C++ cross platform build automation

The bug you reference (bug 4787391) has been fixed in Java 8. Even if you are using an older version of Java, the System.getProperty("user.home") approach is probably still the best. The user.home approach seems to work in a very large number of cases. A 100% bulletproof solution on Windows is hard, because Windows has a shifting concept of what the home directory means.

If user.home isn't good enough for you I would suggest choosing a definition of home directory for windows and using it, getting the appropriate environment variable with System.getenv(String).

In general, there are two issues you need to be concerned with:

1. The requirement that, on Windows, your DLL explicitly exports symbols that should be visible to the outside world (via __declspec(dllexport), and
2. Being able to maintain the build system (ideally, not having to maintain a separate makefile and Microsoft Visual C++ Project/Solution)

For the first, you will need to learn about __declspec(dllexport). On Windows only projects, typically this is implemented in the way I describe in my answer to this question. You can extend this a step further by making sure that your export symbol (such as MY_PROJECT_API) is defined but expands to nothing when building for Linux. This way, you can add the export symbols to your code as needed for Windows without affecting the linux build.

For the second, you can investigate some kind of cross-platform build system.

If you're comfortable with the GNU toolset, you may want to investigate libtool (perhaps in conjunction with automake and autoconf). The tools are natively supported on Linux and supported on Windows through either Cygwin or MinGW/MSYS. MinGW also gives you the option of cross-compiling, that is, building your native Windows binaries while running Linux. Two resources I've found helpful in navigating the Autotools (including libtool) are the "Autobook" (specifically the section on DLLs and Libtool) and Alexandre Duret-Lutz's PowerPoint slides.

As others have mentioned, CMake is also an option, but I can't speak for it myself.