Issue:

The _confg.yml changes are not picked when you deploy to github pages using rake generate deploy

Cause

I had rake preview running another tab, it was started with older version of the _confg.yml. This was also generating the html files into same _deploy folder. Hence when you run rake generate deploy, it was pushing html generated by rake preview task.

Solution

Before running rake generate deploy, make sure you are not running rake preview or rake watch in any window or tab.