improve logging set up to survive multiple command executions

This patch improves geogit cli logging set up to properly resolve
the logging file and current dir upon multiple command executions
and makes geogit-console batch mode (runFile()) to set up logging too,
and also avoids code duplication in cli exception handling between
cli and console.

Conflicts:
	src/cli/src/main/java/org/geogit/cli/GeogitCLI.java
	src/cli/src/main/java/org/geogit/cli/GeogitConsole.java