Towards the beginning of the episode, The Doctor came to Clara's for Christmas dinner. He met her, Naked, in the TARDIS console room. There were several following scenes where people were "clothed" by holograms - Clara introducing The Doctor as her boyfriend, and he'd forgotten to make sure his hologram was visible to the family, so they saw him as naked - meeting the supreme leader of the Papal Mainframe, apparently everyone is nude, but wearing holograms ...
After a few minutes of this the nudity-hidden-by-hologram is not mentioned, but by the statements established in the story that state of nudity continued for awhile.
For example, when Clara and the Doctor are teleported down to Christmas, Trenzalore, and it's snowy and cold, and The Doctor hugs Clara to warm her, they're both still naked and clothed by holograms.
When the Doctor sends the TARDIS to take Clara back, why doesn't his hologram projection disappear?
But did the nudity add anything to the story? Nope. In fact, it detracted from the story, as illustrated by the Gawking Doctor image above.
This nudity plot element converted The Doctor from a minor deity (ergo - River Song's line in The Angels Take Manhattan) to a dirty old man. WHY??!?!?!?
Are we supposed to now believe that in the entire Battle of Demons Run, the soldiers were all naked? That Madama Kovarian was naked in every scene we saw her in? If so, why? What does this add to anything?
Why did the nudity plot element get dropped? Did the writers realize they made a mistake, and never mentioned it again, but if so then why not just remove it entirely from the script?
Maybe oh maybe Moffat has -- well, I'd say, "something up his sleeve" but there might be no sleeve in this case -- something planned for a later episode about nudity. For some unfathomable reason, this was put into the episode, on purpose, and Moffat never does anything without a reason. It's a complete mystery what this would be. In the meantime he's converted the Doctor into a leering goon, and I don't like it.