$
$ cat ch25.txt
First there was nothing. Then there was Calvin[1].
blah blah blah
blah blah blah
"On a long enough timeline, the survival rate for everyone drops to zero" [2].
blah blah blah
"Dr. Livingstone, I presume?" [3]
blah blah blah
$
$ cat footnotes.txt
[1] A memorable quote from Bill Waterson's Calvin and Hobbes.
[2] Spoken by Tyler Durden, in Chuck Palahniuk's "Fight Club".
[3] By Henry Morton Stanley, on meeting Dr. David Livingstone near Lake Tanganyika on Nov. 10th, 1871.
$
$
$ perl -ne 'BEGIN {
>   open(FN,"footnotes.txt");
>   while(<FN>) {chomp; $fnote{$1}=$2 if (/(\[\d+\]) (.*)/)}
>   close(FN)}
> chomp;
> if (/(.*?)(\[\d+\])/) {print "$1\\footnote{$fnote{$2}}\n"}
> else {print $_,"\n"}' ch25.txt
First there was nothing. Then there was Calvin\footnote{A memorable quote from Bill Waterson's Calvin and Hobbes.}
blah blah blah
blah blah blah
"On a long enough timeline, the survival rate for everyone drops to zero" \footnote{Spoken by Tyler Durden, in Chuck Palahniuk's "FightClub".}
blah blah blah
"Dr. Livingstone, I presume?" \footnote{By Henry Morton Stanley, on meeting Dr. David Livingstone near Lake Tanganyika on Nov. 10th, 1871.}
blah blah blah
$
$