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You can setup the JIRA server plugin using the admin client. You will need the following information which is stored on the server

the url of your JIRA server instance, e.g. 'https://jira.mycompany.com',
the rest service of your JIRA server instance, e.g. 'https://jira.mycompany.com/rest/api/2'
a comma separated list of jira projects, e.g. 'PROJECT1,PROJECT2'
a user which has access to JIRA,
the password of the user

The client configuration is done using a JSON object. Please note the text must use double quotes (") around all strings. The following parameters can be set:

enabled: must be set to true if the client should use the JIRA
pluginId: must be set to "101" (unless there is a newer version of the plugin)
defaultProjectId: this is the default project in the create issue dialog
defaultTypeId: that is default issue type in the create issue dialog
projectsAndTypes: an array of projects which should be available, each of them needs
- id: the JIRA project id
- key: a name for humans the project (used in the Matrix client only)
- issueTypes: an array of issue types (tasks or bugs in JIRA), each of them
  - id: the JIRA id of the type (e.g. BUG, TASK, EPIC, ...)
  - name: a name (used in the Matrix client only)
  - icon: a font awesome icon (https://fortawesome.github.io/Font-Awesome/icons/ up to version 4.0)
one2one: a structure which can be set if there should be a one to one mapping between an Matrix item and JIRA bug/task. It has to values
- projectId: the project key
- typeId: the type name
states: an array mapping JIRA states to Matrix states. This can be configured per projectKey and typeName.
- projectKey: the project key (can be empty for the default if there is no better mapping)
- typeName: the type name (can be empty for the default if there is no better mapping)
- states: a list of mappings for this project / type
  - name: the name of the status in matrix, this is computed automatically
  - color: color in display (one to one mapping)
  - background: background color (one to one mapping)
  - done: if set to "true" the ticket will be rendered with strike through