Arduino IDE 1.0.3 can't find libraries in Linux Mint 14

Programs that use libraries fail to compile. Some specifics:
Arduino:Uno
OS: Linux Mint 14
IDE version: 1.0.3 (upgraded from 1.0.1)

Once I put the user into the right group, simple programs compile,upload, and produce expected results on the serial monitor. That seems to indicate that everything is fine, until I start to use libraries. Simple programs like "hello world" and producing an ASCII table work well.

When I try to use libraries, compiles fail, with lots of error messages. Library files are both a header and a c++ file in what look like appropriate locations.
The tree linux program produces:

rc@cerebralcortex ~ $ tree /usr/share/arduino/libraries/usr/share/arduino/libraries
??? Adafruit
? ??? Adafruit_GFX.cpp
? ??? Adafruit_GFX.h
? ??? Adafruit_LEDBackpack.cpp
? ??? Adafruit_LEDBackpack.h
? ??? Wire.h
? -- clipped -- to reduce size -- (unessential libraries are present but not listed)
??? Wire
??? examples
? ??? digital_potentiometer
? ? ??? digital_potentiometer.ino
? ??? master_reader
? ? ??? master_reader.ino
? ??? master_writer
? ? ??? master_writer.ino
? ??? SFRRanger_reader
? ? ??? SFRRanger_reader.ino
? ??? slave_receiver
? ? ??? slave_receiver.ino
? ??? slave_sender
? ??? slave_sender.ino
??? keywords.txt
??? utility
? ??? twi.c
? ??? twi.h
??? Wire.cpp
??? Wire.h

108 directories, 170 files

and

rc@cerebralcortex ~/sketchbook $ tree
.
??? Adafruit_7_SegmntDisplayTest_1_Display
? ??? Adafruit_7_SegmntDisplayTest_1_Display.ino
??? HelloWorld
? ??? HelloWorld.ino
??? HereIsSomeMath
? ??? HereIsSomeMath.ino
??? libraries
? ??? Adafruit_GFX
? ? ??? Adafruit_GFX.cpp
? ? ??? Adafruit_GFX.h
? ? ??? glcdfont.c
? ? ??? license.txt
? ? ??? README.html
? ? ??? readme.txt
? ??? Adafruit_LEDBackpack
? ? ??? Adafruit_LEDBackpack.cpp
? ? ??? Adafruit_LEDBackpack.h
? ? ??? glcdfont.c
? ? ??? README.htm
? ? ??? readme.txt
? ? ??? README.txt
? ??? Wire
? ??? examples
? ? ??? digital_potentiometer
? ? ? ??? digital_potentiometer.ino
? ? ??? master_reader
? ? ? ??? master_reader.ino
? ? ??? master_writer
? ? ? ??? master_writer.ino
? ? ??? SFRRanger_reader
? ? ? ??? SFRRanger_reader.ino
? ? ??? slave_receiver
? ? ? ??? slave_receiver.ino
? ? ??? slave_sender
? ? ??? slave_sender.ino
? ??? keywords.txt
? ??? utility
? ? ??? twi.c
? ? ??? twi.h
? ??? Wire.cpp
? ??? Wire.h
??? NSB_Timer
? ??? NSB_Timer.ino
??? sevenseg
? ??? sevenseg.ino
??? timer
. ??? timer.ino

Adafruit tech support suspected a mislocated Wire program, but it appears to be in the correct place. I have two versions of the file Wire.h and two versions of Wire.cpp, and both have been checked.

Further details, including error dumps are at:

http://forums.adafruit.com/viewtopic.php?f=22&t=36991&p=183060#p183060 so I won't waste too much space. As you can see, I started over on the Adafruit forums, but they didn't have much Linux experience, and suggested this forum. Thanks in advance for the help.