This removes script-wide shellcheck excludes to avoid unintentional
errors and moves the excludes to the scripts where they are necessary.

We don't want OpenWrt packages to replace Gluon packages by accident;
the same logic applies to packages from site feeds.

This gives site feeds a higher precedence than gluon/packages, but that
is unlikely to cause any issues. Gluon base packages still have an even
higher precedence.

modules.sh can't depend on openwrt/feeds.conf.default, otherwise the
initial update will fail.

This fixes `make update` not working correctly when GLUON_SITEDIR is set
manually.