Config files should not need to reference other config files. No config option should contain a path to another config file.

Therefore:

User.properties => AdminUser.properties
Removed CREATE_HOMEDIRECTORY
Removed HOME_DIR_ROOT

AdminDaemon.properties.in => AdminDaemon.properties
Removed USER_PROP
Removed GROUP_PROP
Removed RESOURCE_PROP
Removed RMI_PROP
Removed SQL_PROP
Removed MASTER_AUTH_FILE
Removed ACCESS_COMBINATIONS_FILE

.../conf/{Sql.properties.in => Sql.properties}

com.openexchange.ajp/conf/ajp.properties
changed comment for AJP_SERVLET_CONFIG_DIR

.../conf/{lang-detect.properties.in => lang-detect.properties}

Removed .../conf/TidyConfiguration.properties
Removed .../conf/TidyMessages.properties

com.openexchange.server/conf/contact.properties
Removed property contactldap.configuration.path

.../{import.properties.in => import.properties}
Removed path from com.openexchange.import.mapper.path

com.openexchange.server/conf/mail.properties
Removed path from com.openexchange.mail.JavaMailProperties

com.openexchange.server/conf/system.properties.in => system.properties
Renamed MimeTypeFile to MimeTypeFileName
Removed path from com.openexchange.caching.configfile
Removed properties: Calendar, Infostore, Attachment, Notification, ServletMappingDir, CONFIGPATH, AJPPROPERTIES, IMPORTEREXPORTER, LDAPPROPERTIES, EVENTPROPERTIES, PUSHPROPERTIES, UPDATETASKSCFG, HTMLEntities,
MailCacheConfig, TidyMessages, TidyConfiguration, Whitelist

...{sessiond.properties.in => sessiond.properties}
Removed path from com.openexchange.sessiond.sessionCacheConfig

.../{crawler.properties.in => crawler.properties}
Removed path from com.openexchange.subscribe.crawler.path

.../conf/textxtraction.properties
Removed path from com.openexchange.textxtraction.tikaConfig