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Have you read https://wiki.jenkins-ci.org/display/JENKINS/Publish+Over+... - specifically the section on Transfer sets and the examples at the bottom of the page?
1. it looks like you should set:
Source files: dir1/dir2/dir3/file.zip
Remote directory: dir1
Remove prefix: dir1/dir2/dir3/
NB: the Remote directory is relative to the directory specified in the server configuration (in manage Jenkins) so if that is not root, but is dir1, then the remote directory in the transfer set should be empty.
2. I really cannot understand what problem you are trying to describe here. Can you provide an example?