As your question is rather broad I will give you a rather broad response; normally I wouldn\'t even answer these types of questions but I just so happen to have a relevant script I made a while back.

This is NOT plug and play and has some third-party dependencies from CakePHP that needs to be autoloaded.

The script creates an image of all the specified folders in an array adds a manifest of files and an identifier file e.g. VERSION 2. The image (zip file) can then be uploaded to a site running VERSION 1 as long as it has the same update model. Once uploaded, the model then extracts the files as long as the zip has a valid identifier file in it (to prevent users from uploading an unrelated zip and nuking the system); the script also creates a current image of the site (at VERSION 1) just in case restoration is necessary.

The script also has a restore previous version function that will remove any additional files that were in version 2 and not 1 and will restore the original files of 1.

I offer no support for this. But hopefully you find it a bit helpful - it\'s sort of hacked together but in my limited testing it worked fine.

Controller:

<?php
if (!defined(\'BASEPATH\')) {
exit(\'No direct script access allowed\');
}
/**
* 
* NEOU CMS v4 CI Edition
* @copyright (c) 2018, Alexander Fagard
* @requires PHP version >= 5.6
* 
* You cannot redistribute this document without written permission from the author
* 
*/
class Update extends MY_Backend {
static $perm = [\'admin_only\' => true];
public function __construct() {
parent::__construct();
$this->lang->load(\'core_update\');
$this->load->model(\'backend/core_update_model\', \'update\');
}
public function index() {
$this->tpl->head($this->lang->line(\'update_heading\'));
$this->tpl->body();
$this->output->append_output($this->messages->display());
$data = array(
\'is_local\' => $this->localization->is_local(),
\'previous_exist\' => $this->update->previous_exists()
);
$this->parser->parse(\'backend/core_update\', $data);
$this->tpl->footer();
}
public function restore() {
try {
$this->update->restore_previous();
rmdir_recursive($this->update->updates_folder);
$this->messages->success($this->lang->line(\'update_previous_restored\'));
} catch (Exception $e) {
$this->messages->error($e->getMessage());
} finally {
redirect(CMS_DIR_NAME . \'/update\');
}
}
public function apply() {
$this->load->helper(\'byte_helper\');
try {
$this->update->mk_update_dir();
$config[\'upload_path\'] = $this->update->updates_folder;
$config[\'overwrite\'] = true;
$config[\'allowed_types\'] = \'zip\';
$config[\'max_size\'] = convert_bytes_to_type(file_upload_max_size(), \'KB\');
$config[\'file_ext_tolower\'] = true;
$this->load->library(\'upload\', $config);
if (!$this->upload->do_upload(\'update\')) {
throw new Exception($this->upload->display_errors(\'\', \'\'));
}
$data = $this->upload->data();
$this->update->apply_update($data[\'full_path\']);
$this->messages->success($this->lang->line(\'update_applied\'));
} catch (Exception $e) {
$this->messages->error($e->getMessage());
} finally {
redirect(CMS_DIR_NAME . \'/update\');
}
}
public function create() {
if (!$this->localization->is_local()) {
show_error($this->lang->line(\'update_localhost\'), 500);
}
try {
$this->update->create_update();
$this->messages->success(sprintf($this->lang->line(\'update_created\'), $this->update->files_processed));
} catch (Exception $e) {
$this->messages->error($e->getMessage());
} finally {
redirect(CMS_DIR_NAME . \'/update\');
}
}
}

Model: https://pastebin.com/UuzQ1tds

Upload zip, extract and replace all files.

Something like this:

update.zip

./root/application/controllers/*.*
./root/application/views/*.*
...

This only will be possible if the user running apache/nginx has enough privileges on file system.