Currently, “(Whole Document)” does the entire documents even if some lines are filtered out. I will think about adding a new command that can adjust only filtered lines in the entire document.
I can’t reproduce the bug. I would appreciate if you could let me know how to reproduce it.
As for Issue 2, I assume it is a negative filter, and I will fix it on the next beta.
As for Suggestion, if you choose “Display Coordinates” in the General page of configuration properties, you will see the line number according to the filtered result.