obsolete .h files and #include problems

My first project: MIDI controller (example: http://6be54c364949b623a3c0-4409a68c214f3a9eeca8d0265e9266c0.r0.cf2.rackcdn.com/457/images/mpd26_angle_lg.png)

Im currently experimenting with different parts; potentiometers, encoders, and buttons, and Im stuck on these rotary encoders. I downloaded an encoder .h file from Encoder Library, for Measuring Quadarature Encoded Position or Rotation Signals which was recommended by this people on this forum. My problem is that, based on my research, some of the files referenced in this .h file are obsolete.
Wiring.h
WProgram.h

I get the impression that the functions of these .h files have been incorporated into the arduino.h, and io.h... ect. and I dont need to worry about downloading the supposed "fixes" to these .h files that I've found on github and other places. Is this true?

The other potential problem Im having is that I am using the Visualmicro (http://www.visualmicro.com) plugin which allows me to code and compile in Visual Studio. I think Im having an issue with the automatically generated xx.vsarduino.h file which has definitions like,
#define AVR_ATmega2560
#define ARDUINO 105
#define AVR
#include "C:\Program Files (x86)\Arduino\arduino-1.0.5\hardware\arduino\variants\mega\pins_arduino.h"
#include "C:\Program Files (x86)\Arduino\arduino-1.0.5\hardware\arduino\cores\arduino\arduino.h"
#include "C:\Users\jarmer\Documents\Arduino\doit\XX.ino"

Im a little confused about what #definitions and #includes I need to declare in my .ino file so that my .h files work properly and I dont have duplicates.

Using the Arduino 1.0.5 IDE and the Encoder library from the Teensy website the example programs compile without problems. Have you tried to compile the examples?

Hi jarmerfohn,

You can ignore the vsarduino.h it is used only for intellisense purposes and is not part of the compilation.

Did you sort the other issues out? If not then please do join the free forum and we will help http://www.visualmicro.com/forums/YaBB.pl

Thanks