cd mywebroot/setup php ./index.php --installmode=upgrade-advanced
PHP Warning: Directive 'safe_mode' is deprecated in PHP 5.3 and greater in Unknown on line 0 <html> <head> <title></title> </head> <body> <h1>FATAL ERROR: MODX Setup cannot continue.</h1> <p>To use PHP 5.3.0+, you must set the date.timezone setting in your php.ini. Please do set it to a proper timezone before proceeding. A list can be found <a href="http://us.php.net/manual/en/timezones.php">here</a>.</p> </body> </html>
date.timezone = "Europe/Paris"
http://my-server.com/setup
This question has been answered by multiple community members. See the first response.

safe_mode = on
safe_mode = off
;date.timezone =
date.timezone = Europe/Paris
php ./index.php --installmode=upgrade-advanced
php ./index.php --installmode=upgrade-advanced --core_path=/path/to/.../mypath/to/core
<modx>
<database_type>mysql</database_type>
<database_server>localhost</database_server>
<database>name-of-my-database</database>
<database_user>user-to-connect-database</database_user>
<database_password>password-to-connect-database</database_password>
<database_connection_charset>utf8</database_connection_charset>
<database_charset>utf8</database_charset>
<database_collation>utf8_general_ci</database_collation>
<table_prefix>my-modified-prefix-or-modx__</table_prefix>
<https_port>443</https_port>
<http_host>localhost</http_host>
<cache_disabled>0</cache_disabled>
<!-- Set this to 1 if you are using MODX from Git or extracted it from the full MODX package to the server prior
to installation. -->
<inplace>0</inplace>
<!-- Set this to 1 if you have manually extracted the core package from the file core/packages/core.transport.zip.
This will reduce the time it takes for the installation process on systems that do not allow the PHP time_limit
and Apache script execution time settings to be altered. -->
<unpacked>0</unpacked>
<!-- [b]The language to install MODX for[/b]. This will set the default manager language to this. Use IANA codes. -->
<language>fr</language>
<!-- Paths for your MODX core directory -->
<core_path>path=/path/to/.../mypath/to/core/</core_path>
<!-- Paths for the default contexts that are installed. -->
<context_mgr_path>/path/to/.../mypath/to/httpdocs/manager/</context_mgr_path>
<context_mgr_url>/manager/</context_mgr_url>
<context_connectors_path>/path/to/.../mypath/to/httpdocs/connectors/</context_connectors_path>
<context_connectors_url>/connectors/</context_connectors_url>
<context_web_path>/path/to/.../mypath/to/httpdocs/</context_web_path>
<context_web_url>/</context_web_url>
<!-- Whether or not to remove the setup/ directory after installation. -->
<remove_setup_directory>1</remove_setup_directory>
</modx>php ./index.php --installmode=upgrade-advanced --core_path=/path/to/.../mypath/to/core
Do not forget the --core_path, because it does not get it from the config file (why ?)