Okay you want to build packages from scratch then
should give you some more options.
equo can be there and can be used to recognize emerge / portage changes as portage I think is not yet able to see anything else but will read versions and packages isntalle dby equo or something like this.
equo database gentoosync
Most of the time if you want to update your whole installation then
emerge -u world
equo world --upgrade
should be able to do the job.
If you want to reinstall all packages installed then
equo install world
You can also do a system only update and not extra stuff like amarok or others non esential to the running enviroment liek addon open office chat programs will then be excluded.
Hope this helps.