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I have found that ncftp has this ability to recursive upload directorys. My problem now is that my directory contains a .svn and a .git folder that I do not want uploaded.

ncftpput -R -v -u "user" -p "pass" ftp.own.com /ftp/folder/to/to/place/local/folder/in /local/folder/to/upload

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Actually I got the idea how to do this while writing up this question. Might seem a but hacky but if I not missed something ncftp does not provide some exclude option.

So since I use a script anyway. I just deny ncftp access to that folders temporary. Resulting in creation but empty .git and .svn folders on the ftp server.

chmod 000 .svn
chmod 000 .git
ncftpput -R -v -u "user" -p "pass" ftp.own.com /ftp/folder/to/to/place/local/folder/in /local/folder/to/upload
chmod 700 .svn
chmod 700 .git

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