Emerge updating configuration files
By default your system only accepts packages that are deemed stable.
The Portage tree is a collection of ebuilds, files that contain all information Portage needs to maintain software (install, search, query, ...). The second path leads to Calculate overlay, also containing ebuilds.
When you have installed a package, its documentation is generally found in a subdirectory named after the package under the # ls -l /usr/share/doc/eselect-1.2.11 total 48 -rw-r--r-- 1 root root 296 Jan 26 AUTHORS.bz2 -rw-r--r-- 1 root root 14202 Jan 26 Change Log.bz2 -rw-r--r-- 1 root root 5320 Jan 26 bz2 -rw-r--r-- 1 root root 3837 Jan 26 NEWS.bz2 -rw-r--r-- 1 root root 541 Jan 26 README.bz2 -rw-r--r-- 1 root root 703 Jan 26 bz2 -rw-r--r-- 1 root root 471 Jan 26 TODO.bz2 -rw-r--r-- 1 root root 2067 Jan 26 bz2 ).
This will tell Portage to remove all files installed by that package from your system except the configuration files of that application if you have altered those after the installation.
If you ever want to remove such a package from your system, running on the package will not have much effect as the dependencies remain on the system.
Portage has the functionality to remove orphaned dependencies as well, but since the availability of software is dynamically dependent you first need to update your entire system fully, including the new changes you applied when changing USE flags.