What happened to no indexing certain directories?

You can customize the index locations/folders using tracker-gui .

Install it with this button:

or using the following command:

sudo apt-get install tracker-gui

After installing, go to the Locations tab. Click on the + button and add the specific directories/locations that you want to index.

It goes without saying that the drive has to be mounted already to be able to be indexed.
Hope that helps.

Or You can go here and add to "don't record activity":

Or else, You can also do the following : Install activity-log-manager

sudo add-apt-repository ppa:zeitgeist/ppa
sudo apt-get update && sudo apt-get install activity-log-manager

You can then launch it by searching for it in Unity. Once it's loaded, you'll find the option to prevent certain folders being logged in the Files tab. Hope that helps.