/usr/share/java is where (at least for RedHat/Fedora-style distros), the OS-supplied jars reside. Things like jdbc drivers and stuff like that. You really don't want to dump tomcat's internal jars in there. For one thing, they're not stuff you want to - ahem - "share".
I have been known to go the other direction, however, and place a softlink(s) in TOMCAT_HOME/lib to one or more JDBC driver jars in /usr/share/java. Tomcat's OK with that.
An IDE is no substitute for an Intelligent Developer.