All the problems above are related to python byte code, and the way it
is handled in gentoo. It would be to exhaustive to explain the
problems here but maybe this bug [1] helps to understand the problem.
Also if you want to learn more about python in gentoo you can read
this [2].
In the case of scons and docbook the problem is the same as mentoned
in the bug where python bytecode is installed into the wrong
filesystem location.
Other problems can occur when the python eclasses which handle the
python byte code are not used at all or improperly used with python
applications. For instance when python byte code is not handled by the
eclasses the py{c,o} files are created at runtime when using the
program as root. At deinstallation this files are not removed from the
filesystem because the package manager is not aware of them.
[1] http://bugs.gentoo.org/show_bug.cgi?id=194343
[2] http://www.gentoo.org/proj/en/Python/developersguide.xml
