Hot reload broken for 'applications' extension point contributions

When you add a definition inside an existing 'applications' contribution, hot-reload will because impossible because the whole definition will be removed when the component is reload. This is the same problem that is described in: https://jira.nuxeo.com/browse/NXP-6013?focusedCommentId=84929&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-84929 but limited to the 'applications' extension because it specifically need to have the same name for every contribution that need to be merged with the main theme.