Google announced the Index Status reports within Google Webmaster Tools now lets you differentiate between HTTP, HTTPS and subdirectories.
Google's John Mueller said "If you're a data-driven SEO (or just love to see how your site's indexed), you'll love this change :). In Webmaster Tools, we've now made it possible to differentiate the "index status" information for http / https as well as for subdirectories." Zineb explained "you can now see index status data for your HTTPS sites and subdirectories."
You will see on the report an "update" line that will convey when the reporting changed to handle this.
As of March 9, 2014, the Index Status reflects the data of your specific protocol and site combination as it is verified in Webmaster Tools (i.e. distinguishing www and https variations).
Here are the technical details:
We do not show aggregate data for all versions of your site. While Google crawls and indexes content from your site regardless of whether you have verified the site in Webmaster Tools, the number of indexed URLs reported in Index status are specific to those associated with your site version.For example, suppose you have a site with 10 URLs that people can view without signing in, and 100 URLs that people can only see once they sign into your site. If you have added only one version of your site to Webmaster Tools (e.g. http://www.example.com), you would see Index status totals only for the non-secure portion of your site, which would be a much lower number than for all URLs on your site.
Therefore, in order to see the index count for your secure site, you will need to add it to Webmaster Tools (e.g. https://www.example.com) and then select it from the Site Selector.
Similarly, you can verify a subdirectory of your site with Webmaster Tools, and only data for that subdirectory will be shown in its Index status (www.example.com/blog/). However, the top-level domain will continue to reflect the total count of URLs indexed for that domain.
Forum discussion at Google+.
