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If you create a Beebox project for the purpose of aligning a lot of files, you would of course enable alignment by default (no need to create instructions files). Please note that some languages may encounter difficulties with alignment due to different lengths between phrases in the source language and the target language.
If you integrate the Beebox with a CMS you should use instructions files so that the CMS tells the Beebox exactly which translated content needs to be aligned: The content that was actually edited or annotated by the user.
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