Migrate to Gradle version catalogs for configuration cache compatibility

.gitignore

@@ -13,7 +13,8 @@ target/
 .java-version
 build/
 bin/
-gradle/
+gradle/*
+!gradle/libs.versions.toml
 gradlew
 gradlew.bat
 .idea/

Configure.pl

@@ -269,10 +269,10 @@ sub update_to_latest_versions {
         }
     }
 
-    # Update Gradle dependencies
+    # Update Gradle dependencies using version catalog
     if (-f 'build.gradle') {
-        print "Updating Gradle dependencies to latest versions...\n";
-        my $gradle_output = `./gradlew useLatestVersions`;
+        print "Updating Gradle dependencies to latest versions using version catalog...\n";
+        my $gradle_output = `./gradlew versionCatalogUpdate`;
         my $gradle_status = $? >> 8;
         if ($gradle_status != 0) {
             warn "Failed to update Gradle dependencies. Exit status: $gradle_status\n";

build.gradle

@@ -13,15 +13,13 @@ buildscript {
 // Core plugins configuration
 plugins {
     id 'java'
-    // Plugin for checking dependency updates
-    id 'com.github.ben-manes.versions' version '0.53.0'
-    // Plugin for automatically updating dependencies
-    id 'se.patrikerdes.use-latest-versions' version '0.2.19'
+    // Plugin for updating version catalog with latest versions (configuration cache compatible!)
+    alias(libs.plugins.version.catalog.update)
     id 'application'
     // Plugin for creating OS packages (deb)
-    id 'com.netflix.nebula.ospackage' version '12.1.1'
+    alias(libs.plugins.ospackage)
     // Plugin for creating fat/uber JARs
-    id 'com.gradleup.shadow' version '9.3.0'
+    alias(libs.plugins.shadow)
 }
 
 // Main application class configuration
@@ -68,20 +66,20 @@ repositories {
 // Project dependencies
 dependencies {
     // Core dependencies
-    implementation 'org.ow2.asm:asm:9.9'                           // ByteCode manipulation
-    implementation 'org.ow2.asm:asm-util:9.9'                     // ASM utilities
-    implementation 'com.ibm.icu:icu4j:78.1'                       // Unicode support
-    implementation 'com.alibaba.fastjson2:fastjson2:2.0.60'       // JSON processing
-    implementation 'org.snakeyaml:snakeyaml-engine:3.0.1'           // YAML processing
-    implementation 'org.tomlj:tomlj:1.1.1'                           // TOML processing
-    implementation 'org.apache.commons:commons-csv:1.14.1'          // CSV processing
-    implementation 'net.java.dev.jna:jna:5.18.1'                   // Native access
-    implementation 'net.java.dev.jna:jna-platform:5.18.1'          // Native access
+    implementation libs.asm                           // ByteCode manipulation
+    implementation libs.asm.util                      // ASM utilities
+    implementation libs.icu4j                         // Unicode support
+    implementation libs.fastjson2                     // JSON processing
+    implementation libs.snakeyaml.engine              // YAML processing
+    implementation libs.tomlj                         // TOML processing
+    implementation libs.commons.csv                   // CSV processing
+    implementation libs.jna                           // Native access
+    implementation libs.jna.platform                  // Native access
 
     // Testing dependencies
-    testImplementation 'org.junit.jupiter:junit-jupiter-api:6.1.0-M1'
-    testImplementation 'org.junit.jupiter:junit-jupiter-engine:6.1.0-M1'
-    testImplementation 'org.junit.jupiter:junit-jupiter-params:6.1.0-M1'
+    testImplementation libs.junit.jupiter.api
+    testImplementation libs.junit.jupiter.engine
+    testImplementation libs.junit.jupiter.params
 }
 
 // JUnit configuration
@@ -220,3 +218,16 @@ tasks.register('testUnitParallel') {
     description = 'Runs unit tests in parallel across multiple JVMs. Usage: gradle testUnitParallel --parallel'
     dependsOn 'testUnitShard0', 'testUnitShard1', 'testUnitShard2', 'testUnitShard3'
 }
+
+// Version catalog update configuration
+// The nl.littlerobots.version-catalog-update plugin is configuration cache compatible!
+// Use: ./gradlew versionCatalogUpdate to check and update dependencies
+// Use: ./gradlew versionCatalogUpdate --interactive to review changes interactively
+versionCatalogUpdate {
+    // Sort the catalog keys
+    sortByKey = true
+    // Keep versions not used in the project
+    keep {
+        keepUnusedVersions = true
+    }
+}

dev/design/DEPENDENCY_UPDATES.md

@@ -0,0 +1,82 @@
+# Dependency Management Guide
+
+This project uses **Gradle Version Catalogs** for centralized dependency management. All dependencies are defined in `gradle/libs.versions.toml`.
+
+## Benefits of Version Catalogs
+
+- **Centralized Management**: All versions in one place (`gradle/libs.versions.toml`)
+- **Type-Safe**: IDE autocomplete for dependencies
+- **Configuration Cache Compatible**: Works with Gradle's configuration cache for faster builds
+- **Easy Updates**: Simple commands to check and update dependencies
+
+## Available Tasks
+
+### Check and Update Dependencies
+
+```bash
+# Check for updates and automatically update the version catalog
+./gradlew versionCatalogUpdate
+```
+
+This will:
+- Check all dependencies for newer versions
+- Update `gradle/libs.versions.toml` with the latest versions
+- Maintain proper formatting
+
+### Interactive Mode
+
+```bash
+# Review each update interactively before applying
+./gradlew versionCatalogUpdate --interactive
+```
+
+### Format Version Catalog
+
+```bash
+# Format the libs.versions.toml file (fully configuration cache compatible)
+./gradlew versionCatalogFormat
+```
+
+## Version Catalog Location
+
+All dependencies are defined in: `gradle/libs.versions.toml`
+
+Structure:
+- `[versions]` - Version numbers
+- `[libraries]` - Library dependencies
+- `[plugins]` - Gradle plugins
+
+## Adding New Dependencies
+
+1. Add the version to `[versions]` section
+2. Add the library reference to `[libraries]` section
+3. Use in `build.gradle` with: `implementation libs.library.name`
+
+Example:
+```toml
+[versions]
+gson = "2.10.1"
+
+[libraries]
+gson = { module = "com.google.code.gson:gson", version.ref = "gson" }
+```
+
+Then in `build.gradle`:
+```groovy
+dependencies {
+    implementation libs.gson
+}
+```
+
+## Important Notes
+
+- **Configuration Cache**: Fully compatible! No need to disable features
+- **Review Changes**: Always review updates before committing
+- **Test After Updates**: Run `./gradlew clean build test` after updating
+- **Pin Versions**: Add `# @pin` comment in TOML to prevent auto-updates
+
+## Migration Complete
+
+✅ Migrated from `ben-manes.versions` + `use-latest-versions` to version catalogs
+✅ Configuration cache now works with all tasks
+✅ Cleaner, more maintainable dependency management

gradle/libs.versions.toml

@@ -0,0 +1,28 @@
+[versions]
+asm = "9.9.1"
+commons-csv = "1.14.1"
+fastjson2 = "2.0.60"
+icu4j = "78.1"
+jna = "5.18.1"
+junit-jupiter = "6.1.0-M1"
+snakeyaml-engine = "3.0.1"
+tomlj = "1.1.1"
+
+[libraries]
+asm = { module = "org.ow2.asm:asm", version.ref = "asm" }
+asm-util = { module = "org.ow2.asm:asm-util", version.ref = "asm" }
+commons-csv = { module = "org.apache.commons:commons-csv", version.ref = "commons-csv" }
+fastjson2 = { module = "com.alibaba.fastjson2:fastjson2", version.ref = "fastjson2" }
+icu4j = { module = "com.ibm.icu:icu4j", version.ref = "icu4j" }
+jna = { module = "net.java.dev.jna:jna", version.ref = "jna" }
+jna-platform = { module = "net.java.dev.jna:jna-platform", version.ref = "jna" }
+junit-jupiter-api = { module = "org.junit.jupiter:junit-jupiter-api", version.ref = "junit-jupiter" }
+junit-jupiter-engine = { module = "org.junit.jupiter:junit-jupiter-engine", version.ref = "junit-jupiter" }
+junit-jupiter-params = { module = "org.junit.jupiter:junit-jupiter-params", version.ref = "junit-jupiter" }
+snakeyaml-engine = { module = "org.snakeyaml:snakeyaml-engine", version.ref = "snakeyaml-engine" }
+tomlj = { module = "org.tomlj:tomlj", version.ref = "tomlj" }
+
+[plugins]
+ospackage = "com.netflix.nebula.ospackage:12.1.1"
+shadow = "com.gradleup.shadow:9.3.0"
+version-catalog-update = "nl.littlerobots.version-catalog-update:1.0.1"