Go over the configuration and management chapter
Go over the configuration and management chapter

This fixes the remaining inline code samples and restructures
the sections to make more inline references possible. Also fixes
some minor bugs like links that still have *.md format.

aaronkaplan/intelmq,aaronkaplan/intelmq,certtools/intelmq,aaronkaplan/intelmq,certtools/intelmq,certtools/intelmq