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I want to specify encoding that is used by Lyx when it generates LaTeX source for preview or export. That is not a big problem Document->Settings->Language->Encoding->Other->Select encoding from combo box will do just that. But it will also add command \usepackage[selectedEncoding]{inputenc} to preamble of generated document.

How do I prevent that? I want all my LaTeX documents to be generated in UTF-8 but I do not want that inputenc declaration in preamble.

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Why this automatic inputenc declaration is it a problem? – Paul Gaborit Dec 26 '12 at 2:01
@Paul Gaborit Because LaTeX class of the document may also declare inputenc therefore there is option clash possible. See tex.stackexchange.com/questions/88177/… – drasto Dec 26 '12 at 14:42
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A LaTeX class should not impose specific encoding. – Paul Gaborit Dec 26 '12 at 14:45
@Paul Gaborit Thank you for this! This is what I needed to hear (hope this is not your subjective opinion). Apparently Lyx also expect LaTeX classes to not to impose specific encodings. Would you mind answering my question tex.stackexchange.com/questions/88177/… in this manner? It might be accepted answer. – drasto Dec 26 '12 at 14:59

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You more or less answered your own question:

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By selecting Language Default (no inputenc) as encoding, LyX will not add \usepackage[<encoding>]{inputenc} to the preamble.

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