How can I get an extension method to change the original object?

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You have to modify the contents of the List<string> passed to the extension method, not the variable that holds the reference to the list:

public static void ForceSpaceGroupsToBeTabs(this List<string> lines)
{
    string spaceGroup = new String('.', 4);
    for (int i = 0; i < lines.Count; i++)
    {
        lines[i] = lines[i].Replace(spaceGroup, "T");
    }
}

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