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Reference is added just as a plain text number between brackets
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Translating the Setge de Calanda article from Catalan to Spanish with Apertium, one reference is added to the translation as a plain text number in brackets. Notice the reference [7] in the example below: it appears as a normal reference (in blue) on the source paragraph, but it is added as regular text on the right.

ref-as-text.PNG (79×897 px, 21 KB)

This quick link provides an easy to reproduce example (based on an excerpt with the problematic reference). Note how the issue is present when using Apertium but it is not when using Google Translate. So the issue may be with the algorithm that re-applies references for plain-text translation services like Apertium (the numbers and the colon before the reference may be confusing the algorithm):

With Apertium:

Screenshot 2020-03-24 at 10.29.00.png (296×1 px, 65 KB)

With Google Translate:

Screenshot 2020-03-24 at 10.28.44.png (313×1 px, 69 KB)