Fix pretty permalinks in server auto

The problem is that directory creation code for pages does not update them in --server --auto mode when user modifies the source file. It generates them just during initial generation after launching jekyll.

I introduced pretty_flat mode which behaves consistently in my opinion. It does not create directories /pagename/index.html for pages but generates simple /pagename and works consistently both in batch and --server --auto mode. My other pull requests are solving the problem of mime type with naked /pagename urls (which was probably your original motivation why to implement it as /pagename/index.html)