Better logging for AdminTool and ipa-ldap-updater

- Automatically add a "Logging and output options" group with the --quiet,
    --verbose, --log-file options.
- Set up logging based on these options; details are in the setup_logging
    docstring and in the design document.
- Don't bind log methods as individual methods of the class. This means one
    less linter exception.
- Make the help for command line options consistent with optparse's --help and
    --version options.

Design document: http://freeipa.org/page/V3/Logging_and_output
ipa-replica-prepare: Move parse_options to the framework
ipa-replica-prepare: Move validate_options to the framework
ipa-replica-prepare: More validate_options, start ask_for_options
ipa-replica-prepare: Move more validation code from main to ask_for_options
ipa-replica-prepare: Move the first part of main()
ipa-replica-prepare: copy_ds_certificate
ipa-replica-install: copy_httpd_certificate
ipa-replica-prepare: copy_pkinit_certificate
ipa-replica-prepare: copy_misc_files
ipa-replica-prepare: save_config
ipa-replica-prepare: package_replica_file
ipa-replica-prepare: Remove the temp directory
ipa-replica-prepare: add_dns_records
ipa-replica-prepare: Don't use an extra connection to get the subject base
ipa-replica-prepare: Move the try-except block into export_certdb