diff -u -r1.41 -r1.42
--- JobControlManager.java	27 May 2010 13:01:29 -0000	1.41
+++ JobControlManager.java	3 Jun 2010 03:04:35 -0000	1.42
@@ -364,7 +364,7 @@

 		List<Element> files = root.getChild("inputFiles").getChildren("file");
 		for (Element file : files)
 		{

-			String fileLoc = file.getText();

+			String fileLoc = file.getText().trim();

 			File nextFile = new File(fileLoc);
 			inputFiles.add(nextFile);			
 		}

@@ -468,7 +468,7 @@

 		    List<Element> fsFiles = fileSet.getChildren("file"); 
 		    for (Element file : fsFiles)
 		    {

-		        String filePath = basedir + File.separator + file.getText();

+		        String filePath = basedir + File.separator + file.getText().trim();

 		        inputFiles.add(new File(filePath));
 		    }
 		}

@@ -505,18 +505,6 @@

 		    }
 		}
 		

-		// Check that there are no line breaks and no trailing white spaces in file names
-		for (File file : inputFiles) {
-			String filePath = file.getAbsolutePath();
-			if (filePath.contains(System.getProperty("line.separator")) || filePath.contains(" ")) {
-				filePath = filePath.replace(System.getProperty("line.separator"), "");
-				filePath = filePath.replaceAll("\\s+$", "");
-				inputFiles.remove(file);
-				File newFile = new File(filePath);
-				inputFiles.add(newFile);
-			}
-		}
-		

 		// Check that all files exist.
 		for (File file : inputFiles)
         {