This is an old question, but was a serious PITA for me for a few minutes, so I thought I’d share:
I just ran into this problem, and I believe that the issue is probably platform-dependent. The real tip-off was that the solution from Cyril’s answer wasn’t working as expected: despite my specification of -DgroupId=com.xyz and -DartifactId=whatever on the command-line and the corresponding entry in the POM file, the jar was installed in the local repo under com/whatever.
This led me to experiment with quoting command-line arguments, and the eventual correct result from formatting the command-line like this (after deleting the POM file):
mvn install:install-file "-Dfile=cobra.jar" "-DgroupId=com.cobra" "-DartifactId=cobra" "-Dversion=0.98.4" "-Dpackaging=jar" "-DgeneratePom=true"
Some of the quoting is doubtless redundant, but better safe than sorry, right? I happen to be running Vista on this computer, and would not be surprised if this problem were specific to this OS version…by the way, this was with Maven v3.0.4.