@louiscad i think i found what is wrong with the extra newlines on windows you insert newlines with

appendln()

but in

removeCommentsAddedByUs

you only remove

\n////

and when finding the

indexOfNewLine

you look only for

\n

, but it could be

\r\n

i think the "safest" and laziest way to do this would be to always replace all

\r\n

with

\n

another option is

System.lineSeparator()

or only inserting

\n

(but then if the file somehow does get converted to CRLF its back to the same issue i guess)