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The DIR ccache format is now the default in krb5-server 1.11.2-4 but /run/user/<uid> isn't created for Apache by anything so it has no ccache (and it doesn't have SELinux permissions to write here either). Use KRB5CCNAME to set a file path instead in /etc/sysconfig/httpd. https://fedorahosted.org/freeipa/ticket/3607
Ground rules on adding new schema Brand new schema, particularly when written specifically for IPA, should be added in share/*.ldif. Any new files need to be explicitly loaded in ipaserver/install/dsinstance.py. These simply get copied directly into the new instance schema directory. Existing schema (e.g. in an LDAP draft) may either be added as a separate ldif in share or as an update in the updates directory. The advantage of adding the schema as an update is if 389-ds ever adds the schema then the installation won't fail due to existing schema failing to load during bootstrap. If the new schema requires a new container then this should be added to install/bootstrap-template.ldif.