Eclipse has the CDT (
http://www.eclipse.org/cdt/downloads.php). It definitely does provide some kind of Eclipse integrated tools for examining the glue layer seamlessly with the Java layer. I'll bet you a beer that the guys the wrote the C layer didn't use Eclipse to do it, though, FWIW.
Eclipse likes to be in charge. I've had some luck switching source repos underneath it but it isn't pretty. First of all, you'll have to change the .classpath file if you'd prefer to avoid errors. Also a make, refresh and rebuild. All in all, probably better to keep separate copies for separate versions, if you can afford the space.
G. Blake Meike
Marakana
The second edition of Programming Android is now on-line: