How can we exclude Custom Groovy validations and triggers during execution of merge?

You can add the following Groovy code to exclude validations during execution:

if(userName!='FUSION_APPS_CRM_ESS_APPID' &&
userName!='fusion_apps_crm_ess_appid' &&
userName!='FUSION_APPS_CRM_SOA_APPID' &&
userName!='fusion_apps_crm_soa_appid')
{

}