The following is a list of known directories to add to your IDE for effective code completion using AVR-based Arduinos (version 1.6.*).
{path-to-arduino}/hardware/arduino/avr/cores/arduino/ {path-to-arduino}/hardware/arduino/avr/libraries/EEPROM/ {path-to-arduino}/hardware/arduino/avr/libraries/HID/ {path-to-arduino}/hardware/arduino/avr/libraries/SPI/ {path-to-arduino}/hardware/arduino/avr/libraries/SoftwareSerial/ {path-to-arduino}/hardware/arduino/avr/libraries/Wire/ {path-to-arduino}/hardware/tools/avr/avr/include/ {path-to-arduino}/hardware/tools/avr/avr/include/avr/ {path-to-arduino}/hardware/tools/avr/avr/include/compat/ {path-to-arduino}/hardware/tools/avr/avr/include/util/ {path-to-arduino}/hardware/tools/avr/lib/gcc/avr/4.*.*/include/ {path-to-arduino}/hardware/tools/avr/lib/gcc/avr/4.*.*/include-fixed/
Add any of the following libraries that ship with Ardunio to your IDE project's list of additional directories for code completion only if your project uses the library:
{path-to-arduino}/libraries/Bridge/src/ {path-to-arduino}/libraries/Esplora/src/ {path-to-arduino}/libraries/Ethernet/src/ {path-to-arduino}/libraries/Firmata/src/ {path-to-arduino}/libraries/GSM/src/ {path-to-arduino}/libraries/LiquidCrystal/src/ {path-to-arduino}/libraries/Robot_Control/src/ {path-to-arduino}/libraries/RobotIRremote/src/ {path-to-arduino}/libraries/Robot_Motor/src/ {path-to-arduino}/libraries/SD/src/ {path-to-arduino}/libraries/Servo/src/ {path-to-arduino}/libraries/SpacebrewYun/src/ {path-to-arduino}/libraries/Stepper/src/ {path-to-arduino}/libraries/Temboo/src/ {path-to-arduino}/libraries/TFT/src/ {path-to-arduino}/libraries/WiFi/src/
You can add all of these to the default configuration, but giving your IDE more directories to parse will slow it down.
In addition to the above, you should add any libraries you've downloaded into your {Arduino-install-directory}/libraries
and used by your project to the IDE project's list of additional directories for code completion. These will typically be of the form:
../libraries/{name-of-library}