I am running both maven inside the m2eclipse plugin, windows command line and my cygwin command line.
cygwin\'s bash shell dumps artifacts into the cygwin /home/me/.m2 d
For Cygwin, create a file called ~/.mavenrc and put the following text inside:
MAVEN_OPTS="-Dmaven.repo.local=c:\documents and settings\user\.m2\repository"
export MAVEN_OPTS
Alternatively, you can create the file under /etc/.mavenrc
Another option is to create NTFS junction between .m2 under your windows and your cygwin profile.