Run complex chain of windows batch files in cyg

[geneSmith]

I have a complex chain of windows batch and make files used to build a 
embedded system with vxWorks tools. It was designed to run under windows 
commands with cygwin *not* in mind. I prefer to work in the cygwin 
command line using rxvt terms. However, when I run this complex chain in 
cygwin, which does a lot of environment setting and path mods, it does 
not work (don't see env changes, etc). Is there a way to do this type of 
thing without having to go through the hundreds of files and make them 
look more unix/bash like (e.g., get rid of dos "set", change directions 
of slashes, changed %SYMBOL% to $SYMBOL, etc).

-gene
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