fix cli bugs

for some weird reason the cli arg library I am using removes flags.
Say I have mdoc -logLevel info foo -bar=baz, the job foo would receive
args [bar=baz] when it should be [-bar=baz].  Right now this seems to
happen when using the logLevel flag.  Instead of using the parsed args
I am using the original ones
Merge pull request #75 from metridoc/cli-bug-fix

fix cli bugs