Update cli.markdown

Fix markdown formatting, and add some details about the pre-requisites for multifasta
Merge branch 'master' of github.com:EESI/quikr
Remove debugging version

remove the debugging option for quikr, since there is not a reason to
keep it anymore, consider it cruft. Our users are unlikely to ever use
it and the same for us

- remove from manpage
- remove from quikr.c
update cli.markdown to remove debug
build nbc and c before we install quikr
Merge branch 'master' of github.com:mutantturkey/quikr