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Fixed it
In following function i added the extension validation:
function filedepot_newversion_form($form, &$form_state) {
// I added below to line just before form field
$default_filter = 'jpg png doc docx xls xlsx pdf ppt pptx';
$filter = variable_get('filedepot_filetype_filter', $default_filter);
// And added #upload_validators as shown below
$form['filedepot_file'] = array(
'#type' => 'managed_file',
'#title' => t('Choose a file'),
'#size' => 22,
'#upload_validators' => array(
'file_validate_extensions' => array($filter),
),
);
}
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