core/commands2: Replaced NewDagFromReader with BuildDagFromReader
core/commands2: Restored logging that got removed
core/commands2: Added 'refs' command
core/command2: Make help text match old commands
core/commands2: Made 'resolve' output match old command
core/commands2: Made 'ls' output match old command
commands: Made Command run functions return (interface{}, error) instead of setting the values in the response
core/commands2: Updated commands to new Run function API
commands: Added Option helper constructors
core/commands2: Use Option constructors in commands
commands: Fixed tests