This should be interesting.
Let me see if my poor brain understood the installation instructions.
On step two: I delete everything except for the "user" folder. I installed OXC ver1.0 from the zip file and I have my save games on a subfolder alongside with "data". This step preserves essentially only the save games and the configurations.
My understanding is any .dll files of version 1.0 are not longer needed as the compiled nightly has an exe that is self contained in that regard.
On step three: By "Install OpenXcom" it is meant to say install the contents of the latest nightly, which I see they have obviously the new folder structure. The files of version 1.0 are superseded and not need to be installed again before the installation of the nightly, as it used to be the case.
On step four: The original UFO folders are to be copied on the UFO folder. The universal patch files must be also copied along as well.
On step six: The mods folder that I should create would be "\OpenXcom\user\mods". And there is where I dump the mods to use, each on its own folder.
Future nightlies, for a clean install, would require the "common", "standard" folders, and the "openxcom.exe", "CHANGELOG.txt", and "LICENSE.txt" files, to be deleted. Or the other way around, "UFO", "TFTD", and "user" folders to be preserved while everything else is deleted prior to the new nightly installation.
Did I get right? I ran a quick battle and it appeared fine.