Rework logging to prevent double initialization

Prior to this commit LoggingSystem initialization would happen multiple
times. Once to configure "quiet" logging, and again to configure correct
settings once the Application was initialized. This could cause problems
if `logging.groovy` logback files were used.

The logging system is now only initialized once (when possible) by
following these steps:

- Standard logging initialization occurs via the actual logging
  implementation used (e.g. logback will load a logback.xml file if it
  exists)
- beforeInitization() is called to prevent early log output.
  Implementations now either use a Filter or simply set the root logging
  level.
- initialize() is called with an optional log configuration file (e.g
  a custom logback.xml location) and an optional log output file (the
  default is null indicating console only output).

The initialize() method will attempt to prevent double initialization
by checking if a standard configuration file exists. Double
initialization now only occurs in the following situations:

- The user has a standard configuration file (e.g. classpath:logback.xml)
  but also specifies a logging.config property. Double initialization is
  required since the specified configuration file supersedes the default.
- The user has a standard configuration file (e.g. classpath:logback.xml)
  and specifies a logging.file property. Double initialization is
  required since the standard configuration may use a ${LOG_FILE}
  reference.

In addition this commit removes the `logging.console` option and now
assumes that logging either occurs only to console or to both the
console and a file. This restriction helps simplify the LoggingSystem
implementations. If file only logging is required a custom logback.xml
can be used.

Fixes gh-1091
See gh-1612, gh-1770