Symptoms

If you were using JIRA Linker plugin in the older releases of JIRA (4.x or before) then you have some custom fields of type 'com.atlassian.jira.plugin.linker' in the database but they are not visible on the instance.

There are no errors in the atlassian-jira.log.

Cause

The JIRA Linker plugin should now be bundled with JIRA in the new releases. So the functionality should be working fine. However somehow the fields created using the external plugin are not showing up correctly with the bundled plugin.

Workaround

Run the following query in the JIRA database :

update customfield 
	set customfieldtypekey='com.atlassian.jira.plugin.system.customfieldtypes:url', 
		customfieldsearcherkey='com.atlassian.jira.plugin.system.customfieldtypes:exacttextsearcher' 
	where customfieldtypekey='com.atlassian.jira.plugin.linker:linker';

In general, you are changing the customfield type from Linker to Url field. This seems to be a good idea as Linker field is no longer present in JIRA in the latest releases.