Markdown editor with folders as local libraries
I use Sublime Text with the Markdown Preview package. 

It has Markdown syntax highlighting, color themes, and lets you treat directories as projects, allowing you to search over them, as you requested. The Preview package allows you to see the MD result in your choice of browser, with your choice of renderer (regular/GitHub). 

Sublime is very versatile and open to many more customizations, should you require them.