The javadoc tool has a no-argument `-docfilessubdirs` option to enable deep copying of nested directories in `doc-files` directories, and a `-excludedocfilessubdir name` to exclude specific directories when using the former option. By default, nested directories in `doc-files` are not copied to the output.

These options were introduced in JDK-4468396 in order to deal with subdirectories allocated by version control systems such as SCCS. Since modern version control systems do not create subdirectories within repository directories, the default behaviour seems obsolete. The behaviour most users would expect is for nested directories to be included in the generated documentation.

As a a first step, we should change the default behaviour to include nested directories and deprecating the `-docfilessubdirs` (making it a no-op and possibly triggering a warning). Removal of the `-docfilessubdirs` option and possible deprecation/removal of `-excludedocfilessubdir` should be revisited at a later point in time.