Hey Bill,
thank you for using WPN-XM and raising this issue.
> Is there a method to upgrade the components of an installation without overwriting configuration and database information?
No, an "Upgrade" feature isn't implemented, yet.
I've added backup functionality for some configuration files.
For instance, if "php.ini" is found, it's renamed to "php.ini.old". But that's it.
The database information is not handled at all.
This requires a database dump, followed by the upgrade (replace with newer version) and an import of the dump.
The two folder problem ("nginx" and "nginx-1.9.2") exists, because the rename command fails, if the target folder exists.
The installer needs to check, if it is an upgrade and switch from rename to copy.
Best, Jens