You need Thermal Foundation for Thermal Expansion now.

[05:14:55] [Client thread/ERROR] [FML]: The mod ThermalExpansion (Thermal Expansion) requires mods [ThermalFoundation] to be available

You need thermal foundation for thermal expansion, good, what is the problem with ProjectRed?

PR relies on Thermal Expansion. I cannot remove this dependency.

I found this issue when re-enabling the compatibility modules in #588
I had to remove them from the classpath in order to run, and used a custom gradle dependency configuration to do that. 1b36069 changed to back to normal dependencies.
There's 2 things you can do

1. Remove Thermal Expansion from the class path.
2. Add Thermal Foundation to the mods folder in {RUN_DIR}/mods

I think there's some issues with Tinker's Construct in dev environment too

Theres no need to include the COFH stuff anymore, I used class swapping for that. TConstruct is okay, it doesn't cause problems. I already did this in the other branch. Fixed via e38267c