download.eclipse.org archive does not preserve directory structure

Summary

If I archive a directory that is already on archive.eclipse.org, it archives it into a subdirectory, losing directory structure and causing the https://www.eclipse.org/downloads/download.php script to not be able to find it. This issue led to https://www.eclipse.org/lists/epp-dev/msg06591.html

Steps to reproduce

Create a new directory on download.eclipse.org
Create two files in that directory
Archive one of those files - note how the directory structure has been created on archive.eclipse.org
Archive the directory created in step 1

What is the current bug behavior?

On archive.eclipse.org the directory name will be doubled. The file from step 3 will be in upper dir, the other in the nested one

What is the expected correct behavior?

The files in the directory are archived to the same relative location on archive.eclipse.org
Failing that, an error because the directory exists.

Relevant logs and/or screenshots

You can run this script to setup the condition (step 1 and 2) - this is job#101 in https://ci.eclipse.org/packaging/job/jonah-releng-test/

You can see the result of running all the steps in https://archive.eclipse.org/technology/epp/archivetest/

ssh genie.packaging@projects-storage.eclipse.org /bin/bash << EOF
  set -u # run with unset flag error so that missing parameters cause build failure
  set -e # error out on any failed commands
  set -x # echo all commands used for debugging purposes
  rm -rf /home/data/httpd/archive.eclipse.org/technology/epp/archivetest
  rm -rf /home/data/httpd/download.eclipse.org/technology/epp/archivetest
  mkdir -p /home/data/httpd/download.eclipse.org/technology/epp/archivetest
  touch /home/data/httpd/download.eclipse.org/technology/epp/archivetest/file1
  touch /home/data/httpd/download.eclipse.org/technology/epp/archivetest/file2
EOF