An Alyx model reference has already been found in the sourcefilm maker under a folder titled 'ep3' so it seems Valve are at least working on a new Half-Life game and not just creating Team Fortress hats.
And one last thing to note is a Facepunch forum user has found icons that seem to be for the Source 2 editor. Take a look!
UPDATE: One last subtle clue, Valve added a new line under their description for the source engine on their website. "And it’s about to get even better."