diff --git a/pom.xml b/pom.xml
index 7920727..811c854 100644
--- a/pom.xml
+++ b/pom.xml
@@ -86,7 +86,7 @@
                                 <transformer
                                         implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
                                     <manifestEntries>
-                                        <Main-Class>net.knarcraft.ffmpegconverter.Main</Main-Class>
+                                        <Main-Class>net.knarcraft.ffmpegconverter.FFMpegConvert</Main-Class>
                                     </manifestEntries>
                                 </transformer>
                             </transformers>
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/Main.java b/src/main/java/net/knarcraft/ffmpegconverter/FFMpegConvert.java
similarity index 89%
rename from src/main/java/net/knarcraft/ffmpegconverter/Main.java
rename to src/main/java/net/knarcraft/ffmpegconverter/FFMpegConvert.java
index 9078f65..422775e 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/Main.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/FFMpegConvert.java
@@ -1,5 +1,6 @@
 package net.knarcraft.ffmpegconverter;
 
+import net.knarcraft.ffmpegconverter.config.ConfigHandler;
 import net.knarcraft.ffmpegconverter.converter.AnimeConverter;
 import net.knarcraft.ffmpegconverter.converter.AudioConverter;
 import net.knarcraft.ffmpegconverter.converter.Converter;
@@ -15,11 +16,13 @@ import net.knarcraft.ffmpegconverter.property.MinimalSubtitlePreference;
 import net.knarcraft.ffmpegconverter.utility.FileUtil;
 import net.knarcraft.ffmpegconverter.utility.ListUtil;
 import net.knarcraft.ffmpegconverter.utility.OutputUtil;
+import org.apache.commons.configuration2.Configuration;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Scanner;
 
@@ -28,15 +31,23 @@ import static net.knarcraft.ffmpegconverter.utility.Parser.tokenize;
 /**
  * The main class for starting the software
  */
-class Main {
+public class FFMpegConvert {
 
     private static final String FFPROBE_PATH = "ffprobe"; //Can be just ffprobe if it's in the path
     private static final String FFMPEG_PATH = "ffmpeg"; //Can be just ffmpeg if it's in the path
     private static final Scanner READER = new Scanner(System.in, StandardCharsets.UTF_8);
     private static Converter converter = null;
+    private static final ConfigHandler configHandler = new ConfigHandler();
+    private static boolean debug = false;
 
-    public static void main(String[] args) throws IOException {
+    public static void main(@NotNull String[] arguments) throws IOException {
+        Configuration configuration = configHandler.load();
+        if (configuration.containsKey("debug")) {
+            debug = configuration.getBoolean("debug");
+        }
+        OutputUtil.setDebug(debug);
         converter = loadConverter();
+
         if (converter == null) {
             System.exit(1);
             return;
@@ -62,9 +73,29 @@ class Main {
         OutputUtil.close();
     }
 
+    /**
+     * Gets the configuration handler
+     *
+     * @return <p>The configuration handler</p>
+     */
+    @NotNull
+    public static ConfigHandler getConfigHandler() {
+        return configHandler;
+    }
+
+    /**
+     * Gets whether debug mode is enabled
+     *
+     * @return <p>True if debug mode is enabled</p>
+     */
+    public static boolean isDebugEnabled() {
+        return debug;
+    }
+
     /**
      * Asks the user which converter they want, and assigns a converter instance to the converter variable
      */
+    @Nullable
     private static Converter loadConverter() {
         int choice = getChoice("""
                 Which converter do you want do use?
@@ -101,7 +132,7 @@ class Main {
      * @param recursionSteps <p>The depth to recurse if a folder is given.</p>
      * @throws IOException <p>If conversion or writing fails.</p>
      */
-    private static void convertAllFiles(File fileOrFolder, int recursionSteps) throws IOException {
+    private static void convertAllFiles(@NotNull File fileOrFolder, int recursionSteps) throws IOException {
         if (fileOrFolder.isDirectory()) {
             File[] files = FileUtil.listFilesRecursive(fileOrFolder, converter.getValidFormats(), recursionSteps);
             if (files != null && files.length > 0) {
@@ -113,7 +144,7 @@ class Main {
             }
         } else if (fileOrFolder.exists()) {
             String path = fileOrFolder.getPath();
-            if (Arrays.stream(converter.getValidFormats()).anyMatch((format) -> format.equalsIgnoreCase(
+            if (converter.getValidFormats().stream().anyMatch((format) -> format.equalsIgnoreCase(
                     path.substring(path.lastIndexOf('.') + 1)))) {
                 converter.convert(fileOrFolder);
             } else {
@@ -130,6 +161,7 @@ class Main {
      *
      * @return <p>The initialized downscale converter</p>
      */
+    @Nullable
     private static Converter generateDownScaleConverter() {
         OutputUtil.println("(New width e.x. 1920) (New height e.x. 1080)\nYour input: ");
         List<String> input = readInput(3);
@@ -151,6 +183,7 @@ class Main {
      *
      * @return <p>The initialized transcoder</p>
      */
+    @Nullable
     private static Converter generateMKVToMP4Transcoder() {
         OutputUtil.println("[Audio stream index 0-n] [Subtitle stream index 0-n] [Video stream index 0-n]\nYour input: ");
         List<String> input = readInput(3);
@@ -180,6 +213,7 @@ class Main {
      *
      * @return <p>The initialized anime converter</p>
      */
+    @Nullable
     private static Converter generateAnimeConverter() {
         OutputUtil.println("[Audio languages jpn,eng,ger,fre] [Subtitle languages eng,ger,fre] [Minimal subtitle " +
                 "preference REQUIRE/PREFER/NO_PREFERENCE/AVOID/REJECT] [Forced audio index 0-n] " +
@@ -224,6 +258,7 @@ class Main {
      *
      * @return <p>The initialized anime converter</p>
      */
+    @Nullable
     private static Converter generateWebAnimeConverter() {
         OutputUtil.println("[Audio languages jpn,eng,ger,fre] [Subtitle languages eng,ger,fre] [Convert to stereo if " +
                 "necessary true/false] [Prevent signs&songs subtitles true/false] [Forced audio index 0-n] " +
@@ -274,6 +309,7 @@ class Main {
      * @param max <p>The number of tokens expected.</p>
      * @return <p>A list of tokens.</p>
      */
+    @NotNull
     private static List<String> readInput(int max) {
         List<String> tokens = tokenize(READER.nextLine());
         if (max < tokens.size()) {
@@ -289,7 +325,8 @@ class Main {
      * @param prompt <p>The prompt shown to the user.</p>
      * @return <p>The non-empty choice given by the user.</p>
      */
-    private static String getChoice(String prompt) {
+    @NotNull
+    private static String getChoice(@NotNull String prompt) {
         OutputUtil.println(prompt);
         String choice = "";
         while (choice.isEmpty()) {
@@ -307,7 +344,7 @@ class Main {
      * @param max    The maximum allowed value
      * @return The value given by the user
      */
-    private static int getChoice(String prompt, int min, int max) {
+    private static int getChoice(@NotNull String prompt, int min, int max) {
         OutputUtil.println(prompt);
         int choice = Integer.MIN_VALUE;
         do {
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/config/ConfigHandler.java b/src/main/java/net/knarcraft/ffmpegconverter/config/ConfigHandler.java
new file mode 100644
index 0000000..0f23de8
--- /dev/null
+++ b/src/main/java/net/knarcraft/ffmpegconverter/config/ConfigHandler.java
@@ -0,0 +1,92 @@
+package net.knarcraft.ffmpegconverter.config;
+
+import net.knarcraft.ffmpegconverter.utility.FileHelper;
+import net.knarcraft.ffmpegconverter.utility.OutputUtil;
+import org.apache.commons.configuration2.Configuration;
+import org.apache.commons.configuration2.PropertiesConfiguration;
+import org.apache.commons.configuration2.builder.FileBasedConfigurationBuilder;
+import org.apache.commons.configuration2.builder.fluent.Configurations;
+import org.apache.commons.configuration2.ex.ConfigurationException;
+import org.jetbrains.annotations.NotNull;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.util.Map;
+
+/**
+ * A handler for dealing with configurations
+ */
+public class ConfigHandler {
+
+    private final File configFolder = new File("conf").getAbsoluteFile();
+    private final Configurations configurations = new Configurations();
+    private final File settingsFile = new File(configFolder, "config.properties");
+    private FileBasedConfigurationBuilder<PropertiesConfiguration> builder = configurations.propertiesBuilder(settingsFile);
+
+    /**
+     * Gets a writable configuration used for changing settings
+     *
+     * @return <p>A writable properties configuration</p>
+     */
+    @NotNull
+    public PropertiesConfiguration getWritableConfiguration() {
+        try {
+            return builder.getConfiguration();
+        } catch (ConfigurationException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    /**
+     * Writes the writable configuration to disk
+     */
+    public void writeConfiguration() {
+        OutputUtil.printDebug("Preparing to save config");
+        if (!configFolder.exists() && !configFolder.mkdir()) {
+            throw new RuntimeException("Unable to create config folder. Make sure to run this .jar file from a " +
+                    "writable directory!");
+        }
+        try {
+            if (!settingsFile.exists() && !settingsFile.createNewFile()) {
+                OutputUtil.println("Failed to create configuration file.");
+            }
+        } catch (IOException e) {
+            OutputUtil.println("Failed to create configuration file.");
+        }
+        try {
+            builder.save();
+        } catch (ConfigurationException e) {
+            throw new RuntimeException(e);
+        }
+        OutputUtil.printDebug("Saved available hardware encoder handler");
+    }
+
+    /**
+     * Loads the saved configuration file
+     *
+     * @return <p>The loaded configuration</p>
+     */
+    @NotNull
+    public Configuration load() throws IOException {
+        Configuration configuration;
+        if (!settingsFile.exists()) {
+            configuration = new PropertiesConfiguration();
+            BufferedReader reader = FileHelper.getBufferedReaderForInternalFile("/conf/config.properties");
+            Map<String, String> entries = FileHelper.readKeyValuePairs(reader, "=");
+            for (Map.Entry<String, String> entry : entries.entrySet()) {
+                configuration.setProperty(entry.getKey(), entry.getValue());
+            }
+        } else {
+            try {
+                configuration = configurations.properties(settingsFile);
+            } catch (ConfigurationException e) {
+                throw new RuntimeException(e);
+            }
+        }
+        // Reload contents in the builder
+        builder = configurations.propertiesBuilder(settingsFile);
+        return configuration;
+    }
+
+}
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/AbstractConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/AbstractConverter.java
index 2f3c0c6..b987af0 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/AbstractConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/AbstractConverter.java
@@ -1,12 +1,13 @@
 package net.knarcraft.ffmpegconverter.converter;
 
+import net.knarcraft.ffmpegconverter.FFMpegConvert;
 import net.knarcraft.ffmpegconverter.container.FFMpegCommand;
 import net.knarcraft.ffmpegconverter.container.StreamProbeResult;
 import net.knarcraft.ffmpegconverter.handler.AvailableHardwareEncoderHandler;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
+import net.knarcraft.ffmpegconverter.utility.FileHelper;
 import net.knarcraft.ffmpegconverter.utility.FileUtil;
 import net.knarcraft.ffmpegconverter.utility.OutputUtil;
-import org.apache.commons.configuration2.ex.ConfigurationException;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
@@ -20,12 +21,13 @@ import java.util.List;
  */
 public abstract class AbstractConverter implements Converter {
 
-    final boolean debug = false;
+    final boolean debug = FFMpegConvert.isDebugEnabled();
     private final String newExtension;
     protected String ffprobePath;
     protected String ffmpegPath;
-    protected String[] audioFormats;
-    protected String[] videoFormats;
+    protected List<String> audioFormats;
+    protected List<String> videoFormats;
+    protected List<String> subtitleFormats;
     protected AvailableHardwareEncoderHandler encoderHandler = null;
 
 
@@ -34,31 +36,31 @@ public abstract class AbstractConverter implements Converter {
      */
     AbstractConverter(@Nullable String newExtension) {
         this.newExtension = newExtension;
-        OutputUtil.setDebug(this.debug);
         try {
-            audioFormats = FileUtil.readFileLines("audio_formats.txt");
-            videoFormats = FileUtil.readFileLines("video_formats.txt");
+            this.audioFormats = FileHelper.readLines(FileHelper.getBufferedReaderForInternalFile("/audio_formats.txt"));
+            this.videoFormats = FileHelper.readLines(FileHelper.getBufferedReaderForInternalFile("/video_formats.txt"));
+            this.subtitleFormats = FileHelper.readLines(FileHelper.getBufferedReaderForInternalFile("/subtitle_formats.txt"));
         } catch (IOException e) {
-            System.out.println("Unable to read audio and/or video formats from internal files.");
+            OutputUtil.println("Unable to read audio and/or video formats from internal files.");
             System.exit(1);
         }
     }
 
     @Override
     public void convert(@NotNull File file) throws IOException {
-        StreamProbeResult probeResult = FFMpegHelper.probeFile(ffprobePath, file);
+        StreamProbeResult probeResult = FFMpegHelper.probeFile(this.ffprobePath, file, this.subtitleFormats);
         if (probeResult.parsedStreams().isEmpty()) {
             throw new IllegalArgumentException("The file has no valid streams. Please make sure the file exists and" +
                     " is not corrupt.");
         }
 
-        String outExtension = newExtension != null ? newExtension : FileUtil.getExtension(file.getName());
+        String outExtension = this.newExtension != null ? this.newExtension : FileUtil.getExtension(file.getName());
         String newPath = FileUtil.getNonCollidingPath(file.getParentFile(), file, outExtension);
         OutputUtil.println();
         OutputUtil.println("Preparing to start process...");
         OutputUtil.println("Converting " + file);
 
-        FFMpegCommand ffMpegCommand = generateConversionCommand(ffmpegPath, probeResult, newPath);
+        FFMpegCommand ffMpegCommand = generateConversionCommand(this.ffmpegPath, probeResult, newPath);
         // If the command is null, that means the file does not need conversion
         if (ffMpegCommand == null) {
             return;
@@ -73,11 +75,7 @@ public abstract class AbstractConverter implements Converter {
         ProcessBuilder processBuilder = new ProcessBuilder(command);
         int exitCode = FFMpegHelper.runProcess(processBuilder, file.getParentFile(), "\n", true).exitCode();
         if (exitCode != 0) {
-            try {
-                handleError(ffMpegCommand, file, newPath);
-            } catch (ConfigurationException e) {
-                throw new RuntimeException(e);
-            }
+            handleError(ffMpegCommand, file, newPath);
         }
     }
 
@@ -87,11 +85,10 @@ public abstract class AbstractConverter implements Converter {
      * @param ffMpegCommand <p>The failed ffmpeg command</p>
      * @param file          <p>The file that was to be converted</p>
      * @param newPath       <p>The path of the output file</p>
-     * @throws IOException            <p>If unable to produce output</p>
-     * @throws ConfigurationException <p>If unable </p>
+     * @throws IOException <p>If unable to produce output</p>
      */
     private void handleError(@NotNull FFMpegCommand ffMpegCommand, @NotNull File file,
-                             @NotNull String newPath) throws IOException, ConfigurationException {
+                             @NotNull String newPath) throws IOException {
         File outputFile = new File(newPath);
         if (outputFile.exists() && !outputFile.delete()) {
             OutputUtil.println("Failed to remove failed output file. Please remove it manually");
@@ -118,23 +115,24 @@ public abstract class AbstractConverter implements Converter {
      *
      * @return <p>Available hardware encoding methods</p>
      */
+    @NotNull
     protected List<String> getAvailableHardwareEncodingMethods() {
-        try {
-            if (encoderHandler == null) {
-                encoderHandler = AvailableHardwareEncoderHandler.load();
-                if (encoderHandler.availableHardwareEncodings().isEmpty()) {
-                    List<String> hardwareEncoding = new ArrayList<>(FFMpegHelper.getHWAcceleration(ffmpegPath));
-                    hardwareEncoding.remove(0);
-                    encoderHandler = new AvailableHardwareEncoderHandler(hardwareEncoding);
-                    encoderHandler.save();
+        if (encoderHandler == null) {
+            encoderHandler = AvailableHardwareEncoderHandler.load();
+            if (encoderHandler.availableHardwareEncodings().isEmpty()) {
+                List<String> hardwareEncoding;
+                try {
+                    hardwareEncoding = new ArrayList<>(FFMpegHelper.getHWAcceleration(ffmpegPath));
+                } catch (IOException e) {
+                    throw new RuntimeException(e);
                 }
+                hardwareEncoding.remove(0);
+                encoderHandler = new AvailableHardwareEncoderHandler(hardwareEncoding);
+                encoderHandler.save();
             }
-
-            return encoderHandler.availableHardwareEncodings();
-        } catch (ConfigurationException | IOException exception) {
-            OutputUtil.println("Unable to get available hardware encoders: " + exception.getMessage());
-            return new ArrayList<>();
         }
+
+        return encoderHandler.availableHardwareEncodings();
     }
 
 }
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/AnimeConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/AnimeConverter.java
index 52c70db..872cb85 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/AnimeConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/AnimeConverter.java
@@ -26,6 +26,7 @@ import net.knarcraft.ffmpegconverter.streams.AudioStream;
 import net.knarcraft.ffmpegconverter.streams.SubtitleStream;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -69,6 +70,7 @@ public class AnimeConverter extends AbstractConverter {
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable,
                                                    @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
@@ -118,7 +120,8 @@ public class AnimeConverter extends AbstractConverter {
     }
 
     @Override
-    public @NotNull String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return this.videoFormats;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/AudioConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/AudioConverter.java
index 7e10a69..e12d7f1 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/AudioConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/AudioConverter.java
@@ -9,6 +9,7 @@ import net.knarcraft.ffmpegconverter.converter.module.mapping.NthAudioStreamModu
 import net.knarcraft.ffmpegconverter.converter.module.output.SetOutputFileModule;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -25,13 +26,14 @@ public class AudioConverter extends AbstractConverter {
      * @param ffmpegPath   <p>Path/command to ffmpeg.</p>
      * @param newExtension <p>The extension of the new file.</p>
      */
-    public AudioConverter(String ffprobePath, String ffmpegPath, String newExtension) {
+    public AudioConverter(@NotNull String ffprobePath, @NotNull String ffmpegPath, @NotNull String newExtension) {
         super(newExtension);
         this.ffprobePath = ffprobePath;
         this.ffmpegPath = ffmpegPath;
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
@@ -50,7 +52,8 @@ public class AudioConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return audioFormats;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/Converter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/Converter.java
index 0cb5b7f..8044ffd 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/Converter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/Converter.java
@@ -3,9 +3,11 @@ package net.knarcraft.ffmpegconverter.converter;
 import net.knarcraft.ffmpegconverter.container.FFMpegCommand;
 import net.knarcraft.ffmpegconverter.container.StreamProbeResult;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.io.File;
 import java.io.IOException;
+import java.util.List;
 
 /**
  * This interface describes a file converter
@@ -18,7 +20,7 @@ public interface Converter {
      * @return <p>A list of valid input formats</p>
      */
     @NotNull
-    String[] getValidFormats();
+    List<String> getValidFormats();
 
     /**
      * Converts the given file
@@ -36,6 +38,7 @@ public interface Converter {
      * @param outFile     <p>The output file</p>
      * @return <p>A list of commands</p>
      */
+    @Nullable
     FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                             @NotNull String outFile);
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/DownScaleConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/DownScaleConverter.java
index 9b066d6..5e79c0e 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/DownScaleConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/DownScaleConverter.java
@@ -16,6 +16,7 @@ import net.knarcraft.ffmpegconverter.streams.StreamObject;
 import net.knarcraft.ffmpegconverter.streams.VideoStream;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -36,7 +37,7 @@ public class DownScaleConverter extends AbstractConverter {
      * @param newWidth    <p>The new width of the video</p>
      * @param newHeight   <p>The new height of the video</p>
      */
-    public DownScaleConverter(String ffprobePath, String ffmpegPath, int newWidth, int newHeight) {
+    public DownScaleConverter(@NotNull String ffprobePath, @NotNull String ffmpegPath, int newWidth, int newHeight) {
         super(null);
         this.ffprobePath = ffprobePath;
         this.ffmpegPath = ffmpegPath;
@@ -45,6 +46,7 @@ public class DownScaleConverter extends AbstractConverter {
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         List<StreamObject> streams = probeResult.parsedStreams();
@@ -78,7 +80,8 @@ public class DownScaleConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return videoFormats;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/MKVToMP4Transcoder.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/MKVToMP4Transcoder.java
index 3e2cc75..6fd4d32 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/MKVToMP4Transcoder.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/MKVToMP4Transcoder.java
@@ -13,6 +13,7 @@ import net.knarcraft.ffmpegconverter.converter.module.output.CopyAllModule;
 import net.knarcraft.ffmpegconverter.converter.module.output.SetOutputFileModule;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -46,11 +47,13 @@ public class MKVToMP4Transcoder extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
-        return new String[]{"mkv"};
+    @NotNull
+    public List<String> getValidFormats() {
+        return List.of("mkv");
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH264Converter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH264Converter.java
index bba355f..82afdf4 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH264Converter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH264Converter.java
@@ -15,6 +15,7 @@ import net.knarcraft.ffmpegconverter.converter.module.output.SetOutputFileModule
 import net.knarcraft.ffmpegconverter.streams.StreamObject;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -37,11 +38,13 @@ public class MkvH264Converter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
-        return new String[]{"mkv"};
+    @NotNull
+    public List<String> getValidFormats() {
+        return List.of("mkv");
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH265ReducedConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH265ReducedConverter.java
index 0ad7d70..0cecae6 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH265ReducedConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/MkvH265ReducedConverter.java
@@ -16,6 +16,7 @@ import net.knarcraft.ffmpegconverter.streams.SubtitleStream;
 import net.knarcraft.ffmpegconverter.streams.VideoStream;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -38,11 +39,13 @@ public class MkvH265ReducedConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
-        return new String[]{"mkv"};
+    @NotNull
+    public List<String> getValidFormats() {
+        return List.of("mkv");
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/SubtitleEmbed.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/SubtitleEmbed.java
index d28f5d6..c671214 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/SubtitleEmbed.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/SubtitleEmbed.java
@@ -12,6 +12,7 @@ import net.knarcraft.ffmpegconverter.converter.module.output.MovTextModule;
 import net.knarcraft.ffmpegconverter.converter.module.output.SetOutputFileModule;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -34,11 +35,13 @@ public class SubtitleEmbed extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
-        return new String[]{"mp4"};
+    @NotNull
+    public List<String> getValidFormats() {
+        return List.of("mp4");
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/VideoConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/VideoConverter.java
index 0b2dd2a..e8cfdec 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/VideoConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/VideoConverter.java
@@ -12,6 +12,7 @@ import net.knarcraft.ffmpegconverter.converter.module.output.SetOutputFileModule
 import net.knarcraft.ffmpegconverter.streams.StreamObject;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -35,6 +36,7 @@ public class VideoConverter extends AbstractConverter {
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegGeneralFileCommand(executable, probeResult.parsedFiles());
@@ -57,7 +59,8 @@ public class VideoConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return videoFormats;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/WebAnimeConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/WebAnimeConverter.java
index 541efe2..8516e40 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/WebAnimeConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/WebAnimeConverter.java
@@ -21,6 +21,7 @@ import net.knarcraft.ffmpegconverter.streams.SubtitleStream;
 import net.knarcraft.ffmpegconverter.streams.VideoStream;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -69,6 +70,7 @@ public class WebAnimeConverter extends AbstractConverter {
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegWebVideoCommand(executable, probeResult.parsedFiles());
@@ -114,7 +116,8 @@ public class WebAnimeConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return this.videoFormats;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/converter/WebVideoConverter.java b/src/main/java/net/knarcraft/ffmpegconverter/converter/WebVideoConverter.java
index 76e1cd5..64cf077 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/converter/WebVideoConverter.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/converter/WebVideoConverter.java
@@ -14,6 +14,7 @@ import net.knarcraft.ffmpegconverter.streams.SubtitleStream;
 import net.knarcraft.ffmpegconverter.streams.VideoStream;
 import net.knarcraft.ffmpegconverter.utility.FFMpegHelper;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -39,11 +40,13 @@ public class WebVideoConverter extends AbstractConverter {
     }
 
     @Override
-    public String[] getValidFormats() {
+    @NotNull
+    public List<String> getValidFormats() {
         return videoFormats;
     }
 
     @Override
+    @Nullable
     public FFMpegCommand generateConversionCommand(@NotNull String executable, @NotNull StreamProbeResult probeResult,
                                                    @NotNull String outFile) {
         FFMpegCommand command = FFMpegHelper.getFFMpegWebVideoCommand(executable, probeResult.parsedFiles());
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/handler/AvailableHardwareEncoderHandler.java b/src/main/java/net/knarcraft/ffmpegconverter/handler/AvailableHardwareEncoderHandler.java
index 236de07..4fcdfb6 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/handler/AvailableHardwareEncoderHandler.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/handler/AvailableHardwareEncoderHandler.java
@@ -1,14 +1,12 @@
 package net.knarcraft.ffmpegconverter.handler;
 
+import net.knarcraft.ffmpegconverter.FFMpegConvert;
+import net.knarcraft.ffmpegconverter.config.ConfigHandler;
 import net.knarcraft.ffmpegconverter.utility.OutputUtil;
 import org.apache.commons.configuration2.Configuration;
 import org.apache.commons.configuration2.PropertiesConfiguration;
-import org.apache.commons.configuration2.builder.FileBasedConfigurationBuilder;
-import org.apache.commons.configuration2.builder.fluent.Configurations;
-import org.apache.commons.configuration2.ex.ConfigurationException;
 import org.jetbrains.annotations.NotNull;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
@@ -18,8 +16,7 @@ import java.util.List;
  */
 public record AvailableHardwareEncoderHandler(@NotNull List<String> availableHardwareEncodings) {
 
-    private static final File configFolder = new File("conf").getAbsoluteFile();
-    private static final Configurations configurations = new Configurations();
+    private static final ConfigHandler configHandler = FFMpegConvert.getConfigHandler();
 
     /**
      * Gets all hardware encodings
@@ -42,30 +39,12 @@ public record AvailableHardwareEncoderHandler(@NotNull List<String> availableHar
     }
 
     /**
-     * Saves settings fro this available hardware encoder handler
-     *
-     * @throws ConfigurationException <p>If the configuration file cannot be saved</p>
+     * Saves settings for this available hardware encoder handler
      */
-    public void save() throws ConfigurationException {
-        OutputUtil.printDebug("Preparing to save config");
-        if (!configFolder.exists() && !configFolder.mkdir()) {
-            throw new RuntimeException("Unable to create config folder. Make sure to run this .jar file from a " +
-                    "writable directory!");
-        }
-        File settingsFile = new File(configFolder, "config.properties");
-        try {
-            if (!settingsFile.exists() && !settingsFile.createNewFile()) {
-                OutputUtil.println("Failed to create configuration file.");
-            }
-        } catch (IOException e) {
-            OutputUtil.println("Failed to create configuration file.");
-        }
-
-        FileBasedConfigurationBuilder<PropertiesConfiguration> builder =
-                configurations.propertiesBuilder(settingsFile);
-        PropertiesConfiguration config = builder.getConfiguration();
-        config.setProperty("encoder.hardware", this.availableHardwareEncodings);
-        builder.save();
+    public void save() {
+        PropertiesConfiguration configuration = configHandler.getWritableConfiguration();
+        configuration.setProperty("encoder.hardware", this.availableHardwareEncodings);
+        configHandler.writeConfiguration();
         OutputUtil.printDebug("Saved available hardware encoder handler");
     }
 
@@ -73,14 +52,15 @@ public record AvailableHardwareEncoderHandler(@NotNull List<String> availableHar
      * Loads saved settings for an available hardware encoder handler
      *
      * @return <p>The loaded available hardware encoder handler, or a new one if no data has been saved</p>
-     * @throws ConfigurationException <p>If the configuration file cannot be loaded</p>
      */
-    public static AvailableHardwareEncoderHandler load() throws ConfigurationException {
-        File settingsFile = new File(configFolder, "config.properties");
-        if (!settingsFile.exists()) {
-            return new AvailableHardwareEncoderHandler(new ArrayList<>());
+    @NotNull
+    public static AvailableHardwareEncoderHandler load() {
+        Configuration configuration;
+        try {
+            configuration = configHandler.load();
+        } catch (IOException e) {
+            throw new RuntimeException(e);
         }
-        Configuration configuration = configurations.properties(settingsFile);
         List<String> getEncodings = configuration.getList(String.class, "encoder.hardware");
         return new AvailableHardwareEncoderHandler(getEncodings);
     }
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/parser/ConverterArgument.java b/src/main/java/net/knarcraft/ffmpegconverter/parser/ConverterArgument.java
index 2b5f793..f2db2a0 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/parser/ConverterArgument.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/parser/ConverterArgument.java
@@ -1,6 +1,7 @@
 package net.knarcraft.ffmpegconverter.parser;
 
 import net.knarcraft.ffmpegconverter.utility.ListUtil;
+import org.jetbrains.annotations.NotNull;
 
 /**
  * A class representing a command argument
@@ -20,7 +21,8 @@ public class ConverterArgument {
      * @param valueRequired <p>Whether the argument must be followed by a valid value.</p>
      * @param valueType     <p>The type of value the argument requires.</p>
      */
-    public ConverterArgument(String name, char shorthand, boolean valueRequired, ConverterArgumentValueType valueType) {
+    public ConverterArgument(@NotNull String name, char shorthand, boolean valueRequired,
+                             @NotNull ConverterArgumentValueType valueType) {
         this.name = name;
         this.shorthand = shorthand;
         this.valueRequired = valueRequired;
@@ -60,7 +62,7 @@ public class ConverterArgument {
      * @param value <p>The value to test.</p>
      * @return <p>True if the argument is valid. False otherwise.</p>
      */
-    public boolean testArgumentValue(String value) {
+    public boolean testArgumentValue(@NotNull String value) {
         if (value.isEmpty()) {
             return !valueRequired;
         }
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/streams/AbstractStream.java b/src/main/java/net/knarcraft/ffmpegconverter/streams/AbstractStream.java
index abf94f5..f6f62a9 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/streams/AbstractStream.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/streams/AbstractStream.java
@@ -36,7 +36,8 @@ public abstract class AbstractStream implements StreamObject {
     }
 
     @Override
-    public @NotNull String getCodecName() {
+    @NotNull
+    public String getCodecName() {
         return this.codecName;
     }
 
@@ -51,7 +52,8 @@ public abstract class AbstractStream implements StreamObject {
     }
 
     @Override
-    public @NotNull String getLanguage() {
+    @NotNull
+    public String getLanguage() {
         return this.language;
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/FFMpegHelper.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/FFMpegHelper.java
index 6b44fd1..426bde6 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/utility/FFMpegHelper.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/FFMpegHelper.java
@@ -27,7 +27,6 @@ import java.util.Map;
 public final class FFMpegHelper {
 
     private static final String PROBE_SPLIT_CHARACTER = "øæåÆØå";
-    private static String[] subtitleFormats = null;
 
     private FFMpegHelper() {
 
@@ -70,14 +69,16 @@ public final class FFMpegHelper {
     /**
      * Gets streams from a file
      *
-     * @param ffprobePath <p>The path/command to ffprobe.</p>
-     * @param file        <p>The file to probe.</p>
-     * @return <p>A list of StreamObjects.</p>
-     * @throws IOException <p>If the process can't be readProcess.</p>
+     * @param ffprobePath     <p>The path/command to ffprobe</p>
+     * @param file            <p>The file to probe</p>
+     * @param subtitleFormats <p>The extensions to accept for external subtitles</p>
+     * @return <p>A list of StreamObjects</p>
+     * @throws IOException <p>If the process can't be readProcess</p>
      */
     @NotNull
-    public static StreamProbeResult probeFile(@NotNull String ffprobePath, @NotNull File file) throws IOException {
-        return parseStreams(ffprobePath, probeForStreams(ffprobePath, file), file);
+    public static StreamProbeResult probeFile(@NotNull String ffprobePath, @NotNull File file,
+                                              @NotNull List<String> subtitleFormats) throws IOException {
+        return parseStreams(ffprobePath, probeForStreams(ffprobePath, file), file, subtitleFormats);
     }
 
     /**
@@ -223,7 +224,8 @@ public final class FFMpegHelper {
      * @param fileName <p>The filename to escape.</p>
      * @return <p>A filename with known special characters escaped.</p>
      */
-    public static String escapeSpecialCharactersInFileName(String fileName) {
+    @NotNull
+    public static String escapeSpecialCharactersInFileName(@NotNull String fileName) {
         return fileName.replaceAll("\\\\", "\\\\\\\\\\\\\\\\")
                 .replaceAll("'", "'\\\\\\\\\\\\\''")
                 .replaceAll("%", "\\\\\\\\\\\\%")
@@ -260,7 +262,8 @@ public final class FFMpegHelper {
      * @return <p>A list of streams.</p>
      * @throws IOException <p>If something goes wrong while probing.</p>
      */
-    private static List<String> probeForStreams(String ffprobePath, File file) throws IOException {
+    @NotNull
+    private static List<String> probeForStreams(@NotNull String ffprobePath, @NotNull File file) throws IOException {
         FFMpegCommand probeCommand = new FFMpegCommand(ffprobePath);
         probeCommand.addGlobalOption("-v", "error", "-show_streams");
         probeCommand.addInputFile(file.toString());
@@ -276,13 +279,15 @@ public final class FFMpegHelper {
     /**
      * Takes a list of all streams and parses each stream into one of three objects
      *
-     * @param streams <p>A list of all streams for the current file.</p>
-     * @param file    <p>The file currently being converted.</p>
+     * @param ffprobePath     <p>The path to the ffprobe executable</p>
+     * @param streams         <p>A list of all streams for the current file.</p>
+     * @param file            <p>The file currently being converted.</p>
+     * @param subtitleFormats <p>The extensions to accept for external subtitles</p>
      * @return <p>A list of StreamObjects.</p>
      */
     @NotNull
     private static StreamProbeResult parseStreams(@NotNull String ffprobePath, @NotNull List<String> streams,
-                                                  @NotNull File file) throws IOException {
+                                                  @NotNull File file, @NotNull List<String> subtitleFormats) throws IOException {
         List<StreamObject> parsedStreams = new ArrayList<>();
         int relativeAudioIndex = 0;
         int relativeVideoIndex = 0;
@@ -306,7 +311,7 @@ public final class FFMpegHelper {
             }
         }
         StreamProbeResult probeResult = new StreamProbeResult(List.of(file), parsedStreams);
-        getExternalSubtitles(probeResult, ffprobePath, file.getParentFile(), file.getName());
+        getExternalSubtitles(probeResult, ffprobePath, file.getParentFile(), file.getName(), subtitleFormats);
         return probeResult;
     }
 
@@ -335,17 +340,16 @@ public final class FFMpegHelper {
     /**
      * Tries to find any external subtitles adjacent to the first input file, and appends it to the given probe result
      *
-     * @param ffprobePath    <p>The path/command to ffprobe</p>
-     * @param directory      <p>The directory containing the file</p>
-     * @param convertingFile <p>The first/main file to be converted</p>
+     * @param streamProbeResult <p>The stream probe result to append to</p>
+     * @param ffprobePath       <p>The path/command to ffprobe</p>
+     * @param directory         <p>The directory containing the file</p>
+     * @param convertingFile    <p>The first/main file to be converted</p>
+     * @param subtitleFormats   <p>The extensions to accept for external subtitles</p>
      */
     private static void getExternalSubtitles(@NotNull StreamProbeResult streamProbeResult,
                                              @NotNull String ffprobePath, @NotNull File directory,
-                                             @NotNull String convertingFile) throws IOException {
+                                             @NotNull String convertingFile, @NotNull List<String> subtitleFormats) throws IOException {
         //Find all files in the same directory with external subtitle formats
-        if (subtitleFormats == null) {
-            subtitleFormats = FileUtil.readFileLines("subtitle_formats.txt");
-        }
         File[] subtitleFiles = FileUtil.listFilesRecursive(directory, subtitleFormats, 1);
         // TODO: Generalize this for external audio tracks
 
@@ -382,7 +386,8 @@ public final class FFMpegHelper {
      * @return <p>The output from the readProcess.</p>
      * @throws IOException <p>On reader failure.</p>
      */
-    private static String readProcess(BufferedReader reader, String spacer) throws IOException {
+    @NotNull
+    private static String readProcess(@NotNull BufferedReader reader, @NotNull String spacer) throws IOException {
         String line;
         StringBuilder text = new StringBuilder();
         while (reader.ready() && (line = reader.readLine()) != null && !line.isEmpty() && !line.equals("\n")) {
@@ -398,6 +403,7 @@ public final class FFMpegHelper {
      * @return <p>The available hardware acceleration methods</p>
      * @throws IOException <p>If the process fails</p>
      */
+    @NotNull
     public static List<String> getHWAcceleration(@NotNull String ffmpegPath) throws IOException {
         FFMpegCommand probeCommand = new FFMpegCommand(ffmpegPath);
         probeCommand.addGlobalOption("-v", "error", "-hwaccels");
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/FileHelper.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/FileHelper.java
new file mode 100644
index 0000000..c35c422
--- /dev/null
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/FileHelper.java
@@ -0,0 +1,178 @@
+package net.knarcraft.ffmpegconverter.utility;
+
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * A helper class for dealing with files
+ */
+@SuppressWarnings("unused")
+public final class FileHelper {
+
+    private FileHelper() {
+
+    }
+
+    /**
+     * Gets a buffered reader for an internal file
+     *
+     * @param file <p>The name of the file to get a buffered reader for (start with a '/'). The file should reside in
+     *             the resources directory.</p>
+     * @return <p>A buffered read for reading the file</p>
+     * @throws FileNotFoundException <p>If unable to get an input stream for the given file</p>
+     */
+    @NotNull
+    public static BufferedReader getBufferedReaderForInternalFile(@NotNull String file) throws FileNotFoundException {
+        InputStream inputStream = getInputStreamForInternalFile(file);
+        if (inputStream == null) {
+            throw new FileNotFoundException("Unable to read the given file");
+        }
+        return getBufferedReaderFromInputStream(inputStream);
+    }
+
+    /**
+     * Gets an input stream from a string pointing to an internal file
+     *
+     * <p>This is used for getting an input stream for reading a file contained within the compiled .jar file. The file
+     * should be in the resources directory, and the file path should start with a forward slash ("/") character.</p>
+     *
+     * @param file <p>The file to read</p>
+     * @return <p>An input stream for the file</p>
+     */
+    @Nullable
+    public static InputStream getInputStreamForInternalFile(@NotNull String file) {
+        return FileHelper.class.getResourceAsStream(file);
+    }
+
+    /**
+     * Gets a buffered reader from a string pointing to a file
+     *
+     * @param file <p>The file to read</p>
+     * @return <p>A buffered reader reading the file</p>
+     * @throws FileNotFoundException <p>If the given file does not exist</p>
+     */
+    @NotNull
+
+    public static BufferedReader getBufferedReaderFromString(@NotNull String file) throws FileNotFoundException {
+        FileInputStream fileInputStream = new FileInputStream(file);
+        return getBufferedReaderFromInputStream(fileInputStream);
+    }
+
+    /**
+     * Gets a buffered reader given an input stream
+     *
+     * @param inputStream <p>The input stream to read</p>
+     * @return <p>A buffered reader reading the input stream</p>
+     */
+    @NotNull
+    public static BufferedReader getBufferedReaderFromInputStream(@NotNull InputStream inputStream) {
+        InputStreamReader inputStreamReader = new InputStreamReader(inputStream, StandardCharsets.UTF_8);
+        return new BufferedReader(inputStreamReader);
+    }
+
+    /**
+     * Gets a buffered writer from a string pointing to a file
+     *
+     * @param file <p>The file to write to</p>
+     * @return <p>A buffered writer writing to the file</p>
+     * @throws FileNotFoundException <p>If the file does not exist</p>
+     */
+    @NotNull
+    public static BufferedWriter getBufferedWriterFromString(@NotNull String file) throws FileNotFoundException {
+        FileOutputStream fileOutputStream = new FileOutputStream(file);
+        OutputStreamWriter outputStreamWriter = new OutputStreamWriter(fileOutputStream, StandardCharsets.UTF_8);
+        return new BufferedWriter(outputStreamWriter);
+    }
+
+    /**
+     * Reads key/value pairs from a buffered reader
+     *
+     * @param bufferedReader <p>The buffered reader to read</p>
+     * @param separator      <p>The separator separating a key from a value</p>
+     * @return <p>A map containing the read pairs</p>
+     * @throws IOException <p>If unable to read from the stream</p>
+     */
+    @NotNull
+    public static Map<String, String> readKeyValuePairs(@NotNull BufferedReader bufferedReader,
+                                                        @NotNull String separator) throws IOException {
+        Map<String, String> readPairs = new HashMap<>();
+        List<String> lines = readLines(bufferedReader);
+
+        for (String line : lines) {
+            int separatorIndex = line.indexOf(separator);
+            if (separatorIndex == -1) {
+                continue;
+            }
+
+            //Read the line
+            String key = line.substring(0, separatorIndex);
+            String value = line.substring(separatorIndex + 1);
+            readPairs.put(key, value);
+        }
+
+        return readPairs;
+    }
+
+    /**
+     * Reads a list from a buffered reader
+     *
+     * @param bufferedReader <p>The buffered reader to read</p>
+     * @return <p>A list of the read strings</p>
+     * @throws IOException <p>If unable to read from the stream</p>
+     */
+    @NotNull
+    public static List<String> readLines(@NotNull BufferedReader bufferedReader) throws IOException {
+        List<String> readLines = new ArrayList<>();
+
+        String line = bufferedReader.readLine();
+        boolean firstLine = true;
+        while (line != null) {
+            //Strip UTF BOM from the first line
+            if (firstLine) {
+                line = removeUTF8BOM(line);
+                firstLine = false;
+            }
+            //Split at first separator
+            if (line.isEmpty()) {
+                line = bufferedReader.readLine();
+                continue;
+            }
+
+            readLines.add(line);
+            line = bufferedReader.readLine();
+        }
+        bufferedReader.close();
+
+        return readLines;
+    }
+
+    /**
+     * Removes the UTF-8 Byte Order Mark if present
+     *
+     * @param string <p>The string to remove the BOM from</p>
+     * @return <p>A string guaranteed without a BOM</p>
+     */
+    private static @NotNull String removeUTF8BOM(@NotNull String string) {
+        String UTF8_BOM = "\uFEFF";
+        if (string.startsWith(UTF8_BOM)) {
+            string = string.substring(1);
+        }
+        return string;
+    }
+
+}
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/FileUtil.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/FileUtil.java
index f8d1c13..556ef4d 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/utility/FileUtil.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/FileUtil.java
@@ -1,10 +1,10 @@
 package net.knarcraft.ffmpegconverter.utility;
 
-import java.io.BufferedReader;
+import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
+
 import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
+import java.util.List;
 
 /**
  * A class which helps with file handling
@@ -23,7 +23,8 @@ public final class FileUtil {
      * @param outExtension <p>The extension of the output file.</p>
      * @return <p>A file name with the new extension and without any collisions.</p>
      */
-    public static String getNonCollidingPath(File folder, File file, String outExtension) {
+    @NotNull
+    public static String getNonCollidingPath(@NotNull File folder, @NotNull File file, @NotNull String outExtension) {
         return FileUtil.getNonCollidingFilename(folder.getAbsolutePath() + File.separator +
                 FileUtil.stripExtension(file.getName()) + "." + outExtension, outExtension);
     }
@@ -35,7 +36,8 @@ public final class FileUtil {
      * @param maxRecursions <p>Maximum number of recursions</p>
      * @return A list of files
      */
-    public static File[] listFilesRecursive(File folder, String[] extensions, int maxRecursions) {
+    @Nullable
+    public static File[] listFilesRecursive(@NotNull File folder, @NotNull List<String> extensions, int maxRecursions) {
         //Return if the target depth has been reached
         if (maxRecursions == 0) {
             return null;
@@ -43,6 +45,7 @@ public final class FileUtil {
         //Get a list of all files which are folders and has one of the extensions specified
         File[] foundFiles = folder.listFiles((file) -> file.isFile() &&
                 ListUtil.listContains(extensions, (item) -> file.getName().toLowerCase().endsWith(item)));
+
         //Return if recursion is finished
         if (maxRecursions == 1) {
             return foundFiles;
@@ -68,36 +71,6 @@ public final class FileUtil {
         return foundFiles;
     }
 
-    /**
-     * Reads a file's contents to a string list
-     *
-     * <p>The file must contain the number of lines to read in the first line.</p>
-     *
-     * @param fileName <p>The file to read.</p>
-     * @return <p>A string list where each element is one line of the file.</p>
-     * @throws IOException <p>If the file cannot be read.</p>
-     */
-    public static String[] readFileLines(String fileName) throws IOException {
-        BufferedReader reader = new BufferedReader(new InputStreamReader(getResourceAsStream(fileName)));
-        int numberOfLines = Integer.parseInt(reader.readLine());
-        String[] lines = new String[numberOfLines];
-        for (int i = 0; i < lines.length; i++) {
-            lines[i] = reader.readLine();
-        }
-        return lines;
-    }
-
-    /**
-     * Gets a resource as an InputStream
-     *
-     * @param resourceName <p>The name of the resource you want to read.</p>
-     * @return <p>An input stream which can be used to access the resource.</p>
-     */
-    private static InputStream getResourceAsStream(String resourceName) {
-        ClassLoader classloader = Thread.currentThread().getContextClassLoader();
-        return classloader.getResourceAsStream(resourceName);
-    }
-
     /**
      * Adds parentheses with an integer if the output file already exists
      *
@@ -105,7 +78,8 @@ public final class FileUtil {
      * @param extension  <p>The extension of the target file.</p>
      * @return <p>A filename guaranteed not to collide with other files.</p>
      */
-    private static String getNonCollidingFilename(String targetPath, String extension) {
+    @NotNull
+    private static String getNonCollidingFilename(@NotNull String targetPath, @NotNull String extension) {
         File newFile = new File(targetPath);
         String fileName = stripExtension(targetPath).replaceAll("\\([0-9]+\\)$", "");
         int i = 1;
@@ -121,7 +95,8 @@ public final class FileUtil {
      * @param file <p>The filename to check</p>
      * @return <p>The file's extension</p>
      */
-    public static String getExtension(String file) {
+    @NotNull
+    public static String getExtension(@NotNull String file) {
         if (file.contains(".")) {
             return file.substring(file.lastIndexOf('.') + 1);
         } else {
@@ -135,7 +110,8 @@ public final class FileUtil {
      * @param file <p>A filename.</p>
      * @return <p>A filename without its extension.</p>
      */
-    public static String stripExtension(String file) {
+    @NotNull
+    public static String stripExtension(@NotNull String file) {
         return file.substring(0, file.lastIndexOf('.'));
     }
 
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/ListUtil.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/ListUtil.java
index f8cba56..8854270 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/utility/ListUtil.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/ListUtil.java
@@ -1,5 +1,7 @@
 package net.knarcraft.ffmpegconverter.utility;
 
+import org.jetbrains.annotations.NotNull;
+
 import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.List;
@@ -22,7 +24,8 @@ public final class ListUtil {
      * @param <T>   <p>The type of the two lists.</p>
      * @return <p>A new array containing all elements from the two arrays.</p>
      */
-    static <T> T[] concatenate(T[] listA, T[] listB) {
+    @NotNull
+    public static <T> T[] concatenate(@NotNull T[] listA, @NotNull T[] listB) {
         int listALength = listA.length;
         int listBLength = listB.length;
         @SuppressWarnings("unchecked")
@@ -40,7 +43,7 @@ public final class ListUtil {
      * @param <T>       <p>The type of the list.</p>
      * @return <p>A new list containing all matching elements.</p>
      */
-    static <T> List<T> getMatching(List<T> list, Predicate<T> predicate) {
+    public static <T> List<T> getMatching(List<T> list, Predicate<T> predicate) {
         List<T> matching = new ArrayList<>(list);
         matching.removeIf(predicate.negate());
         return matching;
@@ -54,7 +57,7 @@ public final class ListUtil {
      * @param <T>       Anything which can be stored in a list
      * @return True if at least one element fulfills the predicate
      */
-    static <T> boolean listContains(T[] list, Predicate<T> predicate) {
+    public static <T> boolean listContains(@NotNull List<T> list, @NotNull Predicate<T> predicate) {
         for (T item : list) {
             if (predicate.test(item)) {
                 return true;
@@ -69,7 +72,8 @@ public final class ListUtil {
      * @param string <p>A string which may include commas.</p>
      * @return <p>A string list.</p>
      */
-    public static String[] getListFromCommaSeparatedString(String string) {
+    @NotNull
+    public static String[] getListFromCommaSeparatedString(@NotNull String string) {
         String[] result;
         if (string.contains(",")) {
             result = string.split(",");
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/OutputUtil.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/OutputUtil.java
index 5964e85..b142229 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/utility/OutputUtil.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/OutputUtil.java
@@ -1,5 +1,7 @@
 package net.knarcraft.ffmpegconverter.utility;
 
+import org.jetbrains.annotations.NotNull;
+
 import java.io.BufferedWriter;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
@@ -30,7 +32,7 @@ public final class OutputUtil {
      *
      * @param input <p>The text to print.</p>
      */
-    public static void println(String input) {
+    public static void println(@NotNull String input) {
         if (!input.isEmpty()) {
             try {
                 writer.write(input);
@@ -46,7 +48,7 @@ public final class OutputUtil {
      *
      * @param input <p>The string to print.</p>
      */
-    public static void print(String input) {
+    public static void print(@NotNull String input) {
         try {
             writer.write(input);
             writer.flush();
@@ -82,7 +84,7 @@ public final class OutputUtil {
      *
      * @param message <p>The debug message to show.</p>
      */
-    public static void printDebug(String message) {
+    public static void printDebug(@NotNull String message) {
         if (debug) {
             println(message);
         }
diff --git a/src/main/java/net/knarcraft/ffmpegconverter/utility/Parser.java b/src/main/java/net/knarcraft/ffmpegconverter/utility/Parser.java
index a361299..88f73e4 100644
--- a/src/main/java/net/knarcraft/ffmpegconverter/utility/Parser.java
+++ b/src/main/java/net/knarcraft/ffmpegconverter/utility/Parser.java
@@ -1,6 +1,7 @@
 package net.knarcraft.ffmpegconverter.utility;
 
 import net.knarcraft.ffmpegconverter.parser.ConverterArgument;
+import org.jetbrains.annotations.NotNull;
 
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -23,7 +24,8 @@ public final class Parser {
      * @param validArguments <p>All arguments which are considered valid.</p>
      * @return <p>A map with all parsed arguments.</p>
      */
-    static Map<String, String> parse(String input, List<ConverterArgument> validArguments) {
+    @NotNull
+    static Map<String, String> parse(@NotNull String input, @NotNull List<ConverterArgument> validArguments) {
         return parse(tokenize(input), validArguments);
     }
 
@@ -34,7 +36,8 @@ public final class Parser {
      * @param validArguments <p>A list of arguments which are considered valid.</p>
      * @return <p>A map with all parsed arguments.</p>
      */
-    private static Map<String, String> parse(List<String> tokens, List<ConverterArgument> validArguments) {
+    @NotNull
+    private static Map<String, String> parse(@NotNull List<String> tokens, @NotNull List<ConverterArgument> validArguments) {
         Map<String, String> parsedArguments = new HashMap<>();
 
         while (!tokens.isEmpty()) {
@@ -50,7 +53,8 @@ public final class Parser {
      * @param converterArguments <p>A list of all the valid arguments in existence.</p>
      * @param parsedArguments    <p>The map to store the parsed argument to.</p>
      */
-    private static void parseArgument(List<String> tokens, List<ConverterArgument> converterArguments, Map<String, String> parsedArguments) {
+    private static void parseArgument(@NotNull List<String> tokens, @NotNull List<ConverterArgument> converterArguments,
+                                      @NotNull Map<String, String> parsedArguments) {
         String currentToken = tokens.remove(0);
         List<ConverterArgument> foundArguments;
 
@@ -79,7 +83,8 @@ public final class Parser {
      * @param foundArgument   <p>The found argument to store.</p>
      * @param parsedArguments <p>The map to store parsed arguments to.</p>
      */
-    private static void storeArgumentValue(List<String> tokens, ConverterArgument foundArgument, Map<String, String> parsedArguments) {
+    private static void storeArgumentValue(@NotNull List<String> tokens, @NotNull ConverterArgument foundArgument,
+                                           @NotNull Map<String, String> parsedArguments) {
         String argumentValue;
         if (tokens.isEmpty()) {
             argumentValue = "";
@@ -114,7 +119,8 @@ public final class Parser {
      * @param input <p>A string.</p>
      * @return <p>A list of tokens.</p>
      */
-    public static List<String> tokenize(String input) {
+    @NotNull
+    public static List<String> tokenize(@NotNull String input) {
         List<String> tokens = new ArrayList<>();
         boolean startedQuote = false;
         StringBuilder currentToken = new StringBuilder();
@@ -157,8 +163,8 @@ public final class Parser {
      * @param index        <p>The index of the read character.</p>
      * @param tokens       <p>The list of processed tokens.</p>
      */
-    private static void tokenizeNormalCharacter(StringBuilder currentToken, char character, int inputLength, int index,
-                                                List<String> tokens) {
+    private static void tokenizeNormalCharacter(@NotNull StringBuilder currentToken, char character, int inputLength,
+                                                int index, @NotNull List<String> tokens) {
         currentToken.append(character);
         if (index == inputLength - 1) {
             tokens.add(currentToken.toString());
@@ -173,7 +179,8 @@ public final class Parser {
      * @param tokens       <p>The list of processed tokens.</p>
      * @return <p>True if the token is finished.</p>
      */
-    private static boolean tokenizeSpace(boolean startedQuote, StringBuilder currentToken, List<String> tokens) {
+    private static boolean tokenizeSpace(boolean startedQuote, @NotNull StringBuilder currentToken,
+                                         @NotNull List<String> tokens) {
         if (!startedQuote) {
             //If not inside "", a space marks the end of a parameter
             if (isNotEmpty(currentToken)) {
@@ -192,7 +199,7 @@ public final class Parser {
      * @param builder <p>The string builder to check.</p>
      * @return <p>True if the string builder is non empty.</p>
      */
-    private static boolean isNotEmpty(StringBuilder builder) {
+    private static boolean isNotEmpty(@NotNull StringBuilder builder) {
         return !builder.toString().trim().isEmpty();
     }
 
diff --git a/src/main/resources/audio_formats.txt b/src/main/resources/audio_formats.txt
index 4279515..badc645 100644
--- a/src/main/resources/audio_formats.txt
+++ b/src/main/resources/audio_formats.txt
@@ -1,4 +1,3 @@
-39
 3gp
 aa
 aac
diff --git a/src/main/resources/conf/config.properties b/src/main/resources/conf/config.properties
new file mode 100644
index 0000000..aab92eb
--- /dev/null
+++ b/src/main/resources/conf/config.properties
@@ -0,0 +1 @@
+debug=false
\ No newline at end of file
diff --git a/src/main/resources/subtitle_formats.txt b/src/main/resources/subtitle_formats.txt
index 4dfd314..54de0e5 100644
--- a/src/main/resources/subtitle_formats.txt
+++ b/src/main/resources/subtitle_formats.txt
@@ -1,4 +1,3 @@
-5
 idx
 sub
 srt
diff --git a/src/main/resources/video_formats.txt b/src/main/resources/video_formats.txt
index 4dc9a08..074e447 100644
--- a/src/main/resources/video_formats.txt
+++ b/src/main/resources/video_formats.txt
@@ -1,4 +1,3 @@
-31
 avi
 mpg
 mpeg
diff --git a/src/test/java/net/knarcraft/ffmpegconverter/utility/ListUtilTest.java b/src/test/java/net/knarcraft/ffmpegconverter/utility/ListUtilTest.java
index df97a1b..14c684d 100644
--- a/src/test/java/net/knarcraft/ffmpegconverter/utility/ListUtilTest.java
+++ b/src/test/java/net/knarcraft/ffmpegconverter/utility/ListUtilTest.java
@@ -13,7 +13,7 @@ import static org.junit.Assert.assertFalse;
 
 public class ListUtilTest {
     private static List<Integer> matchesList;
-    private static Integer[] containsList;
+    private static List<Integer> containsList;
 
     @BeforeClass
     public static void setUp() {
@@ -28,7 +28,7 @@ public class ListUtilTest {
         matchesList.add(19);
         matchesList.add(21);
         matchesList.add(23);
-        containsList = new Integer[]{1, 3, 5, 7, 234, 23, 45};
+        containsList = List.of(1, 3, 5, 7, 234, 23, 45);
     }
 
     @Test