For gnome type configurations, I just put at the top or bottom:
And have all my settings put in there.
For script files, it is very much the same:
Generally, the config files are left alone (ie, crontab, gdm, apt), and if they are tinkered with (a good example is me always tinkering with the /boot/grub/menu.lst script). Then when you install a package (at least, via aptitude) it will ask you what want to do with the file.
Of the top of my head, I think its:
- Leave Altered File Unchanged,
- Replace old lines with new.
- Erase over with package maintainer file.
And if it doesn't, the deb scripts are smart enough not to erase your personal settings anyway!
They use a technique where they read the config file line by line and add new configurations/replace old ones using line matching.
ie, you'll read something like this:
So your files are pretty much safe regardless!
This line is unaltered
--Remove this line++Put this here instead
This line remains
++Another new line++
--And completely remove this line--