Here's another eval() solution.

#!/usr/bin/perl

use strict;
use Data::Dumper;

my %hash;
my $value = "determined at run time";
while (<DATA>)
{
    chomp;
    eval '$hash{'
        . join(
            "}{",
            split(/\//)
        )
        . "} = '$value'";
}

print Dumper(\%hash);

__DATA__
root/dir1/file1
root/dir1/file2
root/dir1/file3
root/dir2/file1
[download]

-Matt