Laurent Birtz added the comment:

Thank you for the clarifications on the usage of cmd.exe and shell=True. I tend 
to forget that the shell support in subprocess isn't just about UNIX.

The point of running msys is getting programs to work as if they were in a 
limited UNIX environment without the emulation layer provided by Cygwin. It's 
nice if programs unaware of msys work out-of-the-box, but for use cases like 
mine what is needed is the possibility to write a program that works correctly 
on msys with a minimum of fuss.

Given that, conditionally setting os.dep on program entry and wrapping the 
calls to cmd.exe manually seems to fit the bill. I haven't tested if SCons 
plays nice with that change, so I may be in for a disappointment. Even if it 
doesn't work right, it would still be useful for me to temporarily change 
os.dep and join my paths correctly until I return control to SCons.

On my system, print os.environ["MSYSTEM"] yields MINGW32. That's all I need for 
detecting msys currently. If that ever break I'll find another method.

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<http://bugs.python.org/issue6208>
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