Linux Version of Windows 7 Libraries

Windows 7 has introduced the concept of Library, which is functionally somewhat the same as UnionFS. From How to Use Windows 7's New Library Feature:

You could say Libraries are virtual folders. You add folders to Libraries, where you can view and access the contents of each added folder from the single Library window. A Library itself can’t contain any files as they aren’t real folders, but they offer one-stop access to a collection of folders.

Here are several ways you can make use of Libraries:

• Add folders that are scattered throughout your hard drive(s) to Libraries.
• Create custom Libraries. For example, when I start a new writing assignment, I can create a new Library. I could add related folders such as the one that contains the publication’s guidelines, folders on previous work that I think I’ll want to reference, and folders containing any downloaded research.
• Add network locations (shared folders from other computers) to Libraries.

For some more detailed info, see:

Windows 7 Libraries .NET Sample Library – an Overview
Understanding Windows 7 Libraries

You can make a poor-man's unionfs with symbolic links: reproduce the directory structure of the source, but make links (symbolic or hard) for the files. This should be suitable for your purpose as long as the build system doesn't try to modify source files.

With GNU cp, it's as easy as cp -al or cp -as. But I don't know if there is a port of GNU tools that understands Windows links.

If you need to call the mklink command, it can be done with POSIX tools (warning, typed directly into the browser):

cd SOURCE
find -type d -exec sh -c 'cd BUILDDIR && mkdir "$@"' _ {} +
find -type f -exec sh -c 'mklink "$1" "BUILDDIR/$1"' _ {} \;

I suppose there is a native Windows way involving Powershell, but I have no idea what it looks like. It might be worth investigating if your directory tree is large and your disks are fast because forking under Windows tends to be slow, and the commands above need to fork a lot.