attributes.put(Attributes.Name.MAIN_CLASS, mainClass);
+            }
+        } else {
+            attributes.put(Attributes.Name.MAIN_CLASS, mainClass);
+        }
+        try (OutputStream os = Files.newOutputStream(manifestPath)) {
+            manifest.write(os);
+        }
+    }
+
     private void copyFiles(Path dir, FileSystem fs) throws IOException {
         Files.walk(dir).forEach(new Consumer<Path>() {
             @Override