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Configuration in Administration for MF-2Effect on User Interface
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As you can see 'clones' link type is allowed for source issue, because it appears on the list, but MF-2 issue is associated with Link Scheme which doesn't allow to create 'is cloned by' link type. 

Example

Lets assume that you have issue BUG-32 in Bugs project and issue type is Bug. Let's also assume that you have issue TESTCASE-12 in Tests project and issue type is Test Case.
In Links there is also Bug Origin link type with outward "has a bug" and inward "is a bug from" links.
If you just disable "has a bug" in Bugs project and "is a bug from" in Tests project then it will work like this:

  1. you will be allowed to create
    • link: BUG-32 -> "is a bug from" -> TESTCASE-12
    • Visible on BUG-32: "is a bug from" TESTCASE-12
    • will be visible on TESTCASE-12: "has a bug" BUG-32
  2. but you will not be allowed to create an opposite link
    • TESTCASE-12 -> "is a bug from" -> BUG-32
    • so you will never have a result:
      • Visible on TESTCASE-12: "is a bug from" BUG-32
      • will be visible on BUG-32: "has a bug" TESTCASE-12