Direct Question: If I have two files with the same name (but in different directories), it appears that only Visual Studio 2005 can handle this transparentl
This is easy to fix in the IDE. Click the first file in the folder, Shift+Click the last file so all of them are selected. Right-click, Properties, C++, Output Files. Change the Object File Name from $(IntDir)\
to, say, $(IntDir)\Univariate\
. You can repeat for the Multivariate file group although that's not strictly necessary.