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Yep, there's a notes.ini setting FTBasePath to move the FT indices to a different location, out ot the Domino\Data. I guess this is what you need.
+1, along with the remarks made in the previous comments.
I'd think 'put all .ft directories elsewhere by default' is the right/better approach... because:
a) if I recall right, some of the code is there
b) excluding the .ft directories from backup is comming up often enough, too.
c) Copying directories of databases elsewhere (Server Migration, at hock backups) ofthen don't need that part.