Hi Jeramy,
I tried to answer this earlier but was prevented. I think Moodle security is too strict.
OK to keep this simple I'll just point you in the right direction.
The link IS in the layout/general.php but doesn't look like a link as it's written differently.
Find this line ...
<?php
if ($haslogo) {
echo html_writer::link(new moodle_url('/'), "<img src='".$PAGE->theme->settings->logo."' alt='logo' id='logo' />");
} else { ?>
<img src="<?php echo $OUTPUT->pix_url('logo', 'theme')?>" id="logo">
<?php
} ?>
and change it to this ...
<?php if ($haslogo) { ?>
<a href="URL to site link" ><img id="logo" src="<?php echo $PAGE->theme->settings->logo ;?> " alt="logo" /></a>
<?php } else { ?>
<img src="<?php echo $OUTPUT->pix_url('logo', 'theme')?>" id="logo" />
<?php } ?>