This is the gametypes.txt file that should make mani work for sf. This will make all command except ma_swapteam work. Unfortunately I cannot fix that error because it was generated by the March 12/13th Valve update. If I find a work around for that error I will update the post with the information.
edit, use new url.
EDIT: March 26
Everthing works now even ma_swapteam. Simply install base mani beta 1.2M and use these files. This is for source meta mod version. If you use the regular mani version use the mani_server.cfg and the gametypes.txt file still but get the rev 7 from the mani forums. The dll and so file in this are just the ones form mani beta 1.2m rev 7 if you were wondering.
http://www.kylegar.net/files/mani.rar
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edit: April 17th
This is the files for mani on windows, the same ones BE has now. This is for the non beta of mani. Use this on the last stable release.
http://kylegar.net/files/gametypes_for_windows.rar