Here's a quick overview:
Zeta1 and related code. This stuff is pretty much entirely gone from the repo.
2009-2016 although most theory advances were right at the beginning of the period
Spatial pooling, Temporal Memory, anomaly detection. This is what's in the repo now.
The spatial pooling & TM used to be called the Cortical Learning Algorithm (CLA) but we abandoned that name and have been scrubbing our code and documentation of it for the last couple years. HTM is still used to refer to the algorithms in aggregate and we will continue to include new algorithms under the HTM umbrella.
This covers ongoing work on sensorimotor inference, temporal pooling, disjoint pooling, and possibly motor generation. This all builds on top of the previous work, relying on and extending spatial pooling & TM. Most of this is still very experimental and volatile and lives in nupic.research. It isn't stable or proven enough to meet the NuPIC standards but we still keep it public in case the community wants to follow along.