Change JavaLayerConfiguration.set___Files to use the new API to add source files

[chanseokoh]

Current signature: setExtraFiles(List<Path> extraFiles)

Currently, the source files (extraFiles) should be top-level files and directories. If a source path is a directory, JavaLayerConfiguration calls LayerConfiguration.Builder.addEntryRecursive() to add all the files and sub-directories in the directory recursively. That is, it is not possible to separate files in a directory into different layers (much like the problem of #957). This is also problematic in the WAR case. For example,

WAR-root/
    index.html
    WEB-INF/
        classes/
            HelloServlet.class
            cool.properties
        web.xml

The resources layer should have

index.html                       -->  to be placed in <appRoot>
WEB-INF/web.xml                  -->  to be placed in <appRoot>
WEB-INF/classes/cool.properties  -->  to be placed in <appRoot>

which should be unpacked at the root of the application in an image, whereas the classes layer should have

WEB-INF/classes/HelloServlet.class  -->  to be placed in <appRoot>

or

HelloSevlet.class  -->  to be placed in <appRoot>/WEB-INF/classes

Fortunately, #956 is fixed, so we can now change setExtraFiles() to accept an explicit list of individual files to add. That is, instead of adding fiels with addEntryRecursive(), just add each file with addEntry(). However, it may be inconvenient for callers to always explicitly list all the files, so it'll be good to have setExtraFilesDirectory() and setExtraFilesDirectories() too.

[chanseokoh]

One things to consider is, how this should work with JavaDockerContextGenerator (#1010).