Please refer below link- http://experience-aem.blogspot.com/2014/05/aem-cq-6-msm-setting-jcr-permissions-on-live-copy-components.html 

Kindly follow the steps mentioned in this article- https://helpx.adobe.com/in/experience-manager/kb/how-to-recompile-jsp-files-in-AEM.html 

Could you please add the code so that we can check how it's getting called twice as it's not possible until its called twice.

You can use below command to build your packagemvn clean install -PautoInstallPackage -Dmaven.wagon.http.ssl.insecure=true -Dmaven.wagon.http.ssl.allowall=true  Or you can follow steps mentioned in this thread-https://experienceleaguecommunities.adobe.com/t5/adobe-experience-manager/error-while-mave...

You can use rollout feature in aem to rollout pages from one place to another but it would have inheritance from your source location.

Could you please add the logs here as there must be something in logs or did u check in the browser console what. error you are getting.

Issue is with key store try to reconfiguring it.Step by step details here-https://experienceleaguecommunities.adobe.com/t5/adobe-experience-manager/aem-6-4-saml-integration-with-sso/qaq-p/388634/comment-id/83082#M83082  

Better do it at dialog level.

Try keeping them under apps/urproject folder.

Write a groovy script to update existing nodes ,