use XML::XPath;

use strict;

my $filename = 'test.xml';

my $header = do {
	open my $fh, $filename or die "$filename: $!";
	<$fh>;
};

my $xp = XML::XPath->new(filename => $filename);
$xp->setNodeText("/project/dependencies/dependency[version='1.0']/version", 2.0);

open my $fh, '>', $filename or die "$filename: $!";
print $fh $header;
print $fh XML::XPath::XMLParser::as_string($xp->findnodes('/'));
close $fh;