I couldn't find much info on loading the module/extensions manually.
For anyone who needs to add a module manually ( specifically rep_tax_cash_basis in this example) The extension file is available from https://github.com/apmuthu/frontaccounting/tree/master/extensions
These are placed in the modules directory and info from the \modules\rep_tax_cash_basis\_init\config file and placed in the file \installed_extensions.php extending the array as below:
Instructions are given in this file to increment $next_extension_id also.
0 =>
array (
'name' => 'British COA',
'package' => 'chart_en_GB-general',
'version' => '2.3.0-4',
'type' => 'chart',
'active' => false,
'path' => 'sql',
'sql' => 'en_GB-general.sql',
),
1 =>
array (
'name' => 'Cash Basis Tax Reporting',
'package' => 'rep_tax_cash_basis',
'version' => '2.3.7-4',
'type' => 'extension',
'active' => true,
'path' => 'modules/rep_tax_cash_basis',
'sql' => '',
),
The same needs to be done in the company file for it to be active for that company ie \company\X\installed_extensions.php
And that's it.