New: option defaults by config file

Updated Changes for goal
Added pod describing expected behavior for —config option and new
CONFIG FILE section describing the config file format.
Added --config file options as source of options.

Added test for —config option and expected default value - Failing
Added code for cli parsing - Corrected error in specification - Success
Add conditional test for default config file reading - Not executing?
Rats. Have to implement “fixupTildePath” to deal with paths containing
“~”. Done. Tested. 100%.
Conditional test now failing in correct way. Added config file parsing
with Bio::Seqware::Config, modified to use that module’s
getDefaultFile() call to get default file name. Done, Tested. Added
test for not default file, added test data file and directory. Done,
Tested. Not 100% added test for error undefined filename parameter for
getConfigOptions() Done, tested, Added test for non-exisitng file name.
created makeUuid to enable unique filename, done, tested. Everything
tested, 100%,
Refactoring option parsing.

Refactoring new() by adding an init helper method to do all data
initialization. The is mostly option handling (CLI  and config file).
Also did some refactoring of the cli parser. It might not have been
working correctly. Need to add a test for the internal options _argvAR
and _optHR. Add debug output for cli options, config options, and
initialize object. Also adding second parameter ($object) printing to
say* functions. Tests added, code added, 100% coverage.
Merge branch 'use-config-file'