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The default skin can be set in the portal configuration files. The skin configured as default is used by Platform as the administrator starts/restarts the server.
Simply add a skin tag to the portal.war/WEB-INF/conf/portal/portal/classic/portal.xml configuration file.
To change skin to YourSkin, use the following code:
<portal-config>
<portal-name>classic</portal-name>
<locale>en</locale>
<access-permissions>Everyone</access-permissions>
<edit-permission>*:/platform/administrators</edit-permission>
<skin>MySkin</skin>
...
</portal-config>