As described in bug #349660 (and bug #349824) dev-lang/spidermonkey collides with net-libs/xulrunner (including include files etc. it also cause problems with installing at least one program depending on net-libs/xulrunner).
Can you be more specific about what files collide and what versions you are working with?
At least after uninstalling spidermonkey I had 1 file in /usr/include/xulrunner-1.9.2 instead of nearly 2000. I'll try to produce full list soon. Versions: dev-lang/spidermonkey 1.7.0-r2 net-libs/xulrunner 1.9.2.9-r1
Created attachment 258143 [details] equery files spidermonkey output Here's the file list for spidermonkey on my system; it doesn't own any of the files in /usr/include/xulrunner-1.9.2. It seems like something is very wrong on your system if you get the results you have described.
For one there is no way possible for spidermonkey to install to 1.9.2 unless you using some overlay other then that provided by gentoo. Provide a build.log showing the collision if you really believe this to be a bug.
I'm sorry - my fault but for some reasons (corrupt filesystem? cosmic radiation?) gjs failed to configure just after uninstalling spidermonkey.