In the upgrading instructions on the Wiki, it reads to NOT copy over database.php. I think that it should further include some notable mentions, as follows:
- .htaccess (if no changes in the upgrade) should NOT be copied over. [Because my original install was to a subdirectory, this caused me a great deal of grief when I updated.]
- a warning that template or language files that have any customization using their original file names will be lost if default files are copied over in an upgrade. [Luckily I had copies of the customized files.]