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Avoid maintaining two different installations.
In the long run it will be easier for you to:
- import DB into a new test installation of XOOPS 2.5.5
- update all modules, incl. import of SmartSection data into Publisher
- remove SmartSection and clone Publisher into SmartSection (this will keep the old links working).
- make a backup of the old installation, and replace it with the new one
With that, you would be done, and have it as it is right now.
However, if you want to change your Site from:
http://www.ocaholic.ch/xoops/html/to
http://www.ocaholic.ch/you should then move your files to appropriate directory, or change the setup on your server.
And in order to keep all the saved old links working, you should then use Apache Mod_Rewrite, so your visitors get redirected correctly.