fix: Set -archiveProject trueto avoid flattening

[dominik003]

Previously, the -archiveProject flag was set to false. As a result, the project imported from the T4C repository was made available as a simple directory, but all files of the project were flattened. This resulted in a java.nio.file.File.FileAlreadyExistsException exception when two images with the same name existed in different locations. This PR changes the -archiveProject flag to true, which ensures that the projects are passed as .zip files and their original structure is not changed. The archive is then simply unpacked, and as the original structure is retained using -archiveProject true, the previous unmessing step (i.e., moving images into a images and fragments into a fragments directory) is no longer necessary.

Resolves #151