files in subfolders has not been compiled

[iddq]

Hello,

I'm trying to port my project from 1.6.7 to 1.6.13 and I'm facing following issue.
Files in subfolders of sketch has not been compiled.

[facchinm]

The recursive compilation on sketch subfolders different from src has been removed with 1.6.10 because it was close to a bug than a feature 😄 The relevant issue is #5186 while the commit is arduino/arduino-builder#148 .
Moving the extra (non user-modifiable) files in src will do the trick for both 1.6.7 and latest IDE.