"I thought you realized Mars Direct was an extended stay mission."

My understanding of "Mars Direct" is that it's not some exact plan, but rather an general approach to going to Mars.

"Or maybe I was mistaken in the belief that you and everyone else was talking about extended stays on the Moon vs extended stays on Mars. I didn't realize you or anyone else was pushing for more flags and footprint missions to the Moon."

I'm not for a flag and footprint lunar mission. The time spent on the surface is not relevant to whether something is "flag and footprint"- you could spend a year on the lunar surface and still have it a flags & footprint mission.

"A real mission to look for lunar resources should also be an extended one to be cost effective."

Depends on how you are measuring "cost effective". For instance, achiving a goal for the least amount of time and money is how I would define cost effective. And for the Moon, the main goal would be determine if there was minable deposits of water.

"The shuttle is a huge waste not because each mission costs so much, but because each mission accomplishes so little. The ISS was supposed to change that but its research function has been gutted."

I would characterize the huge waste of the Shuttle as not developing commerical RLVs. The Shuttle was suppose to lower the cost of access to space for NASA, it was also suppose to lead to commerical development of RLV. It didn't do either- and the goal of commerical development of RLV was the higher value which "allowed" the huge amount of money to be spent for it's development. If the goal was merely to lower NASA's launch cost then this would have required far less development costs.
And ISS was also suppose to lead to commerical space development- though this reason wasn't as much a driver- it wasn't believable. ISS was almost axed. The jobs involved, money already spent, and finally involving the Russians tweeked it to passing.