As Pragmatic Programmers, our base material isn't wood or iron, it's knowledge. page 
We gather requirements as knowledge, and then express that knowledge in our designs, implementations, tests, and documents. And we believe that the best format for storing knowledge persistently is plain text. With plain text, we give ourselves the ability to manipulate knowledge, both manually and programmatically, using virtually every tool at our disposal. The problem with most binary formats is that the context necessary to understand the data is separate from the data itself. You are artificially divorcing the data from its meaning. The data may as well be encrypted; it is absolutely meaningless without the application logic ...
Ward via matrix :
A second problem with extensive use of markdown is that programs have trouble understanding it. When we write scripts that build on reading and interpreting pages we find markdown inscrutable and best just ignored. When you write plain text in markdown you are simply hiding it from downstream processing. That may not be a concern of yours today. But this is clearly the growth path for the work we do. Dave Thomas calls this the power of plain text.