Cannot find application with Spotlight (the missing solution)

As a recent user to the Apple world, I've been exploring and optimizing the OS X based on my needs. After playing with my OS X installation I ended up losing access to some applications (native ones!). I managed to restore them by copying the files from another OS X installation. However, Spotlight couldn't find the applications anymore. I searched for solutions but all I got was disappointment. So, I decided to fix it myself and share it with you.

Spotlight cannot find an application that is installed