When initializing a new project directory or updating an existing one with pio init --ide emacs, the directory paths searched for headers listed inside .clang_complete are enclosed in double quotes, which confuses clang-based tools (such as irony) and results in "file not found" errors in Emacs (flycheck-irony).

This is a typical line of .clang_complete that gets generated now:
-I"/home/USER/.platformio/packages/framework-arduinoavr/cores/arduino"
and this is what it should have been generated instead:
-I/home/USER/.platformio/packages/framework-arduinoavr/cores/arduino