Once you have extracted the book and the chapter, you can translate the two together into a single number by multiplying the book rank by 10000 say plus the chapter. Now use the Schwartzian to sort the citations: 

use strict;
use warnings;

my $ctr=0;
my %books=map{$_=>++$ctr}(
'Genesis','Exodus','Leviticus','Numbers','Deuteronomy','Joshua',
'Judges','Ruth','1 Samuel','2 Samuel','1 Kings','2 Kings',
'1 Chronicles','2 Chronicles','Ezra','Nehemiah','Esther',
'Job','Psalm','Proverbs','Ecclesiastes','Song of Solomon',
'Isaiah','Jeremiah','Lamentations','Ezekiel','Daniel',
'Hosea','Joel','Amos','Obadiah','Jonah','Micah','Nahum',
'Habakkuk','Zephaniah','Haggai','Zechariah','Malachi',
'Matthew','Mark','Luke','John','Acts','Romans','1 Corinthians',
'2 Corinthians','Galatians','Ephesians','Philippians',
'Colossians','1 Thessalonians','2 Thessalonians','1 Timothy',
'2 Timothy','Titus','Philemon','Hebrews','James','1 Peter',
'2 Peter','1 John','2 John','3 John','Jude','Revelation');

my @sorted=
map{$_->[0]}
sort{$a->[1]<=>$b->[1]}
map{chomp;/^(\d?\s?\w+)\s+(\d+)/;[$_,10000*$books{$1}+$2]}
<DATA>;

print "$_\n" for @sorted;

__DATA__
Acts 4:29-31
Numbers 14:10
Luke 1:20
John 16:15
Acts 2:4
1 Peter 1:22
Psalm 56:3
2 Corinthians 12:2, 4, 1, 11
Ephesians 3:18, 19
Ephesians 4:14, 13, 17, 18; 5:15, 16
Matthew 24:24
Colossians 2:6-8
Hebrews 10:35-39
Hebrews 4:10-12
Philippians 1:6, 27-29
Matthew 7:6-12, 15
Philippians 2:13-15

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In reply to Re: Regex Substring SORT Conundrum by hdb
in thread Regex Substring SORT Conundrum by Polyglot

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