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Fix CONFIG REWRITE append duplicate newlines
In the old code, everytime we perform a config rewrite, an additional newline is appended, see #1396 Because iostream::eof will only return true after reading the end of the stream. It does not indicate, that the next read will be the end of the stream. So everytime config rewrite is performed, the old loop will append a newline in `lines`, and then we will append it to the conf file. In addition, the same modification has been made to other similar places. This PR fixes #1396
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