zabbix_agentd: Fix agent modules dir and few minor bugs

zabbix_agentd: Fix agent modules dir and few minor bugs

- Add agent modules-dir to backup
- Remove original, not used agent modules dir from rootfile
- Create modules-dir during install if it not already exists
- bugfix: Add existence check before creating log-dir, avoiding error
             messages if it already exists from a previous install
- bugfix: add extract_backup_includes to update.sh script to make
              sure backup includes exist when backup is taken.

Signed-off-by: Robin Roevens <robin.roevens@disroot.org>