G'day immamanatee,

Welcome to the monastery.

You're reading your data an inordinate amount of times:

• Read all input into $text using slurp mode ($/ = undef).
• Read all data to generate @url_list.
• Read all data to remove URL lines.
• Read all remaining lines in an outer loop.
• Read each line in an inner loop to generate link numbers.
• Read the entire @url_list in every pass through the inner loop.

As you're dealing with paragraphs, consider reading your input as paragraphs and processing it just once:

• Read all input into an array using paragraph mode ($/ = '').
• Create a hash, mapping link number to URL, using just the last paragraph of text.
• Loop through all but the last paragraph, printing each paragraph and any associated footnotes.

Here's an example using your data:

#!/usr/bin/env perl -l

use strict;
use warnings;

my @data = do { local $/ = ''; <DATA> };
my %urls = map { /^\[(\d+)/ => $_  } split /^/ => $data[-1];
print $data[$_], @urls{$data[$_] =~ /\[.*?\]\[(\d+)\]/g} for 0 .. $#da
+ta - 1;

__DATA__
This is a an example of [Markdown][1] footer links. I'm trying to use 
+[Perl][2] to organize them more coherently.

But I'm getting too many newlines and I'm hoping the [PerlMonks][3] ca
+n help.

[1]: https://daringfireball.net/projects/markdown/
[2]: http://www.perl.org/
[3]: http://www.perlmonks.org/
[download]

Output:

This is a an example of [Markdown][1] footer links. I'm trying to use 
+[Perl][2] to organize them more coherently.

[1]: https://daringfireball.net/projects/markdown/
[2]: http://www.perl.org/

But I'm getting too many newlines and I'm hoping the [PerlMonks][3] ca
+n help.

[3]: http://www.perlmonks.org/
[download]

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.