Documentation for JIRA 4.3. Documentation for other versions of JIRA is available too. 
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In order to provide fast searching, JIRA creates an index of the text entered into issue fields. This index is stored on the file system, and updated whenever issue text is added or modified. It is sometimes necessary to regenerate this index manually; for instance if issues have been manually entered into the database, or the index has been lost or corrupted.
Screenshot: Indexing JIRA
Choosing a custom Index Path:
If you upgraded JIRA with an XML backup from a JIRA version prior to 4.2 and used a custom directory for your index path, you can choose between using this custom directory (which cannot be edited) or the default directory for your index path location. However, once you switch to using the default directory, you can no longer choose the custom directory option.
(The default directory location is the caches/indexes subdirectory of the JIRA home directory.)