I set some node types in the CND file which loaded while repository initialization. for example

<jj='http://jj.com/1.0'>

[jj:nameable] mixin

  - _name (string) mandatory

[jj:content] > jj:nameable

  - _type (string) mandatory

change the jj:nameable to jj:name, then start application to load the CND file, then stop application, restart again, exception throw while starting:

ERROR jcr.RepositoryNodeTypeManager  - Node types were read from the system content, and appear to be inconsistent or invalid: Test Repository

Message: Supertype 'jj:name' from type 'jj:content' does not exist

Investigate method refreshFromSystem of RepositoryNodeTypeManager, it will also refresh the custom content type from the CND files, but the refresh do not maintain the dependencies

of node type result in the jj:content load before jj:name, that will throw exception.