Fully workable source.

.gitignore

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+*.project
+*.classpath
+/bin/*
+/.settings/*
+/.externalToolBuilders/*
+*.log

run.cmd

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+java -jar ActiveWindowCheck.jar > activewindow.log

src/ru/diowo/activewindowcheck/Main.java

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+package ru.diowo.activewindowcheck;
+
+import com.sun.jna.Native;
+
+import com.sun.jna.Pointer;
+import com.sun.jna.platform.win32.WinDef.HWND;
+import com.sun.jna.platform.win32.WinUser;
+import com.sun.jna.ptr.IntByReference;
+import com.sun.jna.win32.StdCallLibrary;
+
+import com.sun.jna.Native;
+import com.sun.jna.platform.win32.Kernel32;
+import com.sun.jna.platform.win32.User32;
+import com.sun.jna.platform.win32.WinDef.HWND;
+import com.sun.jna.platform.win32.WinDef.RECT;
+import com.sun.jna.platform.win32.WinNT.HANDLE;
+
+import java.util.Timer;
+import java.util.TimerTask;
+
+public class Main {
+
+	private static String lastWindow = ""; 
+	
+	private static final int MAX_TITLE_LENGTH = 1024;
+
+	public interface PsApi extends StdCallLibrary {
+
+	    int GetModuleFileNameExA(HANDLE process, HANDLE module, byte[] name, int i);
+
+	}
+	
+	public static void main(String[] args) throws Exception {
+		
+		Timer timer = new Timer();
+		TimerTask task = new TimerTask() {
+			@Override
+			public void run() {
+				PsApi psapi = (PsApi) Native.loadLibrary("psapi", PsApi.class);
+				
+				char[] buffer = new char[MAX_TITLE_LENGTH * 2];
+			    HWND hwnd = User32.INSTANCE.GetForegroundWindow();
+			    User32.INSTANCE.GetWindowText(hwnd, buffer, MAX_TITLE_LENGTH);
+			    String currWindow = Native.toString(buffer);
+			    if (! lastWindow.equals(currWindow)) {
+			    	lastWindow = currWindow;
+			    	
+				    System.out.println("Active window title: " + Native.toString(buffer));
+				    RECT rect = new RECT();
+				    User32.INSTANCE.GetWindowRect(hwnd, rect);
+				    System.out.println("rect = " + rect);
+				    
+				    IntByReference pid = new IntByReference();
+			        User32.INSTANCE.GetWindowThreadProcessId(hwnd, pid);
+			        
+			        byte[] filename = new byte[1024];
+
+			        HANDLE process = Kernel32.INSTANCE.OpenProcess(0x0400 | 0x0010, false, pid.getValue());
+			        psapi.GetModuleFileNameExA(process, null, filename, 1024);
+			        String filenameString= Native.toString(filename);
+			        
+			        System.out.println("PID "+pid.getValue()+", filename "+filenameString);
+			    }
+			}
+		};
+		
+		timer.schedule(task, 1000, 500);
+		
+    }
+
+}

workspace.xml

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+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<project default="create_run_jar" name="Create Runnable Jar for Project ActiveWindowCheck with Jar-in-Jar Loader">
+    <!--this file was created by Eclipse Runnable JAR file Export Wizard-->
+    <!--ANT 1.7 is required-->
+    <!--define folder properties-->
+    <property name="dir.buildfile" value="."/>
+    <property name="dir.workspace" value="${dir.buildfile}/.."/>
+    <property name="dir.jarfile" value="${dir.workspace}"/>
+    <target name="create_run_jar">
+        <jar destfile="${dir.workspace}/ActiveWindowCheck.jar">
+            <manifest>
+                <attribute name="Main-Class" value="org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader"/>
+                <attribute name="Rsrc-Main-Class" value="ru.diowo.activewindowcheck.Main"/>
+                <attribute name="Class-Path" value="."/>
+                <attribute name="Rsrc-Class-Path" value="./ jna-4.3.0.jar jna-platform-4.3.0.jar"/>
+            </manifest>
+            <zipfileset src="jar-in-jar-loader.zip"/>
+            <fileset dir="${dir.buildfile}/bin"/>
+            <zipfileset dir="${dir.buildfile}/lib" includes="jna-4.3.0.jar"/>
+            <zipfileset dir="${dir.buildfile}/lib" includes="jna-platform-4.3.0.jar"/>
+        </jar>
+    </target>
+</project>