I use gitbook.com to generate the website, and github to store these notes in markdown format.
To make changes I usually edit or create a file on my machine and then sync it to github.
To quickly search my files I have created a simple alfred workflow that searches all content (even inside the files) in knowledge folder.
From alfred I can quickly open a file to edit or get information from. I am using alfred-grep as explained here to quckly search inside all my notes inside alfred.
@nikitavoloboev has been a huge inspiration in the creation of this.