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Even though the generators do different things, there are a couple of settings most of them share:

Permissions to change JIRA data via changes in structure
The scope of the generator (the levels where it works)

Editing Issues via Generators

When you use the Group, Extend or Sort by Rank generators, by default the structure will be able to update some JIRA data as you move issues in the structure:

For the grouper it will update the field by which you group as you move an issue between the groups. For example, if you have issues grouped by assignee, as you move an issue from one group to another, it will be re-assigend.
For the extender it will update the JIRA, Epic links or parent of a sub-task as you move a child from one parent to another. For example, if you move a story from one epic, under the other, the epic field of the story will be updated.
For the sorter by rank it will update the Agile Rank as you move an issue up or down.

If you want to disable this, deselect the Allow changes via Structure checkbox in the generator settings.

Defining Generator Scope

The scope of the generators is defined by its position in the structure and the Levels option.

If you place the generator under the top-level root item, the generator will be applied to the whole structure. If you place it under some static item in the structure, the generator will only affect the descendants of this item.

To limit the scope further you can set on which levels the generator should run.

Structure Plugin for JIRA - Version 3.6 > Generators Options > levels.png

All levels means it will be applied to all descendants of the parent item.
Current level only means it will be applied on the level, where the generator is added.
Manual levels range allows you to define the specific levels, where the generator should work.

The levels created by Group generators are not taken into account when applying the specified manual levels limitation.

The From and To fields define the range of levels to which the generator will be applied. For example, if you want to pull in issue linked to the issues on level 2, you need to set the From field to 2 and To to 2, not 3. Setting the value to 3 will make extender add issues linked to the ones on level 2 and add the issues linked then to the ones that were just added.

This option is especially useful when you are defining generators for the hierarchy, where on different levels you have different types of relations. For example, the top level and the 2nd are connected with issue links, the 2nd to the 3rd with epic links, and on the 4th level you have sub-tasks.

In this case you will have three generators added under the root of the structure with the following Levels settings:

Links extender (Linked Issues) working only on the top level - Current level only
Agile extender (Stories under Epics) working on the second level - Manual levels range: from 2 to 2
Sub-tasks extender working on the third level - Manual levels range: from 3 to 3