In Gentoo:

In the make.conf configuration file, is there a way to disable all USE
flags by default, for example by using a wildcard, then explicitly set the
ones that I want?

For example, all flags disabled, except the foo and bar flags:

USE="-* foo bar"

Is it possible to have more than one USE= line in the
/etc/make.conf file?

For example:

USE="foo"
USE="bar"

Currently my make.conf file has one long USE line which explicitly sets
or clears each of the known global flags.

Regards,

Mark.

--
Mark Hobley,
393 Quinton Road West,
Quinton, BIRMINGHAM.
B32 1QE.