FULL PRODUCT VERSION :
java version "9"
Java(TM) SE Runtime Environment (build 9+181)
Java HotSpot(TM) 64-Bit Server VM (build 9+181, mixed mode)

ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 10.0.16299.192]

A DESCRIPTION OF THE PROBLEM :
I'm the maintainer of the javafx-maven-plugin and discovered a breaking bug inside the JDK/javapackager.

```
// (Open)JDK 9 - WindowsAppImageBuilder
Files.copy(new File(srcdir, fname).toPath(), new File(appDir.toFile(), fname).toPath());
```

```
// (Open)JDK 8 - WinAppBundler
IOUtils.copyFile(new File(srcdir, fname), new File(appDirectory, fname));
```

Inside IOUtils.copyFile there is some code, which creates subfolders:
```
    public static void copyFile(File sourceFile, File destFile)
            throws IOException {
        destFile.getParentFile().mkdirs();
```

This is documented here while trying to make the maven-plugin compatible: https://github.com/javafx-maven-plugin/javafx-maven-plugin/issues/287#issuecomment-360599762

Anything in `StandardBundlerParam.APP_RESOURCES` or `StandardBundlerParam.APP_RESOURCES_LIST` having any item in subfolders (like a "lib"-folder) does not get copied, because `Files.copy` does not create non-existing target subfolders.

This only affects Windows-bundlers, MacOS(X)- and Linux-bundlers do create the required (sub)folder within `writeEntry`-method.

REGRESSION. Last worked in version 8u162

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
some user provided some example-project:
https://github.com/danielpeintner/Java9Test

Works with JDK 8 (using plugin-version 8.8.3), breaks since JDK 9 (using plugin-version 8.9.0-SNAPSHOT).

sorry there is no native javapackager-example u can simply try :(

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Packaging-process copies files from subfolders, creating working windows-bundle.
ACTUAL -
Packaging-process copies no a single files from subfolders, complains at the first encounter while ignoring IOExceptions, but works even further without breaking.

REPRODUCIBILITY :
This bug can be reproduced always.