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Custom fields serve for customization of data which may be stored for an issue of particular project.
(Hence they are defined per-project.)

The purpose of these custom fields are to accomodate custom data, which are project-specific, but are expected to be present for every or most issues of that project - for example, JBoss AS 7 project has a "GitHub pull request" field, which was an important part of the development tracking.

A custom field's definition includes it's name (e.g. githubPR), type (text, number, url, date, user, ...), label (e.g. "Github pull request"), and default value.

When an issue is created/edited/viewed, these custom fields are included in the UI and stored in the database accordingly.

For starters, only text may be supported.

Beware of cyclic dependency in the data model definition (JPA entities).

Each issue may have 1:N relations to other issues.
Relations are oriented.
Relation types are definable globally.

Examples:

Depends / Is dependency
Is related to / relates to
Duplicates / is duplicated by
Cloned from / cloned to
Incorporates / is incorporated by