Update flac.md: Reordering and updating options descriptions - and so…

…me of the examples

I am not sure about the organization of the initial part of the document, to be honest. For example the way it promises examples before options, but before the examples sections it gives examples (on using stdin).

Anyway, here are the most significant changes I made: 
- Some in the examples
- Options are reorganized to match the flac -h order 
- I used _underscores_ for italics, avoiding some formatting issue that arose from triple asterisks 
- Some " " inserted - you will all too easily need them when using -T - but I dared not use too many of them. 

... and some more text tweaks.