It's deprecated because it's insecure, on platforms where other users can see the environment variables passed to pg_dump (which apparently is quite a few variants of Unix). You wouldn't pass the password on the command line either ...
Painful as .pgpass may be for an admin tool, I do not know of any other method I'd recommend on a multiuser machine.
OK, but say you have a phpPgAdmin installation that's servicing 20 users. Then you have to put a .pgpass file in the www home dir (if there is one) with the usernames and passwords of all those users - pretty damn annoying...
Chris
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