Links not getting created for AEM sites output for glossary, citation, footnotes

[maniap]

I'm generating AEM pages using AEM Sites preset with custom component mapping with existing editable template. In the pages created links are not getting generated for glossary. For citation according to documentation it is supported only in Native PDF. Also for foot notes it is coming as a single line of text with no links.
Currently I'm looking at using post processing workflows. Would like to know how we can process the pages created to create links for the same.

[DivrajSingh]

@maniap : with custom component mapping are you also overriding the rules for elements containing the "xref" or glossary? (it may be skipping rendering for those elements like glossary etc.)

Also, is the existing editable template also custom or are you using template shipped with product?

Which specific version of AEM Guides are you using?

[maniap]

@DivrajSingh 
I have not overridden any rules for xref/glossary. If I generate using the default AEM Site preset for the same map it does generate links for the glossary and footnotes. Also one more observation is that for the glossary topics in the map it is creating pages but there is not glossary related content whereas using default AEM Site preset it creates glossary topic pages with the glossary content. 
I'm currently using weretail templates.

AEM Guides version : com.adobe.fmdita-6.5-uuid-5.0.0.211