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TFS on VS2010, merging code issues

Recently we have been having problems with TFS and our code base. We have a section of tests that use Webdriver, and a section that use Coded UI. Lately, we've been having problems merging our code after a new build has been pushed out. Some folders show up as a white outline of a folder, which we can right click and select "include in project". We also notice some files missing, and we can't "get latest" to grab them. We have to go some round about way to do it (shelve code, delete local files, get latest, merge code). Even when we do that we still have some issues.

But the main issue we are having is that our Coded UI maps are breaking. Instead of being the normal structure such as:

.uitest

----.cs

----.designer.cs

When we merge in the new code, the UI maps break out like:

.cs

----.designer.cs

.uitest

I opened the .csproj in notepad++ and noticed that both the .cs and .designer.cs files no longer have a dependancy of the .uitest file. Now the .cs file has no dependancy, and the .designer is dependant on the .cs file. We can fix it with relative ease, but it keeps breaking in every build and we have several maps we need to fix. What exactly could the problem be here? Also, referring to my frist problems of files not being included in the project, what could the issue be there?

I asked the same question on the MSDN forums, but the suggestions I have received I have already tried, like creating a new workspace since the other might be corrupt. Still didn't work.

Thanks in advance

Edit: Had a suggestion on the MSDN forums to run VS as administrator. That didn't work either. Not really sure what could be causing this issue. It doesn't seem to be causing problems for everybody because some new builds cause issues for some people but not others. Some more info would be I run on Windows 7 64bit and Visual Studio Ultimate 2010.

In the past I've had issues with TFS that sound similar, 2 of our developers seemed to periodically create problems when merging files into the data store, folders and files would show as not included while the project file would make it in (breaking everything after get latest). Eventually the problem went away but we never truly found the source. I believe it had something to do with our network - maybe a switch issue in combo with the way we mapped working folders to network drives pointing to a shared dev server. Also one of the workstations seemed to have a problem with windows explorer not seeing file updates on the dev server share... developer would have to hit \\servername\\C$\\sharefolder then hit his mapped network drive again before updates would refresh. (And his check in's created the most problems) ... we ran VS2008, TFS2010

Just some ideas...

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