emaint merges: Replace .append() with .add() for set variables (bug 520542)

pkg_atoms and pkg_invalid_entries were changed to sets, but were not updated
in the function that added to them.
Fix porttree_root deprecation warnings

export PYTHONWARNINGS=d to see the warnings that this fixes.
package_tracker.match: account for unevaluated_atom

This fixes the match cache to properly account for
atom.unevaluated_atom, which is required since match_from_list output
depends on atom.unevaluated_atom (for IUSE matching logic). Note that
similar issues were also fixed in commits
d603f1440c814377fbc1965729fd9b6b008cf76d and
5438bb29c996d777b6343515995176912a7c137f.

X-Gentoo-Bug: 515230
X-Gentoo-Bug-URL: https://bugs.gentoo.org/show_bug.cgi?id=515230
bin/misc-functions.sh: Empty flag variable 'error' before (re-)use

Prevent subsequent .png files from inheriting error status from earlier
file.

Reviewed-By: Michał Górny <mgorny@gentoo.org>
Acked-By: Brian Dolbec <dolsen@gentoo.org>