Is glClear oprates only in the sccisor window? Where can I find reference to this?
Yes, clear operates only within scissored area.
Reference can be found in OpenGL specification, chapter “Clearing the Buffers”:
“When Clear is called, the only per-fragment operations that are applied (if enabled) are the pixel ownership test, the scissor test, and dithering. The masking operations described in the last section (4.2.2) are also effective.”