I have a gripe about web projects in Visual Studio 2005, and it's already come up to bite me in the butt a few times.
The idea that every file in the folder is part of the site never really sat well with me, but I couldn't put my finger on why. But, after using it with a development team, I now know why. When I delete a file, it's removed from my local site, and from source control, which, by the way, is awesome! But here's the problem: when one of the other developers checks in, it picks up that file I deleted (or renamed) as a new file, and adds it back in!
That's not good.
So, now everytime I delete a file, I have to email the team to let them know to remove it locally as well. Or everyone on the team has to watch for newly added files. Something they aren't used to doing. And in my opinion, they shouldn't have to.
I'm sure there are some very good reasons for the new model. I'm getting more and more comfortable with the whole idea of the App_Code folder, but I'm still stuck on the idea of including all files, i.e., no project file.
I know there's a new web project model coming, and that there's an initial release out there, but until it's an officially supported model, it's tough to justify pushing clients that way. Once it's official, I'm pretty sure that's the way we'll go, but until then, we have a few issues to iron out.