Perhaps it's a minor bug with the new update. I'm not seeing the option to adjust the color dots for my projects.
Please edit the project, right click, edit. Then you can click on the dot and change the color.
I'm not seeing the option either. I did as instructed above (the same as always, I think) and the only option that seems to appear is the icon for nesting the project (indent) or moving it back out. I see no color chart as in the past.
To clarify - after you click on "Edit project" and while you have the project input field opened so that you could change its name, you have to left-click on the colored dot. This opens the color selection field.
Definitely not intuitive, but it works for me! (yosemite platform)