Not possible to use features like timer while the clock is hidden

feature is added. try next version. you will find corresponding checkbox on "Experimental" tab. but it may work unreliable, and this is expected, unfortunately...

the reason of such unreliable behavior somewhere deep in Qt, its implementation of window flags changing logic is very strange, and it confuses window managers in mosts cases. setting window flags works fine only on app initialization. I have some workarounds to get it work on runtime, but this is just workarounds. and very likely they will be dropped at all in next major version.

Even official documentation warns that window will disappear when flags are changed on runtime! But this was documented pretty recently, few years there were no such notes... moreover, disappearing is not only problem - it is possible to show window agai, but in most cases window is in some strange state (as I wrote before, Qt' flags changing logic confuses window managers) and flags change has no effect. And this problem not only in my software. Even official exaples or any "hand-made" "hello world" app can demonstrate such behavior.

So do not expect too much. I have no plans to implement own window flags management logic using platform-specific calls, and moreover it is very likely almost impossible to get such things to work correctly because the same logic already exists in Qt framework and it can't be disabled.

Indeed, I couldn't make it work. Moreover, the clock disappears forever and there is no way to put it back, even unticking the option. I had exported the settings before testing, so I just used that to roll back.
Not very aware of why you are using window flags and it sounds weird to me that Qt wouldn't have support for something as common as hotkeys. But if using hotkeys to change settings exceeds Qt possibilities, I'm thinking on an alternative, like operating the Timer not only with mouse clicks, but also with a combination of keys like Ctrl + some user-defined key. In that way, you wouldn't have to deal with the invisibility settings, nor any other setting whatsoever.

ughhh... on my macOS it at least does not disappear... just not always handles clicks. I did not test it on Windows and Linux, because I have these systems only on virtual machines and a lot of strange things can happen on them.

Window flags should be changed to make window "transparent for mouse" (actually make it ignore all input events) and this flag should be vanished to handle clicks. Hotkeys is good idea, I didn't think about it, I'll try. But usal hotkeys (as discussed at your link) will not work - hotkeys are handled only by active window. "global hotkeys" may be an option, but such things are tricky and require platform API usage, fortunately there is very convenient library exists QHotkey. moreover, I already used it in few places.

So, I'll make countdown plugin to work with hotkeys through this library. Please wait few days more until I implement it.

so... it was pretty easy to add global hotkeys support to countdown timer plugin. now it is possible to assign very likely almost any key sequence for timer start/pause/restart actions. feel free to try it. any feedback is welcome. also it is very easy to add hotkey for any other action (in this plugin), feel free to ask/suggest if you need something.

I already updated next version again.

previously implemented very buggy features was removed.

I works great! I would like to promote what you do. Could I send you some bits to the same last address?

sure. this address is permanent

thanks for donation!
closing ticket as solved