nicely done, but do note that currently, the steam release is not compatible with ss2tool.

Thanks, I've added a little update and also to the PCGamingWiki page: http://pcgamingwiki.com/wiki/System_Shock_2

I'd actually like to know more about your statement:

"due to the fact that mods won’t have the correct permissions to access the \Program Files\ folder"

I usually see stuff like this said by people that don't commonly use Steam. I don't have hard evidence that this isn't true, but two things make me believe it's fallacy.

1) I've installed multiple mods to the default steamapps folder structure without any issues
2) Steam atleast semi-supports mods, especially with things like steamworks in place. I think they would change the default folder location if this was always a problem for mods

I HAVE had problems with modding games that I myself install to the program files folder. But my assumption is that when Valve sets up steamapps they adjust the permissions correctly before installing.

Have you actually tried modding SS2 when it's installed into the default steamapps folder location? If you have and it doesn't work, then it's good information for me to know and I stand corrected. If not, then you should atleast try before potentially spreading disinformation.

System Shock2 does not work properly when installed in program files (vista and newer). the game might crash, not work at all, refuse to save user settings and change resolution, corrupt saves, not make them at all, and other nasty stuff.

never, I repeat, NEVER EVER install the game into program files. not even when someone tells you it will cure cancer, save the entire humanity or whatever.

consider this the official statement of the systemshock.org staff.

What's the final situation with the flora mod? Is it all working properly?

yes, it should work, but make sure to get the fixup package, even though it's marked as optional.