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

After non-deliberately deleting some native applications I restored them by copying the files from another OS X installation. However, Spotlight couldn't find the applications anymore (but I could run them).

I tried multiple ways to rebuild the Spotlight index as suggested in the community. Nothing did it.

It turns out that the applications had a wrong set of permissions which made them invisible to Spotlight.

After observing the other native applications' files I discovered that:
  • The main application directory and all its contents must belong to the user root and group wheel;
  • The main application directory and all directories recursively inside of it must have a set of permissions equal to 755 (Traditional Unix permissions);
  • All files recursively inside the main application directory must have a set of permissions equal to 644; 
  • The file inside the Contents/MacOS/ from the main directory must have the set of permissions 755 because it must be executable or the application won't run;
The most important aspect is that the file Contents/Info.plist be readable in the others class so that Spotlight can view it.


Now that we know the theoretical aspects of the issue, let's delve into some Terminal exercise:

  1. Open up Terminal and cd to the directory containing the main directory of the application you want to fix, e.g: cd /Applications/Utilities. Let's assume the application is called MyApp and its main directory MyApp.app;
  2. Set the right owner and group to every file and directory: sudo chown -R root:wheel MyApp.app;
  3. Set the general permissions to every file and directory: sudo chmod -R 775 MyApp.app;
  4. Change the permissions of only the files: find MyApp.app -type f -print0 | xargs -0 sudo chmod 644;
  5. Change the permissions of the actual executable file, to be executable: sudo chmod 775 MyApp.app/Contents/MacOS/MyApp;
Although it doesn't need to be exactly like this, these steps get your application consistent with the other ones.

If the application still doesn't show up in Spotlight, try to force a rebuild of its database:

mdutil -E

Update: Some application files may require specific permissions. Run Disk Utility to verify and repair the disk files' permissions.

References

Traditional Unix permissions