Working directory and website directory differ

Hello,

I've been stumped with this problem for the past day. I have a VS2010 project I'm trying to deploy, via Git. I have two steps: Build a .SLN and then run MSBuild to deploy. Both steps succeed.

However, when I look at the directory where the website is deployed, it's missing about half the files. From what I can tell, it's missing all .cs and .aspx.cs files, but has .aspx files, .css files, etc.

When I look at the working directory (under /TeamCity), _all_ of the files are there.

Any idea what may be causing this? Thank you!