How can I read in a file by paragraphs?

Use the $/ variable (see perlvar for details). You can either set it to "" to eliminate empty paragraphs ("abc\n\n\n\ndef", for instance, gets treated as two paragraphs and not three), or "\n\n" to accept empty paragraphs.

Note that a blank line must have no blanks in it. Thus "fred\n \nstuff\n\n" is one paragraph, but "fred\n\nstuff\n\n" is two.