Users of my arduino eclipse plugin report strange behaviour since Arduino IDE 1.5.7.
After investigation it turns out that avr-gcc sometimes returns wrong information when running the command to get the "included folders and defines" in certain folder setups.
To be concrete when Arduino IDE 1.5.5 is installed in r:/test/ and the following command is run from r:/test/
hardware\tools\avr\bin\avr-g++" -c -g -Os -w -fno-exceptions -ffunction-sections -fdata-sections -fno-threadsafe-statics -MMD -mmcu=atmega328p -DF_CPU=16000000L -DARDUINO=158 -DARDUINO_AVR_PRO -DARDUINO_ARCH_AVR -D__IN_ECLIPSE__=1 -E -P -v -dD R:/Test/Eclipse/workspace/.metadata/.plugins/org.eclipse.cdt.managedbuilder.core/spec.C
it will return (for full listing see http://pastebin.com/ZeLiC7TV)
... ignoring nonexistent directory "r:/test/arduinoide/hardware/tools/avr/lib/gcc/../../avr/include/c++/4.3.2" ignoring nonexistent directory "r:/test/arduinoide/hardware/tools/avr/lib/gcc/../../avr/include/c++/4.3.2/avr/avr5" ignoring nonexistent directory "r:/test/arduinoide/hardware/tools/avr/lib/gcc/../../avr/include/c++/4.3.2/backward" ignoring nonexistent directory "r:/test/arduinoide/hardware/tools/avr/lib/gcc/../../avr/sys-include"

when Arduino 1.5.7 is installed in r:/test/ and the same command is run from r:/test/ you get
`cygwin warning:
MS-DOS style path detected: R:/Test/Eclipse/workspace/.metadata/.plugins/org.eclipse.cdt.managedbuilder.core/spec.C

...
ignoring nonexistent directory "/ArduinoIDE/hardware/tools/avr/bin/../lib/gcc/avr/4.8.1/../../../../avr/include/c++/4.8.1"
ignoring nonexistent directory "/ArduinoIDE/hardware/tools/avr/bin/../lib/gcc/avr/4.8.1/../../../../avr/include/c++/4.8.1/avr/avr5"
...`
As you can see cygwin is reporting a path issue and the R:/test folder is missing from the include paths
With Arduino IDE 1.5.8 the same result is happening.

I think this is a glitch because when using Z:\windows as folder the problem does not occur.
rlogiacco and I have documented our steps in a issue (ignore the title and the part about the missing makefile) #arduino-eclipse-plugin/183
Sloeber/arduino-eclipse-plugin#183 (comment)