When editing or creating a custom field, the administration interface refers to a "Search Template" and a re-index option. There is no reference to how custom field searching differs from non-custom field searching, namely how custom field queries in the "Quick Search" field will not return results. This behavior should be explicitly noted in the documentation and on the interface, otherwise a user or administrator have the potential to be confused and frustrated when trying to implement and use custom fields.

The documentation refers to a search template and to allowing searching through the issue navigator, but says nothing regarding quick search (http://www.atlassian.com/software/jira/docs/v3.8/customfields/overview.html#Search+templates):

Search templates are responsible for indexing a custom field as well as making it searchable through the issue navigator. Each of the default custom field types have a related pre-configured search template.

Suggested correction:

Search templates are responsible for indexing a custom field as well as making it searchable through the issue navigator. Custom fields are not searchable through Quick Search. Each of the default custom field types have a related pre-configured search template.

In the EditCustomField page where it states:

Note that changing a custom field searcher may require a re-index.

needs to be corrected as well. Suggested correction (can be here or in the other location on the page where it says to reindex):

Note that custom fields cannot be searched through Quick Search, only from the Issue Navigator. Changing a custom field searcher may require a re-index.

An alternative and preferable fix would be to implement JRA-7686.