Configuration file taking precedence over command line option

[cluther]

It appears that at least in some circumstances options in the $ZENHOME/etc/*.conf files take precedence over the same option specified on the command line. As far as I'm aware, the command line should always take precedence.

Steps to reproduce:

1. Add device localhost to $ZENHOME/etc/zencommand.conf
2. Run zencommand run --device=otherDevice
3. Note that zencommand collected only for localhost

[kkearney]

(In [11028]) * Refs #3403: Allow command-line params to override config-file defaults

[kkearney]

(In [11035]) * Refs #3403: added inline comment about optparse oddness

[kkearney]

(In [11038]) * Fixes #3403: allow command-line to override config files. Reviewed by JP.

[kkearney]

Documentation Note:
The command-line parameters now override information provided in the configuration files. Also, this change now allows for case-sensitive command-line options and configuration-file options. Any options not understood by the option parser will be output to standard-error and not to a log file, as the determination of the log file is not known at this point, much less whether or not the command is expected to create a log file.