db: rework directory permission handling

Apk used to reset directory permissions always, but this is undesirable
if user has modified the permissions - especially during tmpfs boot.
Though, it is desirable to update the permissions when packaging has
changed permissions, or a new package is installed and the merged
permission mask / owner changes.

Thus the new code updates the permissions only if:
 1) We are booting and directory is not in apkovl
 2) The directory is modified by a package install/remove/upgrade
 3) The filesystem directory permission matched database

Additionally "apk fix --directory-permissions" can be used to reset
all directory permissions to the database defaults.

Fixes #2966

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