A follow up note regarding WP-CLI

@JJJ Even when the paths fix above is applied, creating a new network with WP-CLI results in the new network defaulting to the use of blogs.dir unless the ms_files_rewriting option is explicitly set on the new network. For parity with the defaults in WP_MS_Networks_Admin::handle_add_network() I think it's also worth considering:

Setting the default clone_network to the site ID derived from the --url param
Setting the default options_to_clone to network_options_to_copy() (or at minimum specifying ms_files_rewriting to avoid the bug you identified)

IOW, replacing these lines with something like:

$clone_network = $assoc_args['clone_network'];
if ( empty( $clone_network ) ) {
	$clone_network = get_current_site()->id;
}
$network_exists = get_network( $clone_network );
if ( ! $network_exists ) {
	WP_CLI::error( sprintf( "Clone network %s doesn't exist.", $clone_network ) );
}

$options_to_clone = false;
if ( ! empty( $clone_network ) && $network_exists ) {
	if ( ! empty( $assoc_args['options_to_clone'] ) ) {
		$options_to_clone = explode( ',', $assoc_args['options_to_clone'] );
	} else {
		$options_to_clone = array_keys( network_options_to_copy() );
	}
}

This also fixes what looks like a bug in the current code where $options_to_clone is only ever set when the network specified by clone_network doesn't exist.

Uh oh!

Uplaod problem /uplaod/sites/136/sites/136 #153

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