Certainly there are plenty programs that are designed modularly, componentized, plugin-based, compositional, whatever... They just never feel as good as purpose-built apps with good workflows. If you know of one that does, please do forward it on because I'd love the inspiration.

I think Keybase does what it intends to do, which is to make PKI accessible to non-experts and to cultivate a community of users achieve the usefulness that network effect affords.

If you're really just looking for encryption and signing, encrypted filesystems, encrypted chat, distributed filesystems, and you're an expert, you have the tools you need.