#!/usr/bin/perl

use strict;
use warnings;
use Data::Dumper;

my %dirhash;
while (<DATA>) {
    chomp;
    my $last=\%dirhash;
    $last=$last->{$_} ||= {} for split qr|/|;
}

print Dumper \%dirhash;

__END__
/file.txt
/a/file.txt
/a/b/c
/a/b/c/file.txt
/z/m/w/file.txt