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=== Moving all files to another directory structure ===

 $ find -type f | while read f; do mv -f --backup=t "$f" "../otherdir/$f"; done

=== Removing empty directories ===

 $ find -depth -type d | xargs rmdir

The trick here is that <code>rmdir</code> will not remove non-empty directories.
We use <code>find -depth</code> to act on deeper directories first.