Actually it's quite easy

If you want to hide the child boards in MessageIndex, just remove this chunk of code:
if (!empty($context['boards']) && (!empty($options['show_children']) || $context['start'] == 0))
{
echo '
<div class="tborder childboards" id="board_', $context['current_board'], '_childboards">
<div class="cat_bar">
<h3 class="catbg">', $txt['parent_boards'], '</h3>
</div>
<div class="table_frame">
<table class="table_list">
<tbody id="board_', $context['current_board'], '_children" class="content">';
foreach ($context['boards'] as $board)
{
echo '
<tr id="board_', $board['id'], '" class="windowbg2">
<td class="icon windowbg"', !empty($board['children']) ? ' rowspan="2"' : '', '>
<a href="', ($board['is_redirect'] || $context['user']['is_guest'] ? $board['href'] : $scripturl . '?action=unread;board=' . $board['id'] . '.0;children'), '">';
// If the board or children is new, show an indicator.
if ($board['new'] || $board['children_new'])
echo '
<img src="', $settings['images_url'], '/' .$context['theme_variant_url'], 'on', $board['new'] ? '' : '2', '.png" alt="', $txt['new_posts'], '" title="', $txt['new_posts'], '" />';
// Is it a redirection board?
elseif ($board['is_redirect'])
echo '
<img src="', $settings['images_url'], '/' .$context['theme_variant_url'], 'redirect.png" alt="*" title="*" />';
// No new posts at all! The agony!!
else
echo '
<img src="', $settings['images_url'], '/' .$context['theme_variant_url'], 'off.png" alt="', $txt['old_posts'], '" title="', $txt['old_posts'], '" />';
echo '
</a>
</td>
<td class="info">
<a class="subject" href="', $board['href'], '" name="b', $board['id'], '">', $board['name'], '</a>';
// Has it outstanding posts for approval?
if ($board['can_approve_posts'] && ($board['unapproved_posts'] || $board['unapproved_topics']))
echo '
<a href="', $scripturl, '?action=moderate;area=postmod;sa=', ($board['unapproved_topics'] > 0 ? 'topics' : 'posts'), ';brd=', $board['id'], ';', $context['session_var'], '=', $context['session_id'], '" title="', sprintf($txt['unapproved_posts'], $board['unapproved_topics'], $board['unapproved_posts']), '" class="moderation_link">(!)</a>';
echo '
<p>', $board['description'] , '</p>';
// Show the "Moderators: ". Each has name, href, link, and id. (but we're gonna use link_moderators.)
if (!empty($board['moderators']))
echo '
<p class="moderators">', count($board['moderators']) === 1 ? $txt['moderator'] : $txt['moderators'], ': ', implode(', ', $board['link_moderators']), '</p>';
// Show some basic information about the number of posts, etc.
echo '
</td>
<td class="stats windowbg">
<p>', comma_format($board['posts']), ' ', $board['is_redirect'] ? $txt['redirects'] : $txt['posts'], ' <br />
', $board['is_redirect'] ? '' : comma_format($board['topics']) . ' ' . $txt['board_topics'], '
</p>
</td>
<td class="lastpost">';
/* The board's and children's 'last_post's have:
time, timestamp (a number that represents the time.), id (of the post), topic (topic id.),
link, href, subject, start (where they should go for the first unread post.),
and member. (which has id, name, link, href, username in it.) */
if (!empty($board['last_post']['id']))
echo '
<p><strong>', $txt['last_post'], '</strong> ', $txt['by'], ' ', $board['last_post']['member']['link'], '<br />
', $txt['in'], ' ', $board['last_post']['link'], '<br />
', $txt['on'], ' ', $board['last_post']['time'],'
</p>';
echo '
</td>
</tr>';
// Show the "Child Boards: ". (there's a link_children but we're going to bold the new ones...)
if (!empty($board['children']))
{
// Sort the links into an array with new boards bold so it can be imploded.
$children = array();
/* Each child in each board's children has:
id, name, description, new (is it new?), topics (#), posts (#), href, link, and last_post. */
foreach ($board['children'] as $child)
{
if (!$child['is_redirect'])
$child['link'] = '<a href="' . $child['href'] . '" ' . ($child['new'] ? 'class="new_posts" ' : '') . 'title="' . ($child['new'] ? $txt['new_posts'] : $txt['old_posts']) . ' (' . $txt['board_topics'] . ': ' . comma_format($child['topics']) . ', ' . $txt['posts'] . ': ' . comma_format($child['posts']) . ')">' . $child['name'] . ($child['new'] ? '</a> <a href="' . $scripturl . '?action=unread;board=' . $child['id'] . '" title="' . $txt['new_posts'] . ' (' . $txt['board_topics'] . ': ' . comma_format($child['topics']) . ', ' . $txt['posts'] . ': ' . comma_format($child['posts']) . ')"><img src="' . $settings['lang_images_url'] . '/new.gif" class="new_posts" alt="" />' : '') . '</a>';
else
$child['link'] = '<a href="' . $child['href'] . '" title="' . comma_format($child['posts']) . ' ' . $txt['redirects'] . '">' . $child['name'] . '</a>';
// Has it posts awaiting approval?
if ($child['can_approve_posts'] && ($child['unapproved_posts'] | $child['unapproved_topics']))
$child['link'] .= ' <a href="' . $scripturl . '?action=moderate;area=postmod;sa=' . ($child['unapproved_topics'] > 0 ? 'topics' : 'posts') . ';brd=' . $child['id'] . ';' . $context['session_var'] . '=' . $context['session_id'] . '" title="' . sprintf($txt['unapproved_posts'], $child['unapproved_topics'], $child['unapproved_posts']) . '" class="moderation_link">(!)</a>';
$children[] = $child['new'] ? '<strong>' . $child['link'] . '</strong>' : $child['link'];
}
echo '
<tr id="board_', $board['id'], '_children"><td colspan="3" class="children windowbg"><strong>', $txt['parent_boards'], '</strong>: ', implode(', ', $children), '</td></tr>';
}
}
echo '
</tbody>
</table>
</div>
</div>';
}
OR, you can change the first "if" so that it is always "false", this way you don't delete anything, just have it like this:
if (!empty($context['boards']) && (!empty($options['show_children']) || $context['start'] == 0) && (1==2))
To change it to the bottom, you just need to move that chunk of code and put it BEFORE:
// Show breadcrumbs at the bottom too.
theme_linktree();