I've installed this morning the web deployment project ctp for VS 2008 and immediately had an error with merging connectionStrings for my release build. It presents with error WDP00002: missing section connectionStrings. This is occurring because the project is not copying from the TempBuildDir to the output directory before the merge process. The result is that it's trying to merge the connection string section into a web.config file that doesn't actually exist. This should also work for the missing appSettings posted on some of the forums - but I haven't test that
After a bit of research, I thought I'd found the solution here, but had to modify it slightly. For me, it works when I move it into the AfterMerge target of the deployment project - like thus
<Target Name="AfterMerge">
<CreateItem Include="$(TempBuildDir)\**\*.*">
<Output ItemName="CompiledFiles" TaskParameter="Include" />
</CreateItem>
<Exec Command="if exist "$(WDTargetDir)" rd /s /q "$(WDTargetDir)"" />
<Exec Command="if not exist "$(WDTargetDir)" md "$(WDTargetDir)"" />
<Copy SourceFiles="@(CompiledFiles)" DestinationFolder="$(WDTargetDir)\%(CompiledFiles.SubFolder)%(CompiledFiles.RecursiveDir)" />
<Exec Command="if exist "$(TempBuildDir)" rd /s /q "$(TempBuildDir)"" />
</Target>
Hopefully they'll fix this for the release build.