This is not a question. It is provided as information for those who have added custom links to the OBIEE toolbar in 11g and need to know where to place the customlinks.xml file in 12c.
1. I placed these same three lines (from 11g) into instanceconfig.xml within the <ServerInstance> section:
<CustomLinks>
<Enabled>true</Enabled>
</CustomLinks>
2. Stored customlinks.xml in: c:\Oracle\Middleware\user_projects\domains\bi\bidata\components\OBIPS
3. Restarted BI Presentation Server