how to remove launchpad icons without folder in Applications

3 steps

1) find the launchpad sqlite3 db. This is under the com.apple.dock.launchpad buried in a subdirectory in the /private/var/folder.

In most cases since this was one of the first folders created; it should be in the first folder and first subdirectory of that folder/folder. cd into the first folder after a ls.

In my case it was here: /private/var/folders/mb/br6t4l8d5svbdx8w4r966y1w0000gn/0

localhost:0 dc$ ls

com.apple.LaunchServices-107501.csstore

com.apple.dock.launchpad/

com.apple.notificationcenter/

com.apple.pluginkit/

localhost:0 dc$ 

cd into com.apple.dock.launchpad folder and verify there is a db folder. The sqlite3 database is under this directory in file db. Run sqllite with the path to this file if you aren't in this directory. localhost:db 

dc$ sqlite3 db

SQLite version 3.8.4.1 2014-03-11 15:27:36

Enter ".help" for usage hints.

sqlite> 

List the app names

sqlite> select Title from apps;

App Store

Automator

Calculator

Calendar... (rest deleted)

Delete the app title

>DELETE from app where Title="YouTube";

cntl-D to exit

killall Dock to reset Launchpad; verify gone

Look in /Library, etc.. to clean up application created files.