The ebuild for kdevelop 2.1.3 inhstalls the binary to a different location then previously. The binary is installed to /usr/bin instead of /usr/kde/3/bin and also leaves the 2.1.2 binary around. It also does not create K menu entries for tkdevelop 2.1.3 and kdevelop 2.1.3 setup
3rd party kde apps now install into /usr; this is correct. You can get rid of the older binary by unmergig kdevelop-2.1.2 (you'll have to do it explicitly). And the k menu entries should be there, after perhaps a restart of kde (you have to restart it at least once after installing a kde app in /usr for the first time so that the kde-env changes can take effect).
Nothing to fix.