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>
vdb: Preserve := when storing uninstalled dependency atoms

Make the slot operator processing code not remove the := operator from
vdb dependency entries when the underlying package is not installed.

This fixes a bug where dependencies like || ( A:= B:= ) were stored as
|| ( A:0/1= B ) if B was not installed. This especially confused
dependency comparisons in @changed-deps.

With this patch, Portage stores the original := (or :slot=) atom in the
vdb. This fixes the issue while preserving the same behavior in the
current dependency resolver.

Acked-by: Alexander Berntsen <bernalex@gentoo.org>
Acked-by: Brian Dolbec <dolsen@gentoo.org>
Reviewed-by: Zac Medico <zmedico@gentoo.org>
sets: Introduce @changed-deps to update packages which need dep changes

The @changed-deps set compares the RDEPEND and PDEPEND entries of
installed packages with the metadata of matching ebuilds, triggering
rebuilds whenever a difference in dependencies is detected.

This set can be used to force installed package metadata updates when
ebuild dependencies are changed in-place. In particular, it can be used
to restore dependency tree integrity after disabling --dynamic-deps.

Acked-by: Alexander Berntsen <bernalex@gentoo.org>
Acked-by: Brian Dolbec <dolsen@gentoo.org>
dep_check: fix bug #515230

This fixes dep_check so that graph packages do not mask non-graph
packages (in the same slot) unless the graph packages also match the
dependency atom being satisfied. This requires logic changes in both
_dep_check_composite_db._visible and dep_zapdeps.

Also, fix _dep_check_composite_db match / _cpv_pkg_map
interactions to ensure correct match results.

X-Gentoo-Bug: 515230
X-Gentoo-Bug-URL: https://bugs.gentoo.org/show_bug.cgi?id=515230
QA: Add a set of checks for bash-completion files

Add checks for common mistakes when installing bash completion files:
legacy directory, incorrect naming, missing aliases, deprecated 'have'
function.
Merge branch 'qa-bashcomp' into all-in-one
Merge branch 'all-in-one' into all-in-one-plus-setup.py