Every time i do emerge sync i find out that /etc/make.profile/package.provided is deleted. It is (in my case) a symbolic link to file elsewhere to avoid it being really deleted, but after each emerge sync i have to manually link it again, which is bit annoying.
This belongs to /etc/portage/profile, not /etc/make.profile/. man portage: <snip> /etc/portage/profile/ site-specific overrides of /etc/make.profile/ </snip>
Right. I'd suggest however clearly stating this in the portage man page, because as of now it suggest using this place for storage of self-maintained packages.