Added <file>.cpp and <file>.h to project to implement MVC architecture which in turn uses the RTClib and Wire libraries. The problem is that the Arduino library references do not resove correctly when compiling with the debug option. The same problem occurs when the files are either in the immediate local directory with the controller *.ino file or when they are moved to their own respective library location in the Arduino library hierarchy. 

The error:

Compiling debug version of 'TimeTest2' for 'Arduino Uno'
ChickCoopCtl.cpp.o : : In function `ChickCoopCtl::getTime(char*, char*)':
ChickCoopCtl.cpp : now()'
ChickCoopCtl.cpp : now()'
ChickCoopCtl.cpp.o : : In function `ChickCoopCtl':
ChickCoopCtl.cpp : undefined reference to `Wire'
ChickCoopCtl.cpp : undefined reference to `Wire'
ChickCoopCtl.cpp : begin()'
ChickCoopCtl.cpp : begin()'
avr-objcopy* : : : No such file
avr-objcopy* : : : No such file

The first compiler pass succeeds but the link level fails. This same code compiles and loads successfully if the debug option is set to release. I have changed the references to wire to the underlying TwoWire class and instansiated RTC_DS1307 rather than use the static class reference to no avail - both versions work in release but above errors in debug.

Problem solved

The linker looks at the base Arduino <target>.ino file to resolve core library links. All user library code includes that reference core libraries must also be added to the base <target>.ino file. 

In addition, in the <target>.ino file, the <stdint.h> library must be included before the Wire and RTClib includes in order to resolve the unint<width>_t type references.

The core libraries are added by using the VS Add Arduino Library menu dropdown, the stdint.h reference must be added manually.

I am not an Arduino expert , I found this solution from another post on the web, although my initial suspicion that it was a linker problem proved correct. The Arduino linker uses the library includes in the <target>.ino to resolve link references and does not check user library files for cross references to other or core libraries. 

Any changes would have to be made cognizant of the Arduino environment.

There is a wiki site on Google that documents Arduino and the compile link process - http://code.google.com/p/arduino/. 

There is a compilation section which also points out that references to library files not referenced in the main <target>.ino file must be included in the <target>.ino. Once this accepted and proscribed procedure is followed there is no error between the release and debug compilations. In other words this procedure must be followed to adhere to the Arduino environment.

The original post refers to the fact that the linker failed because I did not include the referenced libraries in the <target>.ino file. The subsequent posts detail the solution, referenced libraries must be included in the <target>.ino file even when not referenced directly in the <target>.ino file. Once the solution procedures are followed there are no errors either in release or debug compilations.

The  the unint<width>_t reference is a compile error, not a linker error. The Arduino compiler does not load stdint.h automatically while VS does.

Referencing stdint.h automatically pre-compile probably will not be affect other compile outcomes.