Fix incremental build losing output under excludedocfilessubdir

[delanym]

When docfilessubdirs is enabled together with excludedocfilessubdir, an incremental build (re-run without a clean) could leave the excluded subdirectory's generated files missing from the output.

copyAllResources() removes the excluded doc-file subdirectories from the output directory before Javadoc runs, relying on Javadoc to regenerate them. However, the staleDataPath up-to-date check (enabled by default) skips the Javadoc invocation when the command line is unchanged, so on a second run the files were deleted but never regenerated.

Move the copyAllResources() call so it runs only when Javadoc is actually (re)generated. When the output is up to date, generation and resource copying are both skipped and the previous output is left intact.

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