Documentation for JIRA 4.0. Documentation for other versions of JIRA is available too. 
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This is all obsolete as of JIRA 3.2, where one can change the scoping of custom fields from within the field interface
In JIRA, custom fields can apply to all issue, all issues of a certain type, or issues in a single project. Occasionally one wants to change the scope of a custom field, eg. to make a project-specific custom field global. JIRA does not yet have a means of doing this in the interface, but it is easy to do by manipulating the database directly. Here we show how to do it.
Load your JIRA database in a SQL console. This operation is database-dependent. Oracle users will run sqlplus, MySQL users mysql or mysqlcc. Users of JIRA Standalone should follow this guide.
By running the query
select * from customfield;
Here, we have one global and one project-specific custom field.
Say we wanted to make the project-specific custom field global. We should set the custom field's project field to null:
Exit the SQL console and restart JIRA. The scope of the custom field should have changed.