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My teacher asked me to move some part to the Annex of the master thesis.

I don't know where should I put this Annex thing,

I have index, list of figures, list of appreviatiosn, then many chapters, then the references.

so where does this Annex sit please ?

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The annex is a separate, standalone document, with information that supports your thesis, but is not part of the thesis.

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Your teacher is requesting that you take the annex (which is a separate, standalone document) and integrate it into the main document. How best to do that is going to depend largely on the content of the annex and how your thesis is structured.

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