eclipse and catkin_make not linking to ros.h dependencies

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Hello all,

So I am working on a project where I basically want to create a node to take information from another, check it, then publish that information elsewhere. I was working on it yesterday and my coding environment was working fine(eclipse mars) however at one point yesterday it stopped recognizing all of my references to ros functions or message types. I thought it was just an eclipse specific thing so I tried to run it with catkin_make in my catkin workspace and that threw the same "undefined reference to ros*" errors as the build did in eclipse. Like I said, all was fine and dandy but now it isn't working. Below is the code for the node I am working with.

#include <ros/ros.h>
#include "/opt/ros/indigo/include/ros/ros.h"
#include <std_msgs/String.h>
#include <geometry_msgs/Twist.h>
#include <string>
#include <vector>

/// ROS node name
const std::string ComponentName = "vel_cmd_filter_node";

const std::string J5CommandTopic = "/j5_cmd";
const std::string MoveBaseCmd = "/cmd_vel";

/// default forward linear velocity command in m/s
const float DefaultVelocityCmd = 0.0;

/// default angular velocity command in rad/s
const float DefaultTurnRateCmd = 0.0;

 /// the rate at which the component will publish commands
const int LoopRate = 10; // Hz

/// input value limits
/// these are just here for safety and do not reflect the actual limits of the platform
const double MaxVelocityCommand = 3.0;
const double MaxTurnRateCommand = 1.0;

geometry_msgs::Twist incoming;

void chatterCallback(const geometry_msgs::Twist& velcmd);
geometry_msgs::Twist getCommandMsg();

int main(int argc, char **argv) {

// get all command line arguments that aren't ROS specific
// these should be the velocity command parameters

// initialize ROS
std::vector<std::string> args;
geometry_msgs::Twist velcmd;


ros::init(argc,argv, ComponentName);
ros::removeROSArgs(argc, argv, args);
ros::NodeHandle nh;
ros::Subscriber sub = nh.subscribe(MoveBaseCmd, 1000, chatterCallback);

// velocity command publisher
ros::Publisher velCmdPub = nh.advertise<geometry_msgs::Twist>(J5CommandTopic, 1000);


// asynchronous spinner to receive ROS messages
ros::AsyncSpinner spinner(0);

// loop rate used to control the frequency of message publication
ros::Rate loop_rate(LoopRate);

// set up message command
geometry_msgs::Twist cmdMsg = getCommandMsg();

// run loop
spinner.start();
while (ros::ok()) {

    // publish velocity command
    ROS_INFO("Sending Velocity Command: {%f, %f}", cmdMsg.linear.x,
            cmdMsg.angular.z);
    if (cmdMsg.linear.x || cmdMsg.angular.z) {
        velCmdPub.publish(cmdMsg);
    }
    ros::spinOnce();
    loop_rate.sleep();
}

// shutdown component
spinner.stop();
ros::shutdown();

return 0;
}

void chatterCallback(const geometry_msgs::Twist& velcmd) {
ROS_INFO("I heard this velocity: [%f]", velcmd.linear.x);
ROS_INFO("I heard this rotation: [%f]", velcmd.angular.z);
incoming = velcmd;
}

geometry_msgs::Twist getCommandMsg() {

geometry_msgs::Twist msg;

// body coordinates
// x is forward linear motion
msg.linear.x = DefaultVelocityCmd;

// rotation around the Z axis
msg.angular.z = DefaultTurnRateCmd;

// all other parameters are ignored in the Twist message
// NOTE:: args[0] is the name of the
if (incoming.linear.x) {
    try {
        msg.linear.x = incoming.linear.x;
        msg.linear.x = std::max(msg.linear.x, -MaxVelocityCommand);
        msg.linear.x = std::min(msg.linear.x, MaxVelocityCommand);
    }

    catch (...) {
        // could not parse the input, use default value
        msg.linear.x = DefaultVelocityCmd;
    }
}

if ...