Difference when building VS solution in VS and msbuild

I'm having an issue building some projects. I´ve found differences between building my solutions in VS (it work fine), and building the solutions with msbuild through command line (it fails).

I've managed to make a small sample that illustrates the problem. [BuildError.zip](https://github.com/Microsoft/msbuild/files/77337/BuildError.zip)

Basically I've got 2 solutions `SolA.sln` and `SolAandB.sln`. `SolA.sln` only contains project `A.csproj` while `SolAandB.sln` contains both `A.csproj` and `B.csproj`. The project `A.csproj` is just a class library, while `B.csproj` is a command line project which references project `A.csproj`. The **subtle peculiarity** about this projects, is that `A.csproj` is configured to not be built in `SolAandB.sln`. The reason of this, is that I've got a lot of projects (more than 300, some of which are C# and others are C++ managed and unmanaged), and some projects are included in more than one solution (mainly to allow adding references to the project), but I only want to build the project once.

When I build `SolAandB.sln` in VS (I'm using `VS2015` with update 1, but don't believe that changes anything), I can see that the invocation to `csc.exe` for `B.csproj` is as follows (I've added line breaks between arguments for clarity):

```
C:\Program Files (x86)\MSBuild\14.0\bin\csc.exe
/noconfig
/nowarn:1701,1702,2008
/nostdlib+
/platform:anycpu32bitpreferred
/errorreport:prompt
/warn:4
/define:DEBUG;TRACE
/errorendlocation
/preferreduilang:en-US
/highentropyva+
/reference:"F:\Visual Studio 2015\Projects\BuildError\A\bin\Debug\A.dll"
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5.2\mscorlib.dll"
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5.2\System.Core.dll"
/debug+
/debug:full
/filealign:512
/optimize-
/out:obj\Debug\B.exe
/ruleset:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\Team Tools\Static Analysis Tools\\Rule Sets\MinimumRecommendedRules.ruleset"
/subsystemversion:6.00
/target:exe
/utf8output
Program.cs
Properties\AssemblyInfo.cs
"C:\Users\Fede\AppData\Local\Temp\.NETFramework,Version=v4.5.2.AssemblyAttributes.cs"
obj\Debug\\TemporaryGeneratedFile_E7A71F73-0F8D-4B9B-B56E-8E70B10BC5D3.cs
obj\Debug\\TemporaryGeneratedFile_036C0B5B-1481-4323-8D20-8F5ADCB23D92.cs
obj\Debug\\TemporaryGeneratedFile_5937a670-0e60-4077-877b-f7221da3dda1.cs
```

Note the `/reference:"F:\Visual Studio 2015\Projects\BuildError\A\bin\Debug\A.dll"` which points correctly to the output of `A.csproj` for the selected build configuration. If I had built in `Release`, the reference would have correctly pointed to the release build output of `A.csproj`.

The result of that build depends on having `A.csproj` already built, which I have. You can see a sample build script in `BuildSolutions.proj` which first builds `SolA.sln` and then `SolAandB.sln`.

Now if I build `SolAandB.sln` through the command line, or as a result of building `BuildSolutions.proj`, I can see that the invocation to `csc.exe` for `B.csproj` is as follows:

```
C:\Program Files (x86)\MSBuild\14.0\bin\csc.exe
/noconfig
/nowarn:1701,1702
/nostdlib+
/platform:anycpu32bitpreferred
/errorreport:prompt
/warn:4
/define:DEBUG;TRACE
/highentropyva+
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5.2\mscorlib.dll"
/reference:"C:\Program Files (x86)\Reference Assemblies\Microsoft\Framework\.NETFramework\v4.5.2\System.Core.dll"
/debug+
/debug:full
/filealign:512
/optimize-
/out:obj\Debug\B.exe
/ruleset:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\Team Tools\Static Analysis Tools\\Rule Sets\MinimumRecommendedRules.ruleset"
/subsystemversion:6.00
/target:exe
/utf8output
Program.cs
Properties\AssemblyInfo.cs
"C:\Users\Fede\AppData\Local\Temp\.NETFramework,Version=v4.5.2.AssemblyAttributes.cs"
```

As you can see, beside several apparently subtle differences, the biggest difference is in that the argument `/reference:"F:\Visual Studio 2015\Projects\BuildError\A\bin\Debug\A.dll"` is missing, and thus the project fails to build with the error `error CS0246: The type or namespace name 'A' could not be found (are you missing a using directive or an assembly reference?)`.

How can I build the solution, in a way that when `csc.exe` is invoked, it's invoked the same way as when I'm building the solution inside visual studio?