Bill, these pants have neither a fly nor sewn in briefs.
While I did consider both during the design, the real goal was to create something that reflected that tenet of "simplicity".
In looking at other pants on the market, I found many of them that had a fly, a brief liner, belt loops, ankle snaps, a second cargo pocket, rear pocket, felted waist liner, knee patches, butt patches, instep patches, etc. etc.
So during design I started hacking those things out, deciding that these pants wouldn't need things. That is backwards to me, so I abandoned that approach and went back to the drawing board with a pair of pull-on pants, and added back only a few things (a few pockets, drawcord).
What I wanted:
Protection from sun, wind, and biting insects for minimal weight.
I had a hard time putting pockets on them even! :)
OK, back to seriousness. Regarding the brief liner, those of us who do wear a separate boxer/brief (stay tuned for a Merino UL version in 2009, mayyyyybe...) would have to cut out a mesh liner in the pant. I think many folks will be able to go commando in these well enough, too, with the absence of the fly.
The combination of the Merino UL and the Thorofare shirt/pants are terrific for cool weather. They are very comfortable for walking, hanging out, sleeping, with the warm inner lining and slicker outer surface that's not clammy like an outer shell of wind/rainwear.