Should fix the problem with multi config files

Multi-file configuration wasn't actually updating configuration with
each file. Unless I am reading this wrong something wrong it looks
like jekyll's deep_merge function doesn't operate on a hash's in place
instead it returns the merged hash.

Also updated the description of the command line description to demo
how you can actually include multiple files. That was confusing, it
doesn't seem to be documented any where in the commander docs.

Fix for pull request 945