The Gutenberg books seem to be formatted with spaces between paragraphs - if you prefer not to have those, then use Calibre to convert (you can do this from epub to epub just to reformat) and in the "Look & Feel" options tick the option to remove space between paragraphs.
You can change the justification if you like, but paragraph indenting would be a custom CSS job - and I think you'll want to keep the para indent once you've got rid of the extra line between the paragraphs.
Coops
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