Hi Joshua,
This is the correct forum for discussing developing issues for apps for Office(Office add-ins).
>>1. Can we develop Word Bookmarks, Word Footnotes and Word endnotes for Office 2016 programmatically using the Javascript API only<<
As far as I know, there is no such API, we can insert the bookmarks, Word footnotes and endnotes in Office.js. However, we can use setSelectedDataAsync methoed to insert the Bookmarks, Footnotes and Endnotes with OOXML.
Here are some helpful links for your reference:
Create better add-ins for Word with Office Open XML
Document.setSelectedDataAsync method (JavaScript API for Office)
>>2. I did find support for creating the same using AJAX calls and C# but we wanted to know if it would be possible with just using Javascript API and if we are using AJAX,C# dlls can it be deployed in a web portal atmosphere like Azure or Sharepoint?<<
The web application in Office add-ins is normal as a web application we developed before. So we can use AJAX and C# dlls as a normal web application. However there are still some difference between it and the normal web application, you can get more
detail about it from link below:
Privacy and security for Office Add-ins
Regards & Fei
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