Lets say I have a file t.txt, a directory t and another file t/t2.txt. If I use the linux zip utility \"zip -r t.zip t.txt t\", I get a zip file with the following entries i
Like others said here to add empty directory add "/" to the directory name.
Pay attention NOT to add File.separator (equals to "\") which actually add an empty file to the zip.
It took me a while to understand what was my mistake - hope I save other some time...