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Create a text field to store company's name, go to CRM Company field configuration and select recently created text field in "Copy to" field. You can filter records to be copied by using "Copy JQL".
Hide field if it has no value
You can select if you want to show empty Company field or not with the setting Hide field if it has no value.
Autocomplete of Company Custom Field
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The field can be filled manually and if it is empty , the system puts 'Not defined' in it so standard JIRA validator of required fields don't return error when no company is written in the required CRM Company field.
CRM Company autocomplete setting requires synchronization of CRM Contacts with Jira Users.