Cleanly sharing a project tree between OSes?

[Al]

My setup is the following. I work on a machine with a windows, linux and
shared partition. When developing a project with autoconf et al., I would
like to be able to use a directory structure like this (on my shared
partition),

$ ls
linux myproj windows

$ ls myproj
AUTHORS    INSTALL      README        bootstrap     doc
COPYING    Makefile.am  etc...

Then I would hope to be able to switch to either the windows directory when
on windows, or the linux directory when on Linux and

$ bootstrap && configure -C && make && make install

from there, and (heres where you come in) have any files that would normally
be created in myproj be created in the current directory. For example, I
dont want a config.cache to be created by say windows, and then be picked up
when doing a configure on Linux. I obviously want to maintain this single
shared project tree for both OSes.

What do I need to change in bootstrap and configure.in to achieve this?

Thanks for any advice.