Change in content bootstrapping results in broken development content after upgrading to v13

While performing an upgrade from 12.6.0 to 13.0.0, I noticed that if there are overlapping content definitions in application and development modules, The following (example) exception is thrown:

[*INFO*] [talledLocalContainer] 29.01.2019 10:34:05 ERROR main [ConfigurationServiceImpl.applyContent:852] Failed to apply all content

[*INFO*] [talledLocalContainer] org.onehippo.cm.model.impl.exceptions.DuplicateNameException: Duplicate Item: 'test[1]'.

[*INFO*] [talledLocalContainer] at org.onehippo.cm.model.impl.OrderableByNameListSorter.sort(OrderableByNameListSorter.java:96) ~[hippo-configuration-management-model-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.model.impl.OrderableByNameListSorter.sort(OrderableByNameListSorter.java:78) ~[hippo-configuration-management-model-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.impl.ContentDefinitionSorter.sort(ContentDefinitionSorter.java:68) ~[hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.ConfigurationContentService.getSortedDefinitions(ConfigurationContentService.java:246) ~[hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.ConfigurationContentService.apply(ConfigurationContentService.java:90) ~[hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.ConfigurationServiceImpl.applyContent(ConfigurationServiceImpl.java:849) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.ConfigurationServiceImpl.init(ConfigurationServiceImpl.java:351) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.onehippo.cm.engine.ConfigurationServiceImpl.start(ConfigurationServiceImpl.java:186) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.LocalHippoRepository.initializeConfiguration(LocalHippoRepository.java:305) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.LocalHippoRepository.initialize(LocalHippoRepository.java:289) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.LocalHippoRepository.create(LocalHippoRepository.java:119) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.LocalHippoRepository.create(LocalHippoRepository.java:109) [hippo-repository-engine-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_161]

[*INFO*] [talledLocalContainer] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_161]

[*INFO*] [talledLocalContainer] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_161]

[*INFO*] [talledLocalContainer] at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_161]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.HippoRepositoryFactory.getHippoRepository(HippoRepositoryFactory.java:147) [hippo-repository-connector-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.hippoecm.repository.RepositoryServlet.init(RepositoryServlet.java:204) [hippo-repository-servlets-13.0.0.jar:13.0.0]

[*INFO*] [talledLocalContainer] at org.apache.catalina.core.StandardWrapper.initServlet(StandardWrapper.java:1124) [catalina.jar:9.0.13]

[*INFO*] [talledLocalContainer] at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1079) [catalina.jar:9.0.13]

.......

I created a project from v13 archetype with the issue reproduced: https://code.onehippo.org/sandbox/content-bootstrap-bug

Note that hcm-action with reload on the folder does not fix the issue.