Fix typos and formatting in the dhcp protocol docs

Also added a link to an RFC and a Bro script (and corrected the name of the
script being referenced).
Fix typos and formatting in the dns protocol docs
Fix typos and formatting in the ftp protocol docs
Fix typos and formatting in the http protocol docs

Also adjusted line numbers in scripting doc due to changes in http/main.bro
Fix typos and formatting in the ssl protocol docs

Also changed one sentence (about setting the Mozilla root CA list) to make
it more clear that the user doesn't need to do anything.
Fix typos and formatting in the other protocol docs
Fix typos and formatting in the base/utils docs
Fix typos and formatting in the BiFs docs
Fix incorrect uses of reST directives

These did not generate any warning messages unfortunately, so had to
find them using grep.