Hi.
This is how I do it. I have just reread the thread and realized that everything I have typed is redundant but hey I'll post anyway
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In the tools configuration where is says for the build something like "make -C %rp/products/mogripserver all_%(BUILD_SUFFIX)" try doing something like "ssh user@machine make -C %rp/products/mogripserver all_%(BUILD_SUFFIX)".
Make sure that your authorized key file is the .ssh directory is setup to allow automagic login.
When editing on windows and building on linux I do something similar. The build line in the tools looks like:
bash c:\data\projects\stuff\buildProduct.sh %rp/products/meshoperatorserver all_%(BUILD_SUFFIX)
where c:\data\projects\stuff\buildProduct.sh is
ssh gbarron@rd-gbarron-linux make -i -C $(echo "$1\.. $2" | sed -e 's~\\~/~g' -e 's#M\:#~#g')
The echo through sed is required to convert the back slashes to forward slashed and to replace the drive letter with ~, thus ending up with the correct command (ssh gbarron@rd-gbarron-linux make -i -C ~/mo/software/products/meshoperatorserver all_lx).
If the cygwin binaries are in the path it all work like a charm.