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Originally Posted by Rev. Bob
1.4.1 saved the modified files with UNIX EOLs (CR only), while 1.5.9 saved them with DOS EOLs (CRLF). One of the short story sections displayed a phantom text-comparison difference that looked like an extra linefeed, but bringing both modified copies into Notepad++ and changing the 1.5.9 version to use UNIX EOLs made them byte-identical. The same behavior showed up in the longer book as well, and I don't see a pattern. Some chapters display several instances, while others show none at all.
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FWIW: UNIX EOL is LF. IIRC Mac is CR, but that might be outdated info. DOS (Windows) is CRLF. This BS has been causing me headaches for nigh-on 45 years.
I am not surprised at the difference. The last change I made was to take out all guesswork about modifying the files. Reason: in calibre V4.3 the system method not only corrected line endings but sometimes changed to encoding to 8-bit ASCII, which broke everything. Taking it out made calibre V5 leave use the "system" line ending. I suspect if you ran the plugin on Linux or Mac you would get slightly different behaviour.
This can be fixed if we are willing to fork.
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I should note that in the case of at least one file for each book, this extends to a known-static file which my copy of calibre custom-generates: titlepage.xhtml. (I use different stock cover page code, but it's a calibre source file mod; it doesn't come from the books.)
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The plugin pays special attention to that file.
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It turns out that loading the beta book into the calibre editor, making and undoing a minimal change to an affected file, resaving the book, and extracting that file results in its EOLs being changed to the CR format, which is why I conclude that this is a quite minor bug in 1.5.9.
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HTML is supposed to ignore EOL differences. I think the rule is any of CR, CRLF, or LF are treated as a space. The line ending should make no difference at all in what the reader app displays.
That said, I am willing to back the changes out if you are willing to support a fork.