Move the FlagAssignment from the project-wide all-packages config to the
per-package config.

Initially it had been easier to do it globally since it gets used as a
solver setting rather than as the other per-package config items, but
obviously it is supposed to be per-package.

So the flags field in the config top-level now applies to all local
packages. And it can also be specified in package-specific sections.

We don't yet check that any of the flags specified actually make sense
for either the local packages or for the specific packages.