core: fix few bugs and clean up code/documentation

- fix typos and remove useless comments
- restore old documentation
- revert BOM changes
- revert adding of `set_anti_aliasing` function in favour of adding new parameters to `configure_app`
- change documentation of some parameters
- remove useless variables like `unsaved_document`
- fix "Mouse clicks count" so that now shows the number of counts and not the button creating them
- implement `_query_dirty` to make the query rects behave correctly inside plots and fix callback for them
- change `DEPRECATED_KEYWORD_ARG` parameter
- hide redundant window in `StackWindow`
- fix bug related to tooltip with angle headers
- restore missing Docking style colors