While editing files longer than one page, Geany manages the scroll position such that the currently edited line is always the bottom-most line. One unfortunate side effect of this is that the spell checking underlining will be hidden beneath the status bar (depending on the height of the window):

In the screenshot above, you can barely see that "Filller" was highlighted as misspelled.

One way other editors (e.g. GitHub right here) handle this, is by leaving some space underneath the last line in the file. As a workaround, you can repeatedly scroll down in Geany, but that gets annoying while editing.

You might need to adjust the height of the Geany window to reproduce the problem.

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