daemon: Add flags argument to command*() functions.

daemon: Add flags argument to command*() functions.

This adds new variations of the command*() functions which
take a 'flags' argument.  Currently the only flag available
is defined as follows:

 COMMAND_FLAG_FOLD_STDOUT_ON_STDERR: For broken external commands
 that send error messages to stdout (hello, parted) but that don't
 have any useful stdout information, use this flag to capture the
 error messages in the *stderror buffer.  If using this flag,
 you should pass stdoutput as NULL because nothing could ever be
 captured in that buffer.

This patch also adds some documentation for command*()
function.