How can in not be HW dependent?
You'd need to output via a USART that you've initialized and plumbed, or use the PB3 / SWO pin for the SWV methods to work.
You provide NO details of your board or the STM32 MCU model you're using.
The IDE does have the ability to turn off breakpoints (it's not the breakpoint window, that works to control each one individually).
It's up in the top tool bar on the left hand side.
You may be able to put in a breakpoint, and see that it is disabled with a small diagonal line through it. Not always so obvious.