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
Port ipa-replica-prepare to the admintool framework

Break the script into several smaller methods.

Use modern idioms: os.path.join instead of string addition; the with statement
for closing files.

Add --quiet, --verbose, and --log-file options. Use logging instead of print
statements. (http://freeipa.org/page/V3/Logging_and_output)

Part of: https://fedorahosted.org/freeipa/ticket/2652
Fixes: https://fedorahosted.org/freeipa/ticket/3285
Make ipapython.dogtag log requests at debug level, not info