How to remove an icon from launchpad that does not appear in the Finder

There is no easy way to do this, but there is a little hack :)

1. Navigate to /System/Library/CoreServices/Dock.app/Contents/Resources/
2. Backup DockMenus.plist
3. Open DockMenus.plist in your favorite text editor with root access

4. Find section finder-running and add new sub-section

   <dict>
       <key>command</key>
       <integer>1004</integer>
       <key>name</key>
       <string>REMOVE_FROM_DOCK</string>
   </dict>
   

   or just Download my version of DockMenus.plist

5. In plist editor file should look like this:

   

6. Open Terminal and run killall Dock.

7. Right click on Finder icon in Dock - Bingo!

   

p.s After Dock restart (manual relaunch or mac reboot) you need manually remove Finder icon from Dock

It may be a bug, but I am thinking it may mean your Spotlight index is corrupt.

I just tried deleting Evernote from my Applications folder. After authenticating, it moved it to the trash. I then checked launchpad again, and it was no longer there. Then, when I dragged it back out of the trash and placed back into Applications folder. Relaunched launchpad, and it was there again on the last page. As in, worked as expected here.

Launchpad keeps its own plist of what files there are, etc, and thats why there are some modification tools to allow to you to edit it. But I am assuming they would use spotlight to 'watch' your Applications folder to add new items not through the Mac App Store. I assume Spotlight because its a great tool for the job, installing Lion does a huge spotlight re-index, and they do use spotlight often behind the scenes.

First, the GUI way I have seen online is to do this (I do the command line way below):

1. In system's preferences -> spotlight -> Privacy add the drive you want to re-index
2. Quit System's preferences
3. Logout of your sessions
4. Login again :-)
5. In system's preferences -> spotlight -> Privacy remove the drive you want to re-index
6. Wait.. a faily long time. You should see mdworker and/or mds running

Personally, I have always done it through the command line.

1. Launch ‘Terminal’ (located in /Applications/Utilities/)
2. At the command prompt, type this exactly: sudo mdutil -E /
3. You will be asked for your password, provide it, as this command requires administrator privelages to run
4. You will receive a confirmation message saying that index will be rebuilt
5. Wait until index is finished rebuilding, this can take a while depending on the size of your hard drive, amount of files, etc.

While I can't find any documentation online that 100% confirms that Launchpad uses Spotlight for this, this would be the first place I would look for the problem you are having.