diff --git a/pom.xml b/pom.xml
index f544f208e..ef11cc871 100644
--- a/pom.xml
+++ b/pom.xml
@@ -232,6 +232,18 @@ along with DependencyCheck.  If not, see <http://www.gnu.org/licenses/>.
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-failsafe-plugin</artifactId>
                 <version>2.12.4</version>
+                <configuration>
+                    <systemProperties>
+                        <property>
+                            <name>cve</name>
+                            <value>../data/cve</value>
+                        </property>
+                        <property>
+                            <name>cpe</name>
+                            <value>../data/cpe</value>
+                        </property>
+                    </systemProperties>
+                </configuration>
                 <executions>
                     <execution>
                         <goals>
diff --git a/src/main/java/org/codesecure/dependencycheck/App.java b/src/main/java/org/codesecure/dependencycheck/App.java
index a0b7ee8dc..0273d125b 100644
--- a/src/main/java/org/codesecure/dependencycheck/App.java
+++ b/src/main/java/org/codesecure/dependencycheck/App.java
@@ -22,6 +22,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.net.URLDecoder;
 import java.util.List;
 import java.util.logging.Level;
 import java.util.logging.LogManager;
@@ -69,11 +70,32 @@ public class App {
         app.run(args);
     }
 
+    private static File getLoggingDirectory() throws IOException {
+        String fileName = "logs";
+        String filePath = App.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (!exePath.isDirectory()) {
+            exePath = exePath.getParentFile();
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+
     private static void prepareLogger() {
         //while java doc for JUL says to use preferences api - it throws an exception...
         //Preferences.systemRoot().put("java.util.logging.config.file", "log.properties");
         //System.getProperties().put("java.util.logging.config.file", "configuration/log.properties");
-        File dir = new File("logs");
+        File dir;
+        try {
+            dir = getLoggingDirectory();
+        } catch (IOException ex) {
+            Logger.getLogger(App.class.getName()).log(Level.SEVERE, "Unable to get default logging location, "
+                    + "using the working directory instead.", ex);
+            dir = new File("logs");
+        }
+
         if (!dir.exists()) {
             dir.mkdir();
         }
diff --git a/src/main/java/org/codesecure/dependencycheck/data/cpe/Index.java b/src/main/java/org/codesecure/dependencycheck/data/cpe/Index.java
index 9e4fa3391..4d7354c87 100644
--- a/src/main/java/org/codesecure/dependencycheck/data/cpe/Index.java
+++ b/src/main/java/org/codesecure/dependencycheck/data/cpe/Index.java
@@ -75,17 +75,32 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * @throws IOException is thrown if an IOException occurs.
      */
     public Directory getDirectory() throws IOException {
-        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
-        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
-        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
-
-        File path = new File(decodedPath + File.separator + fileName);
-        path = new File(path.getCanonicalPath());
+        File path = getDataDirectory();
         Directory dir = FSDirectory.open(path);
 
         return dir;
     }
 
+    /**
+     * Retrieves the directory that the JAR file exists in so that
+     * we can ensure we always use a common data directory.
+     *
+     * @return the data directory for this index.
+     * @throws IOException is thrown if an IOException occurs of course...
+     */
+    protected File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (!exePath.isDirectory()) {
+            exePath = exePath.getParentFile();
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+
     /**
      * Creates an Analyzer for the CPE Index.
      *
@@ -158,8 +173,14 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      *
      * @param timeStamp the timestamp to write.
      */
-    private void writeLastUpdatedPropertyFile(long timeStamp) {
-        String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
+    private void writeLastUpdatedPropertyFile(long timeStamp) throws UpdateException {
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate the last updated properties file.", ex);
+        }
         File cpeProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
         Properties prop = new Properties();
         prop.put(Index.LAST_UPDATED, String.valueOf(timeStamp));
@@ -198,8 +219,10 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * is incorrect.
      * @throws DownloadFailedException is thrown if there is an error
      * downloading the cpe.meta data file.
+     * @throws UpdateException is thrown if there is an error locating the last updated
+     * properties file.
      */
-    public long updateNeeded() throws MalformedURLException, DownloadFailedException {
+    public long updateNeeded() throws MalformedURLException, DownloadFailedException, UpdateException {
         long retVal = 0;
         long lastUpdated = 0;
         long currentlyPublishedDate = retrieveCurrentCPETimestampFromWeb();
@@ -207,12 +230,24 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
             throw new DownloadFailedException("Unable to retrieve valid timestamp from cpe.meta file");
         }
 
-        String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
-        File f = new File(dir);
+        //String dir = Settings.getString(Settings.KEYS.CPE_INDEX);
+        File f;
+        try {
+            f = getDataDirectory(); //new File(dir);
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
         if (!f.exists()) {
             retVal = currentlyPublishedDate;
         } else {
-            File cpeProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
+            File cpeProp;
+            try {
+                cpeProp = new File(f.getCanonicalPath() + File.separatorChar + UPDATE_PROPERTIES_FILE);
+            } catch (IOException ex) {
+                Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+                throw new UpdateException("Unable to find last updated properties file.", ex);
+            }
             if (!cpeProp.exists()) {
                 retVal = currentlyPublishedDate;
             } else {
diff --git a/src/main/java/org/codesecure/dependencycheck/data/nvdcve/Index.java b/src/main/java/org/codesecure/dependencycheck/data/nvdcve/Index.java
index dad110f23..6a381dd21 100644
--- a/src/main/java/org/codesecure/dependencycheck/data/nvdcve/Index.java
+++ b/src/main/java/org/codesecure/dependencycheck/data/nvdcve/Index.java
@@ -67,21 +67,36 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
     private static final String LAST_UPDATED_BASE = "lastupdated.";
 
     /**
-     * Returns the directory that holds the NVD CVE Index.
+     * Returns the directory that holds the NVD CVE Index. Note, this
+     * returns the path where the class or jar file exists.
      *
      * @return the Directory containing the NVD CVE Index.
      * @throws IOException is thrown if an IOException occurs.
      */
     public Directory getDirectory() throws IOException {
+        File path = getDataDirectory();
+        Directory dir = FSDirectory.open(path);
+        return dir;
+    }
+
+    /**
+     * Retrieves the directory that the JAR file exists in so that
+     * we can ensure we always use a common data directory.
+     *
+     * @return the data directory for this index.
+     * @throws IOException is thrown if an IOException occurs of course...
+     */
+    protected File getDataDirectory() throws IOException {
         String fileName = Settings.getString(Settings.KEYS.CVE_INDEX);
         String filePath = Index.class.getProtectionDomain().getCodeSource().getLocation().getPath();
         String decodedPath = URLDecoder.decode(filePath, "UTF-8");
-
-        File path = new File(decodedPath + File.separator + fileName);
+        File exePath = new File(decodedPath);
+        if (!exePath.isDirectory()) {
+            exePath = exePath.getParentFile();
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
         path = new File(path.getCanonicalPath());
-        Directory dir = FSDirectory.open(path);
-
-        return dir;
+        return path;
     }
 
     /**
@@ -171,8 +186,14 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      *
      * @param timeStamp the timestamp to write.
      */
-    private void writeLastUpdatedPropertyFile(Map<String, NvdCveUrl> updated) {
-        String dir = Settings.getString(Settings.KEYS.CVE_INDEX);
+    private void writeLastUpdatedPropertyFile(Map<String, NvdCveUrl> updated) throws UpdateException {
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
         File cveProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
         Properties prop = new Properties();
 
@@ -187,8 +208,10 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
             prop.store(out, dir);
         } catch (FileNotFoundException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to find last updated properties file.", ex);
         } catch (IOException ex) {
             Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to update last updated properties file.", ex);
         } finally {
             try {
                 os.flush();
@@ -212,10 +235,11 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
      * @return the NvdCveUrl of the files that need to be updated.
      * @throws MalformedURLException is thrown if the URL for the NVD CVE Meta
      * data is incorrect.
-     * @throws DownloadFailedException is thrown if there is an error
+     * @throws DownloadFailedException is thrown if there is an error.
      * downloading the nvd cve download data file.
+     * @throws UpdateException Is thrown if there is an issue with the last updated properties file.
      */
-    public Map<String, NvdCveUrl> updateNeeded() throws MalformedURLException, DownloadFailedException {
+    public Map<String, NvdCveUrl> updateNeeded() throws MalformedURLException, DownloadFailedException, UpdateException {
 
         Map<String, NvdCveUrl> currentlyPublished;
         try {
@@ -227,7 +251,14 @@ public class Index extends AbstractIndex implements CachedWebDataSource {
         if (currentlyPublished == null) {
             throw new DownloadFailedException("Unable to retrieve valid timestamp from nvd cve downloads page");
         }
-        String dir = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String dir;
+        try {
+            dir = getDataDirectory().getCanonicalPath();
+        } catch (IOException ex) {
+            Logger.getLogger(Index.class.getName()).log(Level.SEVERE, null, ex);
+            throw new UpdateException("Unable to locate last updated properties file.", ex);
+        }
+
         File f = new File(dir);
         if (f.exists()) {
             File cveProp = new File(dir + File.separatorChar + UPDATE_PROPERTIES_FILE);
diff --git a/src/main/java/org/codesecure/dependencycheck/utils/CliParser.java b/src/main/java/org/codesecure/dependencycheck/utils/CliParser.java
index 9175f9091..6eedcb4be 100644
--- a/src/main/java/org/codesecure/dependencycheck/utils/CliParser.java
+++ b/src/main/java/org/codesecure/dependencycheck/utils/CliParser.java
@@ -93,17 +93,20 @@ public final class CliParser {
             validatePathExists(getScanFiles());
             if (!line.hasOption(ArgumentName.OUT)) {
                 //TODO - need a new exception type here, this isn't really a parseexception.
-                throw new ParseException("Scan cannot be run without specifying a directory to write the reports to via the 'out' argument.");
+                throw new ParseException("Scan cannot be run without specifying a directory "
+                        + "to write the reports to via the 'out' argument.");
             } else {
                 String p = line.getOptionValue(ArgumentName.OUT, "");
                 File f = new File(p);
                 if ("".equals(p) || !(f.exists() && f.isDirectory())) {
                     //TODO - need a new exception type here, this isn't really a parseexception.
-                    throw new ParseException("A valid directory name must be specified for the 'out' argument.");
+                    throw new ParseException("A valid directory name must be specified for "
+                            + "the 'out' argument.");
                 }
             }
             if (!line.hasOption(ArgumentName.APPNAME)) {
-                throw new ParseException("Scan cannot be run without specifying an application name via the 'app' argument.");
+                throw new ParseException("Scan cannot be run without specifying an application "
+                        + "name via the 'app' argument.");
             }
         }
     }
@@ -160,15 +163,25 @@ public final class CliParser {
         Option noupdate = new Option(ArgumentName.DISABLE_AUTO_UPDATE_SHORT, ArgumentName.DISABLE_AUTO_UPDATE,
                 false, "disables the automatic updating of the CPE data.");
 
-        Option appname = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APPNAME).withDescription("the name of the application being scanned.").create(ArgumentName.APPNAME_SHORT);
+        Option appname = OptionBuilder.withArgName("name").hasArg().withLongOpt(ArgumentName.APPNAME)
+                .withDescription("the name of the application being scanned.")
+                .create(ArgumentName.APPNAME_SHORT);
 
-        Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN).withDescription("the path to scan - this option can be specified multiple times.").create(ArgumentName.SCAN_SHORT);
+        Option path = OptionBuilder.withArgName("path").hasArg().withLongOpt(ArgumentName.SCAN)
+                .withDescription("the path to scan - this option can be specified multiple times.")
+                .create(ArgumentName.SCAN_SHORT);
 
-        Option load = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.CPE).withDescription("load the CPE xml file.").create(ArgumentName.CPE_SHORT);
+        Option load = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.CPE)
+                .withDescription("load the CPE xml file.")
+                .create(ArgumentName.CPE_SHORT);
 
-        Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP).withDescription("a property file to load.").create(ArgumentName.PROP_SHORT);
+        Option props = OptionBuilder.withArgName("file").hasArg().withLongOpt(ArgumentName.PROP)
+                .withDescription("a property file to load.")
+                .create(ArgumentName.PROP_SHORT);
 
-        Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT).withDescription("the folder to write reports to.").create(ArgumentName.OUT_SHORT);
+        Option out = OptionBuilder.withArgName("folder").hasArg().withLongOpt(ArgumentName.OUT)
+                .withDescription("the folder to write reports to.")
+                .create(ArgumentName.OUT_SHORT);
 
         //TODO add the ability to load a properties file to override the defaults...
 
@@ -237,7 +250,8 @@ public final class CliParser {
                     + "using the -p <file> argument or by passing them in as system properties." + nl
                     + nl + " " + Settings.KEYS.PROXY_URL + "\t\t    the proxy URL to use when downloading resources."
                     + nl + " " + Settings.KEYS.PROXY_PORT + "\t\t    the proxy port to use when downloading resources."
-                    + nl + " " + Settings.KEYS.CONNECTION_TIMEOUT + "\t    the cconnection timeout (in milliseconds) to use" + nl + "\t\t\t    when downloading resources.";
+                    + nl + " " + Settings.KEYS.CONNECTION_TIMEOUT + "\t    the cconnection timeout (in milliseconds) to use"
+                    + nl + "\t\t\t    when downloading resources.";
         }
 
         formatter.printHelp(Settings.getString("application.name", "DependencyCheck"),
diff --git a/src/test/java/org/codesecure/dependencycheck/data/cpe/BaseIndexTestCase.java b/src/test/java/org/codesecure/dependencycheck/data/cpe/BaseIndexTestCase.java
index 2f13f5daa..96bee0fb5 100644
--- a/src/test/java/org/codesecure/dependencycheck/data/cpe/BaseIndexTestCase.java
+++ b/src/test/java/org/codesecure/dependencycheck/data/cpe/BaseIndexTestCase.java
@@ -9,6 +9,8 @@ import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URLDecoder;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 import junit.framework.TestCase;
@@ -30,8 +32,22 @@ public abstract class BaseIndexTestCase extends TestCase {
         ensureIndexExists();        
     }
     
+    protected static File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String filePath = BaseIndexTestCase.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (!exePath.isDirectory()) {
+            exePath = exePath.getParentFile();
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+    
     public static void ensureIndexExists() throws Exception {
-        String indexPath = Settings.getString(Settings.KEYS.CPE_INDEX);
+        //String indexPath = Settings.getString(Settings.KEYS.CPE_INDEX);
+        String indexPath = getDataDirectory().getCanonicalPath();
         java.io.File f = new File(indexPath);
         if (!f.exists()) {
             f.mkdirs();
diff --git a/src/test/java/org/codesecure/dependencycheck/data/nvdcve/BaseIndexTestCase.java b/src/test/java/org/codesecure/dependencycheck/data/nvdcve/BaseIndexTestCase.java
index 3efbc6aa6..1898b15d3 100644
--- a/src/test/java/org/codesecure/dependencycheck/data/nvdcve/BaseIndexTestCase.java
+++ b/src/test/java/org/codesecure/dependencycheck/data/nvdcve/BaseIndexTestCase.java
@@ -10,6 +10,8 @@ import java.io.BufferedOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.net.URLDecoder;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipInputStream;
 import junit.framework.TestCase;
@@ -31,8 +33,23 @@ public abstract class BaseIndexTestCase extends TestCase {
         ensureIndexExists();        
     }
     
+    
+    protected static File getDataDirectory() throws IOException {
+        String fileName = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String filePath = BaseIndexTestCase.class.getProtectionDomain().getCodeSource().getLocation().getPath();
+        String decodedPath = URLDecoder.decode(filePath, "UTF-8");
+        File exePath = new File(decodedPath);
+        if (!exePath.isDirectory()) {
+            exePath = exePath.getParentFile();
+        }
+        File path = new File(exePath.getCanonicalFile() + File.separator + fileName);
+        path = new File(path.getCanonicalPath());
+        return path;
+    }
+        
     public static void ensureIndexExists() throws Exception {
-        String indexPath = Settings.getString(Settings.KEYS.CVE_INDEX);
+        //String indexPath = Settings.getString(Settings.KEYS.CVE_INDEX);
+        String indexPath = getDataDirectory().getCanonicalPath();
         java.io.File f = new File(indexPath);
         if (!f.exists()) {
             f.mkdirs();
diff --git a/src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexTest.java b/src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexTest.java
index 02c2a0b4b..135c63cdb 100644
--- a/src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexTest.java
+++ b/src/test/java/org/codesecure/dependencycheck/data/nvdcve/IndexTest.java
@@ -45,6 +45,8 @@ public class IndexTest extends BaseIndexTestCase {
         Index instance = new Index();
         String exp = File.separatorChar + "target" + File.separatorChar + "data" + File.separatorChar + "cve";
         Directory result = instance.getDirectory();
-        assertTrue(result.toString().contains(exp));
+        
+        assertTrue("Recieved '" + result.toString() + "' and excpected '" + exp + "'.",
+                result.toString().contains(exp));
     }
 }
diff --git a/src/test/java/org/codesecure/dependencycheck/utils/SettingsTest.java b/src/test/java/org/codesecure/dependencycheck/utils/SettingsTest.java
index 4edcd7032..8f2e5a6fa 100644
--- a/src/test/java/org/codesecure/dependencycheck/utils/SettingsTest.java
+++ b/src/test/java/org/codesecure/dependencycheck/utils/SettingsTest.java
@@ -38,7 +38,7 @@ public class SettingsTest extends TestCase {
     public void testGetString() {
         System.out.println("getString");
         String key = Settings.KEYS.CPE_INDEX;
-        String expResult = "target/data/cpe";
+        String expResult = "../data/cpe";
         String result = Settings.getString(key);
         assertTrue(result.endsWith(expResult));
     }