Ensure Pixel gets disabled, PDF ToC support (#3659)

# Description of Changes

Please provide a summary of the changes, including:

- What was changed
- Why the change was made
- Any challenges encountered

Closes #(issue_number)

---

## Checklist

### General

- [ ] I have read the [Contribution
Guidelines](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/CONTRIBUTING.md)
- [ ] I have read the [Stirling-PDF Developer
Guide](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/DeveloperGuide.md)
(if applicable)
- [ ] I have read the [How to add new languages to
Stirling-PDF](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/HowToAddNewLanguage.md)
(if applicable)
- [ ] I have performed a self-review of my own code
- [ ] My changes generate no new warnings

### Documentation

- [ ] I have updated relevant docs on [Stirling-PDF's doc
repo](https://github.com/Stirling-Tools/Stirling-Tools.github.io/blob/main/docs/)
(if functionality has heavily changed)
- [ ] I have read the section [Add New Translation
Tags](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/HowToAddNewLanguage.md#add-new-translation-tags)
(for new translation tags only)

### UI Changes (if applicable)

- [ ] Screenshots or videos demonstrating the UI changes are attached
(e.g., as comments or direct attachments in the PR)

### Testing (if applicable)

- [ ] I have tested my changes locally. Refer to the [Testing
Guide](https://github.com/Stirling-Tools/Stirling-PDF/blob/main/DeveloperGuide.md#6-testing)
for more details.

---------

Co-authored-by: Dario Ghunney Ware <[email protected]>
Co-authored-by: Connor Yoh <[email protected]>
Co-authored-by: a <a>
Co-authored-by: Reece <[email protected]>

stirling-pdf/build.gradle

@@ -1,8 +1,17 @@
+apply plugin: 'org.springframework.boot'
+
 repositories {
     maven { url = 'https://build.shibboleth.net/maven/releases' }
     maven { url = 'https://maven.pkg.github.com/jcefmaven/jcefmaven' }
 }
 
+configurations {
+    developmentOnly
+    runtimeClasspath {
+        extendsFrom developmentOnly
+    }
+}
+
 dependencies {
     if (System.getenv('STIRLING_PDF_DESKTOP_UI') != 'false'
         || (project.hasProperty('STIRLING_PDF_DESKTOP_UI')
@@ -71,25 +80,58 @@ sourceSets {
         resources {
             srcDirs += ['../configs']
         }
+        java {
+            if (System.getenv('STIRLING_PDF_DESKTOP_UI') == 'false') {
+                exclude 'stirling/software/SPDF/UI/impl/**'
+            }
+
+        }
     }
+    test {
+        java {
+            if (System.getenv('DOCKER_ENABLE_SECURITY') == 'false' || System.getenv('DISABLE_ADDITIONAL_FEATURES') == 'true'
+                || (project.hasProperty('DISABLE_ADDITIONAL_FEATURES')
+                && System.getProperty('DISABLE_ADDITIONAL_FEATURES') == 'true')) {
+                exclude 'stirling/software/proprietary/security/**'
+            }
+            if (System.getenv('STIRLING_PDF_DESKTOP_UI') == 'false') {
+                exclude 'stirling/software/SPDF/UI/impl/**'
+            }
+        }
+    }
+    
 }
 
+
+// Disable regular jar
 jar {
+    enabled = false
+}
+
+// Configure and enable bootJar for this project
+bootJar {
+    enabled = true
     duplicatesStrategy = DuplicatesStrategy.EXCLUDE
     zip64 = true
 
-    from {
-        configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
-    }
+    // Don't include all dependencies directly like the old jar task did
+    // from {
+    //     configurations.runtimeClasspath.collect { it.isDirectory() ? it : zipTree(it) }
+    // }
+    
+    // Exclude signature files to prevent "Invalid signature file digest" errors
+    exclude 'META-INF/*.SF'
+    exclude 'META-INF/*.DSA'
+    exclude 'META-INF/*.RSA'
+    exclude 'META-INF/*.EC'
 
     manifest {
         attributes(
-            'Main-Class': 'stirling.software.SPDF.SPDFApplication',
             'Implementation-Title': 'Stirling-PDF',
             'Implementation-Version': project.version
         )
     }
 }
 
-jar.dependsOn ':common:jar'
-jar.dependsOn ':proprietary:jar'
+bootJar.dependsOn ':common:jar'
+bootJar.dependsOn ':proprietary:jar'