...

Starting with JCLI 6.1, the cloneProject action will now create a project with a shared configuration just like the UI option for this. See 

Jira Legacy
JCLI-349 JCLI-349

. More over, even on the createProject action you can get a shared configuration by referencing an existing project via the template parameter. See 

Jira Legacy
JCLI-1055 JCLI-1055

 for more details. When a create or clone is done in this way, JIRA will not create extraneous and unwanted project specific schemes.  Here is an excerpt from JCLI-1055:

cloneProject will now create the clone using the "shared configuration" option shown on the UI. This means ALL schemes will be the same as the base project unless specifically overridden. The old behavior that involved creating project specific schemes will no longer be an option (create an issue if you need this behavior resurrected). While this is an incompatibility, this new behavior is more the expected behavior from a *clone* operation.

Project Templates

JIRA 7.x has renamed a number of templates and removed some (like the JIRA Classic Template). Also, if you built private templates via the JIRA plugin exit point, that has also changed in an incompatible way and will need to be redone.

...