The IFA didn't exactly object to the partition of football in Ireland now, did they?
I'm sure you and most (all?) IFA fans are not that concerned about it either. Unless you secretly wish there was one association to govern football in Ireland?
If the FAI was founded with the intention of being the main governing body on the island, then that is hardly partitionist. Rather, circumstances (those damn circumstances again!) meant that that was the ultimate effect.
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