I'm doing a new install of the game cleaning most of the mods. On the Wiki page it gave a list of mods that need to be cleaned. I am going to do a full Fcom install. It was noted that you should not clean any of the Fcom files. It said that WarCry and Bob's Armory need to be cleaned. Two questions:
What about Fran's, MMM and OOO, should they be cleaned also? Also, is there a recommended install order for the mods, e.g. OOO first, MMM next, etc.
All enlightenment will be greatly appreciated.

WarCry and Bob's Armory are not core FCOM components. The last three mods you mentioned are, and they absolutely should not be cleaned. Leave the to the modders. You really have to know what your doing. I would not even suggest how to tweak such plugins to anyone less than an advanced mod, preferably FCOM, user. Here is a link to the best FCOM install guide: http://www.gamesas.com/index.php?/topic/1079933-50-steps-to-ctd-almost-free-fcom-game/.

Edit: http://www.gamesas.com/index.php?/topic/1079991-relz-fcomconvergance/page__view__findpost__p__15769697

Thabks for the info. Will do some more reading and hopefully learning.

You do not know how happy it makes me to read that statement. Reading is good. ^__^