diff --git a/src/main/java/stirling/software/SPDF/utils/FileToPdf.java b/src/main/java/stirling/software/SPDF/utils/FileToPdf.java
index ca06c5c2..ebdbf4fa 100644
--- a/src/main/java/stirling/software/SPDF/utils/FileToPdf.java
+++ b/src/main/java/stirling/software/SPDF/utils/FileToPdf.java
@@ -35,15 +35,17 @@ public class FileToPdf {
                 command.add("weasyprint");
             } else {
                 command.add("wkhtmltopdf");
+                command.add("--enable-local-file-access");
             }
+
             command.add(tempInputFile.toString());
             command.add(tempOutputFile.toString());
             ProcessExecutorResult returnCode;
             if (fileName.endsWith(".zip")) {
 
                 if (htmlFormatsInstalled) {
-                    command.add("--allow");
-                    command.add(tempOutputFile.getParent().toString());
+                    // command.add(1, "--allow");
+                    // command.add(2, tempInputFile.getParent().toString());
                 }
                 returnCode =
                         ProcessExecutor.getInstance(ProcessExecutor.Processes.WEASYPRINT)
diff --git a/src/main/java/stirling/software/SPDF/utils/ProcessExecutor.java b/src/main/java/stirling/software/SPDF/utils/ProcessExecutor.java
index 18bc925a..23311bde 100644
--- a/src/main/java/stirling/software/SPDF/utils/ProcessExecutor.java
+++ b/src/main/java/stirling/software/SPDF/utils/ProcessExecutor.java
@@ -4,15 +4,22 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.io.InterruptedIOException;
 import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.Semaphore;
+import java.util.concurrent.TimeUnit;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 public class ProcessExecutor {
 
+    private static final Logger logger = LoggerFactory.getLogger(ProcessExecutor.class);
+
     public enum Processes {
         LIBRE_OFFICE,
         OCR_MY_PDF,
@@ -26,7 +33,7 @@ public class ProcessExecutor {
     private static final Map<Processes, ProcessExecutor> instances = new ConcurrentHashMap<>();
 
     public static ProcessExecutor getInstance(Processes processType) {
-        return getInstance(processType, false);
+        return getInstance(processType, true);
     }
 
     public static ProcessExecutor getInstance(Processes processType, boolean liveUpdates) {
@@ -43,16 +50,29 @@ public class ProcessExecutor {
                                 case INSTALL_APP -> 1;
                                 case CALIBRE -> 1;
                             };
-                    return new ProcessExecutor(semaphoreLimit, liveUpdates);
+
+                    long timeoutMinutes =
+                            switch (key) {
+                                case LIBRE_OFFICE -> 30;
+                                case OCR_MY_PDF -> 30;
+                                case PYTHON_OPENCV -> 30;
+                                case GHOSTSCRIPT -> 5;
+                                case WEASYPRINT -> 30;
+                                case INSTALL_APP -> 60;
+                                case CALIBRE -> 30;
+                            };
+                    return new ProcessExecutor(semaphoreLimit, liveUpdates, timeoutMinutes);
                 });
     }
 
     private final Semaphore semaphore;
     private final boolean liveUpdates;
+    private long timeoutDuration;
 
-    private ProcessExecutor(int semaphoreLimit, boolean liveUpdates) {
+    private ProcessExecutor(int semaphoreLimit, boolean liveUpdates, long timeout) {
         this.semaphore = new Semaphore(semaphoreLimit);
         this.liveUpdates = liveUpdates;
+        this.timeoutDuration = timeout;
     }
 
     public ProcessExecutorResult runCommandWithOutputHandling(List<String> command)
@@ -62,12 +82,12 @@ public class ProcessExecutor {
 
     public ProcessExecutorResult runCommandWithOutputHandling(
             List<String> command, File workingDirectory) throws IOException, InterruptedException {
-        int exitCode = 1;
         String messages = "";
+        int exitCode = 1;
         semaphore.acquire();
         try {
 
-            System.out.print("Running command: " + String.join(" ", command));
+            logger.info("Running command: " + String.join(" ", command));
             ProcessBuilder processBuilder = new ProcessBuilder(command);
 
             // Use the working directory if it's set
@@ -91,8 +111,11 @@ public class ProcessExecutor {
                                     String line;
                                     while ((line = errorReader.readLine()) != null) {
                                         errorLines.add(line);
-                                        if (liveUpdates) System.out.println(line);
+                                        if (liveUpdates) logger.info(line);
                                     }
+                                } catch (InterruptedIOException e) {
+                                    logger.warn(
+                                            "Error reader thread was interrupted due to timeout.");
                                 } catch (IOException e) {
                                     e.printStackTrace();
                                 }
@@ -109,8 +132,11 @@ public class ProcessExecutor {
                                     String line;
                                     while ((line = outputReader.readLine()) != null) {
                                         outputLines.add(line);
-                                        if (liveUpdates) System.out.println(line);
+                                        if (liveUpdates) logger.info(line);
                                     }
+                                } catch (InterruptedIOException e) {
+                                    logger.warn(
+                                            "Error reader thread was interrupted due to timeout.");
                                 } catch (IOException e) {
                                     e.printStackTrace();
                                 }
@@ -120,8 +146,17 @@ public class ProcessExecutor {
             outputReaderThread.start();
 
             // Wait for the conversion process to complete
-            exitCode = process.waitFor();
+            boolean finished = process.waitFor(timeoutDuration, TimeUnit.MINUTES);
 
+            if (!finished) {
+                // Terminate the process
+                process.destroy();
+                // Interrupt the reader threads
+                errorReaderThread.interrupt();
+                outputReaderThread.interrupt();
+                throw new IOException("Process timeout exceeded.");
+            }
+            exitCode = process.exitValue();
             // Wait for the reader threads to finish
             errorReaderThread.join();
             outputReaderThread.join();
@@ -130,13 +165,13 @@ public class ProcessExecutor {
                 if (outputLines.size() > 0) {
                     String outputMessage = String.join("\n", outputLines);
                     messages += outputMessage;
-                    System.out.println("Command output:\n" + outputMessage);
+                    logger.info("Command output:\n" + outputMessage);
                 }
 
                 if (errorLines.size() > 0) {
                     String errorMessage = String.join("\n", errorLines);
                     messages += errorMessage;
-                    System.out.println("Command error output:\n" + errorMessage);
+                    logger.warn("Command error output:\n" + errorMessage);
                     if (exitCode != 0) {
                         throw new IOException(
                                 "Command process failed with exit code "
diff --git a/src/main/resources/settings.yml.template b/src/main/resources/settings.yml.template
index 1245c9e0..00c5998e 100644
--- a/src/main/resources/settings.yml.template
+++ b/src/main/resources/settings.yml.template
@@ -13,7 +13,9 @@ system:
   defaultLocale: 'en-US' # Set the default language (e.g. 'de-DE', 'fr-FR', etc)
   googlevisibility: false # 'true' to allow Google visibility (via robots.txt), 'false' to disallow
   enableAlphaFunctionality: false # Set to enable functionality which might need more testing before it fully goes live (This feature might make no changes)
-#  customExternalPort: 8000 used for when port mappings do not work correctly
+  customApplications:
+    installBookFormats: false # Installs Calibre for book format conversion (For non docker it must be manually downloaded but will need to be true to show in UI)
+    installAdvancedHtmlToPDF: false # DO NOT USE EXTERNALLY, NOT SAFE! Install wkHtmlToPDF (For non docker it must be manually downloaded but will need to be true to show in UI)
   
 #ui:
 #  appName: exampleAppName # Application's visible name