We are using the pro-plan for paper.li and to support SSL we use cloudflare SSL which makes an SSL tunnel to the paper.li website. The custom domain through which paper.li loads is fine except for the JS and CSS which loads through http.
Here is a simple change through which paper.li can support SSL ->
<script src="http://paper.li/something.js" />
you can load it using
<script src="//paper.li/something.js" />
This small change solves the whole problem.
As a test you can check out our custom domain at paper.li -> https://news.appknox.com (This loads inseured JS and CSS for the same reason).
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