Whoa! That second regex will Do Weird Things after the first. (It picks up the newlines after the fresh tag). Here's another approach:
my $str = TEXT;
Foo is on this line,
and bar is in this paragraph.
Baz is in a new paragraph.
TEXT
my @para = split(/\n\n/, $str);
s!\n!<br>\n! foreach @para;
$str = join "\n<p>\n", @para;
print ">>$str<<\n";
For extra credit, put that in a one-liner. *sigh*
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