You might be able to use something like this to suspend the build process:
http://www.codeproject.com/KB/threads/pausep.aspx
http://www.beyondlogic.org/solutions...rocessutil.htm
Or if you call the GUI app from the command-line, you could send keystrokes to it to pause/resume the build (pausing would pause the build when the current step finishes). The default shortcuts for pause and resume are Esc and F7.
http://www.kinook.com/VisBuildPro/Ma...nd_linegui.htm