Code review comment: I wouldn't have a warn here. It's not something that needs special attention or something on which the user can do something.

Code under review:
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();
        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);
        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);
        }
    }

Line commented on: "Seems like you have a pre-existing MANIFEST.MF. Since quarkus generates an executable JAR, some entries will be added.");

Revised code:
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)) {
            try (InputStream is = Files.newInputStream(manifestPath)) {
                manifest.read(is);
            }
        }
        Attributes attributes = manifest.getMainAttributes();
        attributes.put(Attributes.Name.MANIFEST_VERSION, "1.0");
        if (attributes.containsKey(Attributes.Name.CLASS_PATH)) {
            log.warn(
                    "Your MANIFEST.MF already defined a CLASS_PATH entry. Quarkus has overwritten this existing entry.");
        }
        attributes.put(Attributes.Name.CLASS_PATH, classPath);
        if (attributes.containsKey(Attributes.Name.MAIN_CLASS)) {
            String existingMainClass = attributes.getValue(Attributes.Name.MAIN_CLASS);
            if (!mainClass.equals(existingMainClass)) {
                log.warn("Your MANIFEST.MF already defined a MAIN_CLASS entry. Quarkus has overwritten your existing entry.");
            }
        }
        attributes.put(Attributes.Name.MAIN_CLASS, mainClass);
        try (OutputStream os = Files.newOutputStream(manifestPath)) {
            manifest.write(os);
        }
    }