<p>Did some more tests, and result is always the same - freeze after deleting line via shortcut (no matter which key binding was used) in both "normal" and "default config without plugins" modes. But it only happens when editing existing (saved) file. If I create a new file, paste thousands of lines into it and use CTRL + K, everything works until the moment I save the file on disk.</p>
<p>For this reason, I believe it might be somehow related to one file monitoring options (because Geany has plenty of them that are used to monitor files for external changes, do auto reload, etc)</p>

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