JDK25 - Integrate Stirling-Tools JPDFium for PDF operations (#6387)

.github/workflows/backend-build.yml

@@ -1,7 +1,7 @@
 name: Backend build, format check, and coverage
 
-# Reusable workflow called from build.yml. Runs the full backend build matrix
+# Reusable workflow called from build.yml. Runs the backend build matrix
-# (JDK 21/25 × spring-security on/off), Spotless formatting check, JUnit, and
+# (JDK 25 × spring-security on/off), Spotless formatting check, JUnit, and
 # posts Jacoco coverage to PRs.
 on:
   workflow_call:
@@ -24,7 +24,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        jdk-version: [21, 25]
+        jdk-version: [25]
         spring-security: [true, false]
     steps:
       - name: Harden Runner

.github/workflows/multiOSReleases.yml

@@ -94,21 +94,21 @@ jobs:
           if [ "${{ github.event_name }}" = "workflow_dispatch" ]; then
             case "${{ github.event.inputs.platform }}" in
               "windows")
-                echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64"}]}' >> $GITHUB_OUTPUT
+                echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64","jpdfium_platforms":"windows-x64"}]}' >> $GITHUB_OUTPUT
                 ;;
               "macos")
-                echo 'matrix={"include":[{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal"}]}' >> $GITHUB_OUTPUT
+                echo 'matrix={"include":[{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal","jpdfium_platforms":"darwin-arm64,darwin-x64"}]}' >> $GITHUB_OUTPUT
                 ;;
               "linux")
-                echo 'matrix={"include":[{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64"}]}' >> $GITHUB_OUTPUT
+                echo 'matrix={"include":[{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64","jpdfium_platforms":"linux-x64"}]}' >> $GITHUB_OUTPUT
                 ;;
               *)
-                echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64"},{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal"},{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64"}]}' >> $GITHUB_OUTPUT
+                echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64","jpdfium_platforms":"windows-x64"},{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal","jpdfium_platforms":"darwin-arm64,darwin-x64"},{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64","jpdfium_platforms":"linux-x64"}]}' >> $GITHUB_OUTPUT
                 ;;
             esac
           else
             # For push/release events, build all platforms
-            echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64"},{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal"},{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64"}]}' >> $GITHUB_OUTPUT
+            echo 'matrix={"include":[{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64","jpdfium_platforms":"windows-x64"},{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal","jpdfium_platforms":"darwin-arm64,darwin-x64"},{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64","jpdfium_platforms":"linux-x64"}]}' >> $GITHUB_OUTPUT
           fi
 
   build-jars:
@@ -263,15 +263,17 @@ jobs:
         if: matrix.platform == 'macos-15'
         env:
           AARCH64_JAVA_HOME: ${{ env.JAVA_HOME }}
+          JPDFIUM_PLATFORMS: ${{ matrix.jpdfium_platforms }}
         run: task desktop:jlink:universal-mac
 
       - name: Prepare desktop build
-        run: task desktop:prepare
         env:
           MAVEN_USER: ${{ secrets.MAVEN_USER }}
           MAVEN_PASSWORD: ${{ secrets.MAVEN_PASSWORD }}
           MAVEN_PUBLIC_URL: ${{ secrets.MAVEN_PUBLIC_URL }}
           DISABLE_ADDITIONAL_FEATURES: true
+          JPDFIUM_PLATFORMS: ${{ matrix.jpdfium_platforms }}
+        run: task desktop:prepare
 
       # DigiCert KeyLocker Setup (Cloud HSM)
       - name: Setup DigiCert KeyLocker
@@ -440,6 +442,10 @@ jobs:
           echo "Generated tauri.windows.conf.json (alias masked):"
           sed "s/${KEYPAIR_ALIAS}/***/g" ./frontend/src-tauri/tauri.windows.conf.json
 
+      - name: Sign JPDFium dylibs inside bootJar (macOS only)
+        if: matrix.platform == 'macos-15' && env.APPLE_CERTIFICATE != ''
+        run: bash frontend/scripts/sign-jpdfium-dylibs-in-bootjar.sh
+
       - name: Import release GPG signing key (Linux)
         if: matrix.platform == 'ubuntu-22.04' && env.RELEASE_GPG_PRIVATE_KEY != '' && (github.event_name == 'release' || (github.event_name == 'workflow_dispatch' && github.event.inputs.sign != 'false') || github.ref == 'refs/heads/V2-master')
         run: |

.github/workflows/tauri-build.yml

@@ -47,12 +47,10 @@ jobs:
           APPLE_CERTIFICATE: ${{ secrets.APPLE_CERTIFICATE }}
           PLATFORM: ${{ inputs.platform }}
         run: |
-          WINDOWS='{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64"}'
+          WINDOWS='{"platform":"windows-latest","args":"--target x86_64-pc-windows-msvc","name":"windows-x86_64","jpdfium_platforms":"windows-x64"}'
-          MACOS='{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal"}'
+          MACOS='{"platform":"macos-15","args":"--target universal-apple-darwin","name":"macos-universal","jpdfium_platforms":"darwin-arm64,darwin-x64"}'
-          LINUX='{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64"}'
+          LINUX='{"platform":"ubuntu-22.04","args":"","name":"linux-x86_64","jpdfium_platforms":"linux-x64"}'
 
-          # Resolve requested platform — populated by either workflow_dispatch
-          # or workflow_call inputs; both paths default to "all".
           case "$PLATFORM" in
             windows) ENTRIES=("$WINDOWS") ;;
             macos)   ENTRIES=("$MACOS") ;;
@@ -113,10 +111,6 @@ jobs:
           toolchain: stable
           targets: ${{ matrix.platform == 'macos-15' && 'aarch64-apple-darwin,x86_64-apple-darwin' || '' }}
 
-      # x86_64 JDK is set up first so the aarch64 step below can leave its
-      # JAVA_HOME as the active one. The macOS universal JRE build needs
-      # jmods from both arches; the x64 path is captured into the env
-      # before the second setup-java overwrites JAVA_HOME.
       - name: Set up x86_64 JDK 25 (macOS universal JRE)
         if: matrix.platform == 'macos-15'
         uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
@@ -143,21 +137,21 @@ jobs:
       - name: Setup Task
         uses: go-task/setup-task@3be4020d41929789a01026e0e427a4321ce0ad44 # v2.0.0
 
-      # Build the universal JRE before desktop:prepare so the jlink:runtime
-      # task short-circuits on its `test -d runtime/jre` status check.
       - name: Build universal macOS JRE
         if: matrix.platform == 'macos-15'
         env:
           AARCH64_JAVA_HOME: ${{ env.JAVA_HOME }}
+          JPDFIUM_PLATFORMS: ${{ matrix.jpdfium_platforms }}
         run: task desktop:jlink:universal-mac
 
       - name: Prepare desktop build
-        run: task desktop:prepare
         env:
           MAVEN_USER: ${{ secrets.MAVEN_USER }}
           MAVEN_PASSWORD: ${{ secrets.MAVEN_PASSWORD }}
           MAVEN_PUBLIC_URL: ${{ secrets.MAVEN_PUBLIC_URL }}
           DISABLE_ADDITIONAL_FEATURES: true
+          JPDFIUM_PLATFORMS: ${{ matrix.jpdfium_platforms }}
+        run: task desktop:prepare
 
       # DigiCert KeyLocker Setup (Cloud HSM)
       - name: Setup DigiCert KeyLocker
@@ -270,6 +264,10 @@ jobs:
           echo "APPLE_SIGNING_IDENTITY=$CERT_ID" >> $GITHUB_ENV
           echo "Certificate imported successfully."
 
+      - name: Sign JPDFium dylibs inside bootJar (macOS only)
+        if: matrix.platform == 'macos-15' && env.APPLE_CERTIFICATE != ''
+        run: bash frontend/scripts/sign-jpdfium-dylibs-in-bootjar.sh
+
       - name: Check DMG creation dependencies (macOS only)
         if: matrix.platform == 'macos-15'
         run: |

.taskfiles/desktop.yml

@@ -3,6 +3,22 @@ version: '3'
 vars:
   JLINK_MODULES: "java.base,java.compiler,java.desktop,java.instrument,java.logging,java.management,java.naming,java.net.http,java.prefs,java.rmi,java.scripting,java.security.jgss,java.security.sasl,java.sql,java.transaction.xa,java.xml,java.xml.crypto,jdk.crypto.ec,jdk.crypto.cryptoki,jdk.unsupported"
 
+  # Override via JPDFIUM_PLATFORMS env (csv of platform keys, or 'all').
+  JPDFIUM_PLATFORMS:
+    sh: |
+      if [ -n "${JPDFIUM_PLATFORMS:-}" ]; then
+          echo "$JPDFIUM_PLATFORMS"
+      else
+          case "{{OS}}-{{ARCH}}" in
+              darwin-arm64)  echo "darwin-arm64";;
+              darwin-amd64)  echo "darwin-x64";;
+              linux-amd64)   echo "linux-x64";;
+              linux-arm64)   echo "linux-arm64";;
+              windows-amd64) echo "windows-x64";;
+              *)             echo "all";;
+          esac
+      fi
+
 tasks:
   prepare:
     desc: "Prepare desktop build dependencies"
@@ -71,15 +87,16 @@ tasks:
     deps: [jlink:jar, jlink:runtime]
 
   jlink:jar:
-    desc: "Build backend JAR for Tauri bundling"
+    desc: "Build backend JAR for Tauri bundling (host-OS natives only by default)"
     run: once
     dir: ..
     env:
       DISABLE_ADDITIONAL_FEATURES: "true"
     cmds:
-      - cmd: cmd /c gradlew.bat bootJar --no-daemon
+      - echo "Building bootJar with JPDFium natives for {{.JPDFIUM_PLATFORMS}}"
+      - cmd: cmd /c gradlew.bat bootJar --no-daemon -PjpdfiumPlatforms={{.JPDFIUM_PLATFORMS}}
         platforms: [windows]
-      - cmd: ./gradlew bootJar --no-daemon
+      - cmd: ./gradlew bootJar --no-daemon -PjpdfiumPlatforms={{.JPDFIUM_PLATFORMS}}
         platforms: [linux, darwin]
       - mkdir -p frontend/src-tauri/libs
       - cp app/core/build/libs/stirling-pdf-*.jar frontend/src-tauri/libs/

AGENTS.md

@@ -431,7 +431,7 @@ The frontend is organized with a clear separation of concerns:
 
 ## Important Notes
 
-- **Java Version**: Minimum JDK 21, supports and recommends JDK 25
+- **Java Version**: Requires JDK 25.
 - **Lombok**: Used extensively - ensure IDE plugin is installed
 - **File Persistence**:
   - **Backend**: Designed to be stateless - files are processed in memory/temp locations only

DeveloperGuide.md

@@ -11,7 +11,7 @@ This guide focuses on developing for Stirling 2.0, including both the React fron
 **Stirling 2.0** is built using:
 
 **Backend:**
-- Spring Boot (Java 21+, JDK 25 recommended)
+- Spring Boot (requires JDK 25)
 - PDFBox for core PDF operations
 - LibreOffice for document conversions
 - qpdf for PDF optimization
@@ -45,7 +45,7 @@ This guide focuses on developing for Stirling 2.0, including both the React fron
 - [Task](https://taskfile.dev/installation/) — unified command runner (recommended)
 - Docker
 - Git
-- Java JDK 21 or later (JDK 25 recommended)
+- Java JDK 25
 - Node.js 18+ and npm (required for frontend development)
 - Gradle 7.0 or later (Included within the repo)
 - [uv](https://docs.astral.sh/uv/) — Python package manager (required for engine development)
@@ -61,7 +61,7 @@ This guide focuses on developing for Stirling 2.0, including both the React fron
    cd Stirling-PDF
    ```
 
-2. Install Docker and JDK 21 (or JDK 25 recommended) if not already installed.
+2. Install Docker and JDK 25 if not already installed.
 
 3. Install a recommended Java IDE such as Eclipse, IntelliJ, or VSCode
    1. Only VSCode

app/common/build.gradle

@@ -60,6 +60,24 @@ dependencies {
         exclude group: 'com.google.code.gson', module: 'gson'
     }
 
+    api 'com.stirling:jpdfium:1.0.0'
+
+    // -PjpdfiumPlatforms=all|<csv of linux-x64,linux-arm64,darwin-x64,darwin-arm64,windows-x64>
+    def jpdfiumPlatformsProp = (project.findProperty('jpdfiumPlatforms') ?: 'all').toString().trim()
+    def jpdfiumAllPlatforms = ['linux-x64', 'linux-arm64', 'darwin-x64', 'darwin-arm64', 'windows-x64']
+    def jpdfiumPlatforms = jpdfiumPlatformsProp == 'all'
+            ? jpdfiumAllPlatforms
+            : jpdfiumPlatformsProp.split(',').collect { it.trim() }.findAll { it }
+    def jpdfiumInvalid = jpdfiumPlatforms.findAll { !jpdfiumAllPlatforms.contains(it) }
+    if (jpdfiumInvalid) {
+        throw new GradleException("Unknown jpdfiumPlatforms value(s): ${jpdfiumInvalid.join(', ')}. " +
+                "Valid: ${jpdfiumAllPlatforms.join(', ')} or 'all'.")
+    }
+    logger.lifecycle("JPDFium native platforms: ${jpdfiumPlatforms.join(', ')}")
+    jpdfiumPlatforms.each { platform ->
+        runtimeOnly "com.stirling:jpdfium-natives-${platform}:1.0.0"
+    }
+
     // ArchUnit: enforces module dependency direction (see ArchitectureTest)
     testImplementation 'com.tngtech.archunit:archunit-junit5:1.4.2'
 }

app/common/src/test/java/stirling/software/common/jpdfium/JPDFiumSmokeTest.java

@@ -0,0 +1,32 @@
+package stirling.software.common.jpdfium;
+
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+
+import stirling.software.jpdfium.PdfDocument;
+
+class JPDFiumSmokeTest {
+
+    @Test
+    void opensExamplePdfAndReadsPageCount(@TempDir Path tmp) throws IOException {
+        Path pdf = tmp.resolve("example.pdf");
+        try (InputStream in = getClass().getResourceAsStream("/example.pdf")) {
+            assertNotNull(in, "example.pdf must exist under src/test/resources");
+            Files.copy(in, pdf);
+        }
+
+        try (PdfDocument doc = PdfDocument.open(pdf)) {
+            assertTrue(
+                    doc.pageCount() >= 1,
+                    "PdfDocument should report at least one page for example.pdf");
+        }
+    }
+}

app/core/build.gradle

@@ -162,7 +162,8 @@ bootJar {
     manifest {
         attributes(
             'Implementation-Title': 'Stirling-PDF',
-            'Implementation-Version': project.version
+            'Implementation-Version': project.version,
+            'Enable-Native-Access': 'ALL-UNNAMED'
         )
     }
 }

app/core/src/main/java/stirling/software/SPDF/controller/api/MergeController.java

@@ -3,13 +3,14 @@ package stirling.software.SPDF.controller.api;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
 import java.util.regex.Pattern;
 
-import org.apache.pdfbox.multipdf.PDFMergerUtility;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDDocumentCatalog;
 import org.apache.pdfbox.pdmodel.PDDocumentInformation;
@@ -47,6 +48,11 @@ import stirling.software.common.util.PdfErrorUtils;
 import stirling.software.common.util.TempFile;
 import stirling.software.common.util.TempFileManager;
 import stirling.software.common.util.WebResponseUtils;
+import stirling.software.jpdfium.PdfDocument;
+import stirling.software.jpdfium.PdfMerge;
+import stirling.software.jpdfium.doc.Bookmark;
+import stirling.software.jpdfium.doc.PdfBookmarkEditor;
+import stirling.software.jpdfium.doc.PdfBookmarkEditor.BookmarkTree;
 
 @GeneralApi
 @Slf4j
@@ -57,7 +63,6 @@ public class MergeController {
     private final CustomPDFDocumentFactory pdfDocumentFactory;
     private final TempFileManager tempFileManager;
 
-    // Merges a list of PDDocument objects into a single PDDocument
     public PDDocument mergeDocuments(List<PDDocument> documents) throws IOException {
         PDDocument mergedDoc = pdfDocumentFactory.createNewDocument();
         boolean success = false;
@@ -76,11 +81,8 @@ public class MergeController {
         }
     }
 
-    // Re-order files to match the explicit order provided by the front-end.
-    // fileOrder is newline-delimited original filenames in the desired order.
     private static MultipartFile[] reorderFilesByProvidedOrder(
             MultipartFile[] files, String fileOrder) {
-        // Split by various line endings and trim each entry
         String[] desired =
                 stirling.software.common.util.RegexPatternUtils.getInstance()
                         .getNewlineSplitPattern()
@@ -107,7 +109,6 @@ public class MergeController {
         return ordered.toArray(new MultipartFile[0]);
     }
 
-    // Returns a comparator for sorting MultipartFile arrays based on the given sort type
     private Comparator<MultipartFile> getSortComparator(String sortType) {
         return switch (sortType) {
             case "byFileName" ->
@@ -155,18 +156,16 @@ public class MergeController {
                             return 0;
                         }
                     };
-            case "orderProvided" -> (file1, file2) -> 0; // Default is the order provided
+            case "orderProvided" -> (file1, file2) -> 0;
-            default -> (file1, file2) -> 0; // Default is the order provided
+            default -> (file1, file2) -> 0;
         };
     }
 
-    // Parse client file IDs from JSON string
     private String[] parseClientFileIds(String clientFileIds) {
         if (clientFileIds == null || clientFileIds.trim().isEmpty()) {
             return new String[0];
         }
         try {
-            // Simple JSON array parsing - remove brackets and split by comma
             String trimmed = clientFileIds.trim();
             if (trimmed.startsWith("[") && trimmed.endsWith("]")) {
                 String inside = trimmed.substring(1, trimmed.length() - 1).trim();
@@ -186,39 +185,29 @@ public class MergeController {
         return new String[0];
     }
 
-    // Adds a table of contents to the merged document using filenames as chapter titles
     private void addTableOfContents(PDDocument mergedDocument, MultipartFile[] files) {
-        // Create the document outline
         PDDocumentOutline outline = new PDDocumentOutline();
         mergedDocument.getDocumentCatalog().setDocumentOutline(outline);
 
-        int pageIndex = 0; // Current page index in the merged document
+        int pageIndex = 0;
-
-        // Iterate through the original files
         for (MultipartFile file : files) {
-            // Get the filename without extension to use as bookmark title
             String filename = file.getOriginalFilename();
             String title = GeneralUtils.removeExtension(filename);
 
-            // Create an outline item for this file
             PDOutlineItem item = new PDOutlineItem();
             item.setTitle(title);
 
-            // Set the destination to the first page of this file in the merged document
             if (pageIndex < mergedDocument.getNumberOfPages()) {
                 PDPage page = mergedDocument.getPage(pageIndex);
                 item.setDestination(page);
             }
-
-            // Add the item to the outline
             outline.addLast(item);
 
-            // Increment page index for the next file
             try (PDDocument doc = pdfDocumentFactory.load(file)) {
                 pageIndex += doc.getNumberOfPages();
             } catch (IOException e) {
                 ExceptionUtils.logException("document loading for TOC generation", e);
-                pageIndex++; // Increment by at least one if we can't determine page count
+                pageIndex++;
             }
         }
     }
@@ -236,7 +225,6 @@ public class MergeController {
                     }
                 }
 
-                // Fallback to XMP metadata if Info dates are missing
                 PDMetadata metadata = doc.getDocumentCatalog().getMetadata();
                 if (metadata != null) {
                     try (InputStream is = metadata.createInputStream()) {
@@ -287,7 +275,7 @@ public class MergeController {
             @ModelAttribute MergePdfsRequest request,
             @RequestParam(value = "fileOrder", required = false) String fileOrder)
             throws IOException {
-        List<File> filesToDelete = new ArrayList<>(); // List of temporary files to delete
+        List<File> filesToDelete = new ArrayList<>();
         TempFile outputTempFile = null;
 
         boolean removeCertSign = Boolean.TRUE.equals(request.getRemoveCertSign());
@@ -298,48 +286,35 @@ public class MergeController {
             files = new MultipartFile[0];
         }
 
-        // If front-end provided explicit visible order, honor it and override backend sorting
         if (fileOrder != null && !fileOrder.isBlank()) {
             log.info("Reordering files based on fileOrder parameter");
             files = reorderFilesByProvidedOrder(files, fileOrder);
         } else {
             log.info("Sorting files based on sortType: {}", request.getSortType());
-            Arrays.sort(
+            Arrays.sort(files, getSortComparator(request.getSortType()));
-                    files,
-                    getSortComparator(
-                            request.getSortType())); // Sort files based on requested sort type
         }
 
         try (TempFile mt = new TempFile(tempFileManager, ".pdf")) {
 
-            PDFMergerUtility mergerUtility = new PDFMergerUtility();
+            List<Path> inputPaths = new ArrayList<>(files.length);
-            long totalSize = 0;
             List<Integer> invalidIndexes = new ArrayList<>();
             for (int index = 0; index < files.length; index++) {
                 MultipartFile multipartFile = files[index];
-                totalSize += multipartFile.getSize();
+                File tempFile = tempFileManager.convertMultipartFileToFile(multipartFile);
-                File tempFile =
+                filesToDelete.add(tempFile);
-                        tempFileManager.convertMultipartFileToFile(
+                inputPaths.add(tempFile.toPath());
-                                multipartFile); // Convert MultipartFile to File
-                filesToDelete.add(tempFile); // Add temp file to the list for later deletion
 
-                // Pre-validate each PDF so we can report which one(s) are broken
+                try (PdfDocument ignored = PdfDocument.open(tempFile.toPath())) {
-                // Use the original MultipartFile to avoid deleting the tempFile during validation
+                } catch (Exception e) {
-                try (PDDocument ignored = pdfDocumentFactory.load(multipartFile)) {
-                    // OK
-                } catch (IOException e) {
                     ExceptionUtils.logException("PDF pre-validate", e);
                     invalidIndexes.add(index);
                 }
-                mergerUtility.addSource(tempFile); // Add source file to the merger utility
             }
 
-            mergerUtility.setDestinationFileName(mt.getFile().getAbsolutePath());
+            int[] pageCounts;
-
             try {
-                mergerUtility.mergeDocuments(
+                pageCounts =
-                        pdfDocumentFactory.getStreamCacheFunction(
+                        mergeWithJpdfium(inputPaths, files, generateToc, mt.getFile().toPath());
-                                totalSize)); // Merge the documents
             } catch (IOException e) {
                 ExceptionUtils.logException("PDF merge", e);
                 if (PdfErrorUtils.isCorruptedPdfError(e)) {
@@ -348,10 +323,26 @@ public class MergeController {
                 throw e;
             }
 
-            // Load the merged PDF document and operate on it inside try-with-resources
+            boolean sigFlattenNeeded = false;
-            try (PDDocument mergedDocument = pdfDocumentFactory.load(mt.getFile())) {
+            if (removeCertSign) {
-                // Remove signatures if removeCertSign is true
+                try (PdfDocument check = PdfDocument.open(mt.getFile().toPath())) {
-                if (removeCertSign) {
+                    sigFlattenNeeded = !check.signatures().isEmpty();
+                } catch (Exception e) {
+                    log.debug(
+                            "JPDFium signature pre-check failed; falling back to PDFBox flatten:"
+                                    + " {}",
+                            e.getMessage());
+                    sigFlattenNeeded = true;
+                }
+                if (!sigFlattenNeeded) {
+                    log.info(
+                            "removeCertSign requested but merged document has no signature"
+                                    + " fields; skipping PDFBox flatten pass");
+                }
+            }
+
+            if (sigFlattenNeeded) {
+                try (PDDocument mergedDocument = pdfDocumentFactory.load(mt.getFile())) {
                     PDDocumentCatalog catalog = mergedDocument.getDocumentCatalog();
                     PDAcroForm acroForm = catalog.getAcroForm();
                     if (acroForm != null) {
@@ -359,24 +350,26 @@ public class MergeController {
                                 acroForm.getFields().stream()
                                         .filter(PDSignatureField.class::isInstance)
                                         .toList();
-
                         if (!fieldsToRemove.isEmpty()) {
-                            acroForm.flatten(
+                            acroForm.flatten(fieldsToRemove, false);
-                                    fieldsToRemove,
-                                    false); // Flatten the fields, effectively removing them
                         }
                     }
+                    outputTempFile = new TempFile(tempFileManager, ".pdf");
+                    try {
+                        mergedDocument.save(outputTempFile.getFile());
+                    } catch (Exception e) {
+                        outputTempFile.close();
+                        outputTempFile = null;
+                        throw e;
+                    }
                 }
-
+            } else {
-                // Add table of contents if generateToc is true
-                if (generateToc && files.length > 0) {
-                    addTableOfContents(mergedDocument, files);
-                }
-
-                // Save the modified document to a temporary file
                 outputTempFile = new TempFile(tempFileManager, ".pdf");
                 try {
-                    mergedDocument.save(outputTempFile.getFile());
+                    Files.copy(
+                            mt.getFile().toPath(),
+                            outputTempFile.getFile().toPath(),
+                            java.nio.file.StandardCopyOption.REPLACE_EXISTING);
                 } catch (Exception e) {
                     outputTempFile.close();
                     outputTempFile = null;
@@ -395,7 +388,7 @@ public class MergeController {
             throw ex;
         } finally {
             for (File file : filesToDelete) {
-                tempFileManager.deleteTempFile(file); // Delete temporary files
+                tempFileManager.deleteTempFile(file);
             }
         }
 
@@ -405,4 +398,113 @@ public class MergeController {
 
         return WebResponseUtils.pdfFileToWebResponse(outputTempFile, mergedFileName);
     }
+
+    private int[] mergeWithJpdfium(
+            List<Path> inputPaths, MultipartFile[] files, boolean generateToc, Path outputPath)
+            throws IOException {
+        if (inputPaths.isEmpty()) {
+            try (PdfDocument empty = PdfDocument.open(new byte[0])) {
+                empty.save(outputPath);
+            } catch (Exception ignored) {
+                Files.write(outputPath, new byte[0]);
+            }
+            return new int[0];
+        }
+
+        List<PdfDocument> docs = new ArrayList<>(inputPaths.size());
+        int[] pageCounts = new int[inputPaths.size()];
+        int[] pageOffsets = new int[inputPaths.size()];
+        List<List<Bookmark>> sourceBookmarks = new ArrayList<>(inputPaths.size());
+        int runningOffset = 0;
+        try {
+            for (int i = 0; i < inputPaths.size(); i++) {
+                Path p = inputPaths.get(i);
+                PdfDocument doc = PdfDocument.open(p);
+                docs.add(doc);
+                pageCounts[i] = doc.pageCount();
+                pageOffsets[i] = runningOffset;
+                sourceBookmarks.add(doc.bookmarks());
+                runningOffset += pageCounts[i];
+            }
+
+            BookmarkTree combinedTree =
+                    buildCombinedBookmarkTree(files, pageOffsets, sourceBookmarks, generateToc);
+
+            try (PdfDocument merged = PdfMerge.merge(docs)) {
+                if (combinedTree.entries().isEmpty()) {
+                    merged.save(outputPath);
+                } else {
+                    PdfBookmarkEditor.setBookmarks(merged, combinedTree, outputPath);
+                }
+            }
+        } catch (RuntimeException e) {
+            throw new IOException("JPDFium merge failed", e);
+        } finally {
+            for (PdfDocument doc : docs) {
+                try {
+                    doc.close();
+                } catch (Exception ignored) {
+                }
+            }
+        }
+        return pageCounts;
+    }
+
+    private BookmarkTree buildCombinedBookmarkTree(
+            MultipartFile[] files,
+            int[] pageOffsets,
+            List<List<Bookmark>> sourceBookmarks,
+            boolean generateToc) {
+        BookmarkTree.Builder builder = BookmarkTree.builder();
+
+        if (generateToc) {
+            for (int i = 0; i < files.length; i++) {
+                String filename = files[i].getOriginalFilename();
+                String title = GeneralUtils.removeExtension(filename);
+                if (title == null || title.isBlank()) {
+                    title = "Document " + (i + 1);
+                }
+                builder.add(title, pageOffsets[i]);
+            }
+        }
+
+        for (int i = 0; i < sourceBookmarks.size(); i++) {
+            int offset = pageOffsets[i];
+            for (Bookmark bm : sourceBookmarks.get(i)) {
+                addBookmarkFlat(builder, bm, offset);
+            }
+        }
+
+        return builder.build();
+    }
+
+    private void addBookmarkFlat(BookmarkTree.Builder builder, Bookmark root, int offset) {
+        final int maxNodes = 100_000;
+        java.util.Deque<Bookmark> stack = new java.util.ArrayDeque<>();
+        java.util.Set<Bookmark> visited =
+                java.util.Collections.newSetFromMap(new java.util.IdentityHashMap<>());
+        stack.push(root);
+        int processed = 0;
+        while (!stack.isEmpty() && processed < maxNodes) {
+            Bookmark bm = stack.pop();
+            if (!visited.add(bm)) {
+                continue;
+            }
+            processed++;
+            if (bm.isInternal() && bm.title() != null) {
+                builder.add(bm.title(), offset + bm.pageIndex());
+            }
+            if (bm.hasChildren()) {
+                List<Bookmark> children = bm.children();
+                for (int i = children.size() - 1; i >= 0; i--) {
+                    stack.push(children.get(i));
+                }
+            }
+        }
+        if (processed >= maxNodes) {
+            log.warn(
+                    "Source bookmark traversal hit {}-node cap; remaining bookmarks dropped",
+                    maxNodes);
+        }
+    }
 }

build.gradle

@@ -31,12 +31,12 @@ ext {
     googleJavaFormatVersion = "1.28.0"
     logback = "1.5.32"
     // junit-platform-launcher version managed by Spring Boot BOM
-    modernJavaVersion = 21
+    modernJavaVersion = 25
 }
 
 java {
-    sourceCompatibility = JavaVersion.VERSION_21
+    sourceCompatibility = JavaVersion.VERSION_25
-    targetCompatibility = JavaVersion.VERSION_21
+    targetCompatibility = JavaVersion.VERSION_25
     toolchain {
         languageVersion = JavaLanguageVersion.of(project.findProperty('javaVersion')?.toString() ?: '25')
     }
@@ -158,8 +158,8 @@ subprojects {
     apply plugin: 'jacoco'
 
     java {
-        sourceCompatibility = JavaVersion.VERSION_21
+        sourceCompatibility = JavaVersion.VERSION_25
-        targetCompatibility = JavaVersion.VERSION_21
+        targetCompatibility = JavaVersion.VERSION_25
         toolchain {
             languageVersion = JavaLanguageVersion.of(25)
         }
@@ -444,7 +444,8 @@ subprojects {
                 "-XX:G1HeapRegionSize=4m",
                 "-XX:+ExplicitGCInvokesConcurrent",
                 "-XX:+UseStringDeduplication",
-                "-XX:+UseCompactObjectHeaders"
+                "-XX:+UseCompactObjectHeaders",
+                "--enable-native-access=ALL-UNNAMED"
             ]
         }
     }

frontend/scripts/sign-jpdfium-dylibs-in-bootjar.sh

@@ -0,0 +1,111 @@
+#!/usr/bin/env bash
+# Sign every .dylib inside the bootJar's JPDFium native jars.
+# Requires APPLE_SIGNING_IDENTITY set to a Developer ID identity in the keychain.
+#
+# Usage: sign-jpdfium-dylibs-in-bootjar.sh [path/to/stirling-pdf-*.jar]
+
+set -u
+
+echo "sign-jpdfium-dylibs-in-bootjar.sh: start  ($(uname -s) $(uname -m))"
+
+case "$(uname -s)" in
+    Darwin*) ;;
+    *) echo "Not macOS, skipping"; exit 0;;
+esac
+
+if [ -z "${APPLE_SIGNING_IDENTITY:-}" ]; then
+    echo "APPLE_SIGNING_IDENTITY not set; skipping"
+    exit 0
+fi
+if ! command -v codesign >/dev/null 2>&1; then
+    echo "codesign not on PATH; skipping"
+    exit 0
+fi
+if ! command -v jar >/dev/null 2>&1; then
+    echo "jar not on PATH (need a JDK setup-action earlier); skipping"
+    exit 0
+fi
+
+BOOTJARS=()
+if [ -n "${1:-}" ]; then
+    BOOTJARS+=("$1")
+else
+    for cand in app/core/build/libs/stirling-pdf-*.jar \
+                frontend/src-tauri/libs/stirling-pdf-*.jar; do
+        [ -f "$cand" ] || continue
+        BOOTJARS+=("$cand")
+    done
+fi
+if [ "${#BOOTJARS[@]:-0}" = 0 ]; then
+    echo "bootJar not found (expected app/core/build/libs/stirling-pdf-*.jar" \
+         "or frontend/src-tauri/libs/stirling-pdf-*.jar)"
+    exit 0
+fi
+
+for BOOTJAR in "${BOOTJARS[@]}"; do
+    BOOTJAR=$(cd "$(dirname "$BOOTJAR")" && pwd)/$(basename "$BOOTJAR")
+    echo ""
+    echo "=== Target bootJar: $BOOTJAR ($(du -h "$BOOTJAR" | cut -f1)) ==="
+
+    WORK=$(mktemp -d)
+    # shellcheck disable=SC2064
+    trap "rm -rf '$WORK'" EXIT
+
+    NATIVE_JAR_PATHS=()
+    while IFS= read -r line; do
+        [ -n "$line" ] || continue
+        NATIVE_JAR_PATHS+=("$line")
+    done < <(jar tf "$BOOTJAR" \
+        | grep -E '^BOOT-INF/lib/jpdfium-natives-darwin-(x64|arm64)-.*\.jar$' || true)
+
+    if [ "${#NATIVE_JAR_PATHS[@]:-0}" = 0 ]; then
+        echo "  No JPDFium darwin natives in this bootJar; skipping"
+        rm -rf "$WORK"
+        continue
+    fi
+
+    ( cd "$WORK" && jar xf "$BOOTJAR" ${NATIVE_JAR_PATHS[@]+"${NATIVE_JAR_PATHS[@]}"} ) \
+        || { echo "jar xf failed to extract natives jars" >&2; exit 1; }
+
+    ANY_SIGNED=0
+    for nat_jar in "$WORK/BOOT-INF/lib"/jpdfium-natives-darwin-*.jar; do
+        [ -f "$nat_jar" ] || continue
+        base=$(basename "$nat_jar")
+        echo "  Processing $base"
+
+        exp_dir="$WORK/${base%.jar}.expanded"
+        mkdir -p "$exp_dir"
+        ( cd "$exp_dir" && jar xf "$nat_jar" )
+
+        signed=0
+        while IFS= read -r dylib; do
+            codesign --force --sign "$APPLE_SIGNING_IDENTITY" \
+                     --options runtime --timestamp "$dylib" 2>&1 | sed 's/^/      /'
+            signed=$((signed + 1))
+        done < <(find "$exp_dir" -name '*.dylib' -type f)
+
+        if [ "$signed" = 0 ]; then
+            echo "    (no .dylibs found)"
+            continue
+        fi
+        echo "    signed $signed dylib(s)"
+
+        rm -f "$nat_jar"
+        ( cd "$exp_dir" && jar cfM0 "$nat_jar" . )
+        ANY_SIGNED=1
+    done
+
+    if [ "$ANY_SIGNED" = 0 ]; then
+        echo "  No .dylibs signed; skipping update"
+        rm -rf "$WORK"
+        continue
+    fi
+
+    # `jar uf` always DEFLATEs; Spring Boot's nested-jar loader only reads
+    # STORED entries. Use `zip -0` to update in place with no compression.
+    ( cd "$WORK" && zip -q0 "$BOOTJAR" ${NATIVE_JAR_PATHS[@]+"${NATIVE_JAR_PATHS[@]}"} ) \
+        || { echo "zip update failed" >&2; exit 1; }
+
+    echo "  Updated: $BOOTJAR ($(du -h "$BOOTJAR" | cut -f1))"
+    rm -rf "$WORK"
+done

testing/test.sh

@@ -442,8 +442,10 @@ compare_file_lists() {
             echo "New files created during test:"
             cat "${diff_file}.added" | sed 's/^> //'
 
-            # Check for tmp files
+            # Exclude JPDFium native cache (deleteOnExit-registered, not a leak).
-            grep -i "tmp\|temp" "${diff_file}.added" > "${diff_file}.tmp" || true
+            grep -i "tmp\|temp" "${diff_file}.added" \
+                | grep -v '/jpdfium-[0-9]\+/' \
+                > "${diff_file}.tmp" || true
             if [ -s "${diff_file}.tmp" ]; then
                 echo "WARNING: Temporary files detected:"
                 cat "${diff_file}.tmp"