fromStructured flag is true, then the structured configuration (i.e., Configuration.properties) is merged into the latest raw configurations returned from the plugin. The Configuration object returned will consist of the structured configuration along with the merged raw configurations. If fromStructured is false, then the raw configurations (i.e., Configuration.rawConfigurations) is merged into the latest structured configurations returned from the plugin. The returned Configuration will then consist of the raw configuration along with the merged structured configuration.
@param configuration The Configuration with the changes to be merged
@param resourceId The id of the resource to which the configuration belongs
@param fromStructured A flag that if true indicates the merge should be from structured to raw,otherwise merge from raw to structured.
@return The merged configuration, where a merge consists of a refresh of the side being mergedfollowed by the values of the side merging from being applied to the side being merged into.
@throws PluginContainerException if a runtime or plugin error occurs.
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