diff --git a/src/it/replace-file-content/pom.xml b/src/it/replace-file-content/pom.xml
index ed1ccd6..a8b1fad 100644
--- a/src/it/replace-file-content/pom.xml
+++ b/src/it/replace-file-content/pom.xml
@@ -84,9 +84,9 @@
 						<configuration>
 							<filesets>
 								<fileset>
-									<directory>${basedir}</directory>
+									<directory>${basedir}/folder1</directory>
 									<includes>
-										<include>folder1/file12.txt</include>
+										<include>file12.txt</include>
 									</includes>
 									<outputDirectory>${project.build.directory}/replace-linestart</outputDirectory>
 								</fileset>
@@ -139,7 +139,7 @@
 									<type>md5</type>
 								</requireFileChecksum>
 								<requireFileChecksum>
-									<file>${project.build.directory}/replace-linestart/folder1/file12.txt</file>
+									<file>${project.build.directory}/replace-linestart/file12.txt</file>
 									<checksum>fb1f2b040970526fc99b1339f22465f1</checksum>
 									<type>md5</type>
 								</requireFileChecksum>
diff --git a/src/main/java/com/inteligr8/maven/regex/MatchFileContentMojo.java b/src/main/java/com/inteligr8/maven/regex/MatchFileContentMojo.java
index e4864ba..69bffa6 100644
--- a/src/main/java/com/inteligr8/maven/regex/MatchFileContentMojo.java
+++ b/src/main/java/com/inteligr8/maven/regex/MatchFileContentMojo.java
@@ -14,6 +14,7 @@
  */
 package com.inteligr8.maven.regex;
 
+import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -57,9 +58,11 @@ public class MatchFileContentMojo extends AbstractMatchMojo {
 		
 		try {
 	    	for (FileSet fileSet : this.filesets) {
+	    		Path baseInputPath = this.resolveDirectory(basepath, fileSet.getDirectory(), "fileset input");
+	    		
 	    		String[] filePathsAndNames = fsman.getIncludedFiles(fileSet);
 	    		for (String filePathAndName : filePathsAndNames) {
-	    			Path file = basepath.resolve(filePathAndName);
+	    			Path file = baseInputPath.resolve(filePathAndName);
 	    			if (!Files.isDirectory(file))
 	    				if (this.matches(file, this.chunkSize))
 	    					return true;
@@ -72,6 +75,20 @@ public class MatchFileContentMojo extends AbstractMatchMojo {
     	return this.negate;
     }
     
+    private Path resolveDirectory(Path basepath, String directory, String errorName) throws IOException, MojoExecutionException {
+		Path path = new File(directory).toPath();
+		if (!path.isAbsolute())
+			path = basepath.resolve(path);
+		
+		if (!Files.exists(path))
+			throw new MojoExecutionException("A " + errorName + " directory does not exist: " + directory);
+		
+		if (!Files.isDirectory(path))
+			throw new MojoExecutionException("A " + errorName + " does reference a directory: " + directory);
+		
+		return path;
+    }
+    
     @Override
     protected void normalizeParameters() throws MojoFailureException {
     	super.normalizeParameters();
diff --git a/src/main/java/com/inteligr8/maven/regex/ReplaceFileContentMojo.java b/src/main/java/com/inteligr8/maven/regex/ReplaceFileContentMojo.java
index 99a00e1..5ff1f2b 100644
--- a/src/main/java/com/inteligr8/maven/regex/ReplaceFileContentMojo.java
+++ b/src/main/java/com/inteligr8/maven/regex/ReplaceFileContentMojo.java
@@ -52,16 +52,12 @@ public class ReplaceFileContentMojo extends AbstractReplaceMojo {
 		
 		try {
 	    	for (FileSet fileSet : this.filesets) {
-	    		String outputDir = fileSet.getOutputDirectory();
-	    		Path baseOutputPath = new File(outputDir).toPath();
-	    		if (!Files.exists(baseOutputPath))
-	    			Files.createDirectories(baseOutputPath);
-	    		if (!Files.isDirectory(baseOutputPath))
-	    			throw new MojoExecutionException("A fileset output directory does not reference a directory: " + outputDir);
+	    		Path baseInputPath = this.resolveDirectory(basepath, fileSet.getDirectory(), false, "fileset input");
+	    		Path baseOutputPath = this.resolveDirectory(basepath, fileSet.getOutputDirectory(), true, "fileset output");
 	    		
 	    		String[] filePathsAndNames = fsman.getIncludedFiles(fileSet);
 	    		for (String filePathAndName : filePathsAndNames) {
-	    			Path file = basepath.resolve(filePathAndName);
+	    			Path file = baseInputPath.resolve(filePathAndName);
 	    			Path tofile = baseOutputPath.resolve(filePathAndName);
 	    			if (!Files.exists(tofile.getParent()))
 	    				Files.createDirectories(tofile.getParent());
@@ -77,6 +73,25 @@ public class ReplaceFileContentMojo extends AbstractReplaceMojo {
     	return didReplace;
     }
     
+    private Path resolveDirectory(Path basepath, String directory, boolean createIfMissing, String errorName) throws IOException, MojoExecutionException {
+		Path path = new File(directory).toPath();
+		if (!path.isAbsolute())
+			path = basepath.resolve(path);
+		
+		if (!Files.exists(path)) {
+			if (createIfMissing) {
+    			Files.createDirectories(path);
+			} else {
+				throw new MojoExecutionException("A " + errorName + " directory does not exist: " + directory);
+			}
+		}
+		
+		if (!Files.isDirectory(path))
+			throw new MojoExecutionException("A " + errorName + " does reference a directory: " + directory);
+		
+		return path;
+    }
+    
     @Override
     protected void normalizeParameters() throws MojoFailureException {
     	super.normalizeParameters();
diff --git a/src/test/java/com/inteligr8/maven/regex/FileSetUnitTest.java b/src/test/java/com/inteligr8/maven/regex/FileSetUnitTest.java
new file mode 100644
index 0000000..5e1fffb
--- /dev/null
+++ b/src/test/java/com/inteligr8/maven/regex/FileSetUnitTest.java
@@ -0,0 +1,29 @@
+package com.inteligr8.maven.regex;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import org.apache.maven.shared.model.fileset.FileSet;
+import org.apache.maven.shared.model.fileset.util.FileSetManager;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class FileSetUnitTest {
+	
+	@Test
+	public void srcMainJava() {
+		FileSet fileset = new FileSet();
+		fileset.setDirectory("src/main/java");
+		fileset.setIncludes(Arrays.asList("**/*.java"));
+		
+		String fs = File.separator;
+		FileSetManager fsman = new FileSetManager();
+		Set<String> files = new HashSet<>(Arrays.asList(fsman.getIncludedFiles(fileset)));
+		Assert.assertTrue(files.size() > 15);
+		System.err.println(files);
+		Assert.assertTrue(files.contains("com"+fs+"inteligr8"+fs+"maven"+fs+"regex"+fs+"AbstractFileMojo.java"));
+	}
+
+}