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To invoke the debugger, you will need to put the /h into the command box, which is only available on main screens (modal windows). So how to invoke the debugger in popup screen (popup window) ? Use a SAPGUI shortcut.

A SAPGUI shortcut is a simple text file in which the action you want to shortcut to is described. The file has a predefined setup and extension. When you drag-drop the file onto the popup, the command specified in the shortcut is executed. This is available not only for /H debugging, but for any other user command as well. Try it !. 

The file should be called: debugger.SAP, (where only the .SAP bit is required). Edit the file (notepad) and set

[Function]
Title=Debug
Command=/H
Type=SystemCommand 

Now drag drop the file to your SAP screen (works on popup as well as modal windows). It's not only systemcommand settings that can be arranged in SAPGUI shortcuts, here's an example with some more settings: 

[System]
Name=YD1
Description=04 - **** Solman ****
Client=100
[User]
Name=WIM
Language=
[Function]
Title=Debug
Command=/H
Type=SystemCommand
[Configuration]
WorkDir=C:\Documents and Settings\albert\SapWorkDir
[Options]
Reuse=1