find . -type f | ../test.php

files-first.php

#!/usr/bin/env php
<?php
$input = stream_get_contents(fopen("php://stdin", "r"));
$files = explode("\n", $input);
$treeFiles = [];

foreach ($files as $file) {
    if (empty($file)) {
        continue;
    }
    $parts = explode('/', $file);

    $filename = array_pop($parts);
    $parts = array_reverse($parts);
    $tree = [$filename => $file];
    foreach ($parts as $part) {
        if ($part === '.') {
            continue;
        }
        $tree = [$part => $tree];
    }
    $treeFiles = array_merge_recursive($treeFiles, $tree);
}
$format = function($tree, $format, $nesting = 0) {
    ksort($tree, SORT_STRING);
    $folders = [];
    $return = '';
    foreach ($tree as $name => $value) {
        if (!is_string($value)) {
            $folders[$name] = $value;
            continue;
        }
        $return .= sprintf(
            "%s [%s]%s\n",
            str_repeat('*', $nesting + 1),
            $value,
            pathinfo($value, PATHINFO_FILENAME)
        );
    }
    foreach ($folders as $name => $value) {
        $return .= sprintf(
            "%s %s\n",
            str_repeat('*', $nesting + 1),
            ucfirst($name)
        );
        $return .= $format($tree[$name], $format, $nesting + 1);
    }
    return $return;
};

echo $format($treeFiles, $format);

new.php

#!/usr/bin/env php
<?php
$input = stream_get_contents(fopen("php://stdin", "r"));
$files = explode("\n", $input);
$treeFiles = [];

foreach ($files as $file) {
    if (empty($file)) {
        continue;
    }
    $parts = explode('/', $file);

    $filename = array_pop($parts);
    $parts = array_reverse($parts);
    $tree = [$filename => $file];
    foreach ($parts as $part) {
        if ($part === '.') {
            continue;
        }
        $tree = [$part => $tree];
    }
    $treeFiles = array_merge_recursive($treeFiles, $tree);
}
$format = function($tree, $format, $nesting = 0) {
    ksort($tree, SORT_STRING);
    $files = [];
    $return = '';
    foreach ($tree as $name => $value) {
        if (is_string($value)) {
            $files[$name] = $value;
            continue;
        }
        $return .= sprintf(
            "%s %s\n",
            str_repeat('*', $nesting + 1),
            ucfirst($name)
        );
        $return .= $format($tree[$name], $format, $nesting + 1);
    }
    foreach ($files as $name => $file) {
        $return .= sprintf(
                "%s [%s]%s\n",
                str_repeat('*', $nesting + 1),
                $file,
                pathinfo($file, PATHINFO_FILENAME)
        );
    }
    return $return;
};

echo $format($treeFiles, $format);

test.php

#!/usr/bin/env php
<?php
$input = stream_get_contents(fopen("php://stdin", "r"));
$files = explode("\n", $input);
$treeFiles = [];

foreach ($files as $file) {
    if (empty($file)) {
        continue;
    }
    $parts = explode('/', $file);

    $filename = array_pop($parts);
    $parts = array_reverse($parts);
    $tree = [$filename => $filename];
    foreach ($parts as $part) {
        if ($part === '.') {
            continue;
        }
        $tree = [$part => $tree];
    }
    $treeFiles = array_merge_recursive($treeFiles, $tree);
}
$format = function($tree, $format, $nesting = 0) {
    ksort($tree, SORT_STRING);
    $files = [];
    $return = '';
    foreach ($tree as $name => $value) {
        if ($name === $value) {
            $files[] = $value;
            continue;
        }
        $return .= str_repeat('    ', $nesting) . $name . "\n";
        $return .= $format($tree[$name], $format, $nesting + 1);
    }
    foreach ($files as $file) {
        $return .= str_repeat('    ', $nesting) . $file . "\n";
    }
    return $return;
};

echo $format($treeFiles, $format);

Thanks @Xerkus