Fix sqlite on FS without proper locking mechanism
Option are always strings of a boolean is found then enforce "on"/"off"
Rework repo update to avoid early repo destruction.

Do not touch repository unless we could really download it.
Fix forced update.
Update errors are now not fatal.

All utilities that tries to update repos should not fail if it is
impossible. pkg-update, on the contrary should treat update as fatal
failure.
Fix warnings.
Use one mtime, not the most recent one.
Fix realpath usage.
Fix pkg set -o