Is it really any easier to deal with popups than to just close the documents? (Ctrl+W)

The best solution would be either:

require a switch to create new documents, and change the default to not open new documents from the CLI without it.
to only allow one new file from the command-line, and not show a dialog. Is creating multiple new documents from the CLI really needed?

Either would solve the problem.

Pay more attention to what you're typing? (Mistyped commands can do a lot of damage.)

geany some_filename_glob will only open files or open new documents. How can that do a lot of damage?

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