By default, the SQC Plugin only processes files with "xsd", "wsdl" or "xfm" extension. In order to process files with other extensions, you would have to create a new plugin which provides extensions to the following extension points:
The creation of this plugin only requires that you create a new plugin manifest file like pluginExtensionExample.xml. To install your new plugin, you will have to create a new directory, MyPluginDir say, in EclipseDirOrWSADDir/plugins (where EclipseDirOrWSADDir is the directory where Eclipse or WSAD has been installed). Then put the plugin manifest at EclipseDirOrWSADDir/plugins/MyPlugin/plugin.xml and restart Eclipse or WSAD.