diff --git a/apps/niftest/find_bad_nifs.sh b/apps/niftest/find_bad_nifs.sh
deleted file mode 100755
index 4b599f442..000000000
--- a/apps/niftest/find_bad_nifs.sh
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/bin/bash
-#Script to test all nif files (both loose, and in BSA archives) in data files directory
-
-#The user input as an absolute path
-DATAFILESDIR="`readlink -m "$1"`"
-#Program used to test
-TEST_PROG="`pwd`/niftest"
-
-#Make sure our files don't bother anyone
-NIFTEST_TMP_DIR="/tmp/niftest_$RANDOM/"
-mkdir "$NIFTEST_TMP_DIR"
-cd "$NIFTEST_TMP_DIR"
-
-find "$DATAFILESDIR" -iname *bsa > nifs.txt
-find "$DATAFILESDIR" -iname *nif >> nifs.txt
-
-sed -e 's/.*/\"&\"/' nifs.txt > quoted_nifs.txt
-
-xargs --arg-file=quoted_nifs.txt "$TEST_PROG" 2>&1 | tee nif_out.txt
-# xargs --arg-file=quoted_nifs.txt "$TEST_PROG" 2> nif_out.txt >/dev/null
-
-echo "List of bad NIF Files:"
-cat nif_out.txt|grep File:|cut -d ' ' -f 2-
-
-rm nifs.txt
-rm quoted_nifs.txt
-rm nif_out.txt
-rmdir "$NIFTEST_TMP_DIR"
diff --git a/apps/niftest/niftest.cpp b/apps/niftest/niftest.cpp
index 20c8597f3..72393db40 100644
--- a/apps/niftest/niftest.cpp
+++ b/apps/niftest/niftest.cpp
@@ -2,12 +2,20 @@
 
 #include <iostream>
 #include <fstream>
+#include <cstdlib>
 
 #include <components/nif/niffile.hpp>
 #include <components/files/constrainedfilestream.hpp>
 #include <components/vfs/manager.hpp>
 #include <components/vfs/bsaarchive.hpp>
+#include <components/vfs/filesystemarchive.hpp>
 
+#include <boost/program_options.hpp>
+#include <boost/filesystem.hpp>
+
+// Create local aliases for brevity
+namespace bpo = boost::program_options;
+namespace bfs = boost::filesystem;
 
 ///See if the file has the named extension
 bool hasExtension(std::string filename, std::string  extensionToFind)
@@ -35,32 +43,97 @@ bool isBSA(std::string filename)
     return hasExtension(filename,"bsa");
 }
 
-///Check all the nif files in the given BSA archive
-void readBSA(std::string filename)
+/// Check all the nif files in a given VFS::Archive
+/// \note Takes ownership!
+/// \note Can not read a bsa file inside of a bsa file.
+void readVFS(VFS::Archive* anArchive,std::string archivePath = "")
 {
-    VFS::Manager myManager(false);
-    myManager.addArchive(new VFS::BsaArchive(filename));
+    VFS::Manager myManager(true);
+    myManager.addArchive(anArchive);
     myManager.buildIndex();
 
     std::map<std::string, VFS::File*> files=myManager.getIndex();
     for(std::map<std::string, VFS::File*>::const_iterator it=files.begin(); it!=files.end(); ++it)
     {
-      std::string name = it->first;
-      if(isNIF(name))
-      {
-//           std::cout << "Decoding: " << name << std::endl;
-          Nif::NIFFile temp_nif(myManager.get(name),name);
-      }
+        std::string name = it->first;
+
+        try{
+            if(isNIF(name))
+            {
+            //           std::cout << "Decoding: " << name << std::endl;
+                Nif::NIFFile temp_nif(myManager.get(name),archivePath+name);
+            }
+            else if(isBSA(name))
+            {
+                if(!archivePath.empty() && !isBSA(archivePath))
+                {
+//                     std::cout << "Reading BSA File: " << name << std::endl;
+                    readVFS(new VFS::BsaArchive(archivePath+name),archivePath+name+"/");
+//                     std::cout << "Done with BSA File: " << name << std::endl;
+                }
+            }
+        }
+        catch (std::exception& e)
+        {
+            std::cerr << "ERROR, an exception has occurred:  " << e.what() << std::endl;
+        }
     }
 }
 
+std::vector<std::string> parseOptions (int argc, char** argv)
+{
+    bpo::options_description desc("Ensure that OpenMW can use the provided NIF and BSA files\n\n"
+        "Usages:\n"
+        "  niftool <nif files, BSA files, or directories>\n"
+        "      Scan the file or directories for nif errors.\n\n"
+        "Allowed options");
+    desc.add_options()
+        ("help,h", "print help message.")
+        ("input-file", bpo::value< std::vector<std::string> >(), "input file")
+        ;
+
+    //Default option if none provided
+    bpo::positional_options_description p;
+    p.add("input-file", -1);
+
+    bpo::variables_map variables;
+    try
+    {
+        bpo::parsed_options valid_opts = bpo::command_line_parser(argc, argv).
+            options(desc).positional(p).run();
+        bpo::store(valid_opts, variables);
+    }
+    catch(std::exception &e)
+    {
+        std::cout << "ERROR parsing arguments: " << e.what() << "\n\n"
+            << desc << std::endl;
+        exit(1);
+    }
+
+    bpo::notify(variables);
+    if (variables.count ("help"))
+    {
+        std::cout << desc << std::endl;
+        exit(1);
+    }
+    if (variables.count("input-file"))
+    {
+        return variables["input-file"].as< std::vector<std::string> >();
+    }
+
+    std::cout << "No input files or directories specified!" << std::endl;
+    std::cout << desc << std::endl;
+    exit(1);
+}
+
 int main(int argc, char **argv)
 {
+    std::vector<std::string> files = parseOptions (argc, argv);
 
-    std::cout << "Reading Files" << std::endl;
-     for(int i = 1; i<argc;i++)
-     {
-         std::string name = argv[i];
+//     std::cout << "Reading Files" << std::endl;
+    for(std::vector<std::string>::const_iterator it=files.begin(); it!=files.end(); ++it)
+    {
+         std::string name = *it;
 
         try{
             if(isNIF(name))
@@ -70,12 +143,17 @@ int main(int argc, char **argv)
              }
              else if(isBSA(name))
              {
-                std::cout << "Reading BSA File: " << name << std::endl;
-                readBSA(name);
+//                 std::cout << "Reading BSA File: " << name << std::endl;
+                readVFS(new VFS::BsaArchive(name));
+             }
+             else if(bfs::is_directory(bfs::path(name)))
+             {
+//                 std::cout << "Reading All Files in: " << name << std::endl;
+                readVFS(new VFS::FileSystemArchive(name),name);
              }
              else
              {
-                 std::cerr << "ERROR:  \"" << name << "\" is not a nif or bsa file!" << std::endl;
+                 std::cerr << "ERROR:  \"" << name << "\" is not a nif file, bsa file, or directory!" << std::endl;
              }
         }
         catch (std::exception& e)