How to compile a sketch using arduino-builder?
You need to specify the path to the tools-builder folder, which is where ctags is. Try this:

arduino-builder \
  -compile \
  -hardware /usr/share/arduino/hardware \
  -tools /usr/share/arduino/hardware/tools \
  -tools /usr/share/arduino/tools-builder \
  -libraries lib \
  -fqbn arduino:avr:uno \
  -build-path .build \
  src/main.ino