The secret chats presumably are (if you trust Telegram). Secret chats are 1 to 1. So anything outside of those that most people on Telegram access (massive channels and groups, smaller groups, private groups and channels) is NOT encrypted.
The article claims that "Contacts and calendars are built on industry standards (CalDAV and CardDAV) that do not provide built-in support for end-to-end encryption." but it seems like a weak argument. Nobody actually cares what protocol is used between a device and a cloud.
There is a feature that can be enabled to create an end-to-end encrypted chat between strictly two users, but most people do not actually use it.
Telegram is largely a social network masquerading as a messaging app. There is a deep network of “channels” that interlink with each other to provide a community for users. None of that is encrypted.
Good luck with that. And that's a seriously big issue. Moderators (and "moderators" in Telegram mean an alleged team of people they hire to moderate all content in Telegram - if you report content, the group administrators won't even be notified about that so they can act by themselves first) in most cases won't do absolutely anything.
