New report:
1.Your codelite version = 8.2.1
2. Is it a self compiled version of codelite = No
3. Your OS = Win 8.1, 32-bit
4. Compiler version = Node.js v0.12.7
Now both for debugging and running, all output is in an external COMMAND.COM window,
with both keyboard input works fine

Feedback:
Maybe its the best for a web tool where the console output is a mandatory feature, to let display it in an external window? I think so..
But besides that, on computers with small screens, its bad to have 2 different windows, and I know from other IDEs that they can display the output both of run and debug mode in an "internal" console window.
But its more important that it works at all

Thanks for the fast feedback & improvement.
I setup a notice to your software on
http://www.hemmerling.com/doku.php/en/webtech04.html

Sincerely
Rolf