[Java] Tidy up dependency declarations.

build.gradle

@@ -150,10 +150,10 @@ allprojects {
         resolutionStrategy {
             failOnVersionConflict()
             // patching conflicting Checkstyle dependencies
-            force "org.codehaus.plexus:plexus-utils:3.3.0",
-                  "org.apache.commons:commons-lang3:3.8.1",
-                  "org.apache.httpcomponents:httpcore:4.4.14",
-                  "commons-codec:commons-codec:1.15"
+            force libs.commons.codec,
+                  libs.commons.lang3,
+                  libs.httpcore,
+                  libs.plexus.utils
         }
     }
 
@@ -284,7 +284,7 @@ project(':sbe-tool') {
                     implementation files("${layout.buildDirectory.get()}/classes/java/generated")
                     implementation libs.hamcrest
                     implementation libs.mockito
-                    implementation platform("org.junit:junit-bom:${libs.versions.junit.get()}")
+                    implementation platform(libs.junit.bom)
                     implementation "org.junit.jupiter:junit-jupiter-params"
                 }
             }

gradle/libs.versions.toml

@@ -1,19 +1,34 @@
 [versions]
 agrona = "2.0.1"
 checkstyle = "10.21.1"
-junit = "5.11.4"
-jmh = "1.37"
+commons-codec = "1.15"
+commons-lang3 = "3.8.1"
 gradle = "8.11.1"
+hamcrest = "3.0"
+httpcore = "4.4.14"
+jqwik = "1.9.2"
+jmh = "1.37"
+json = "20250107"
+junit = "5.11.4"
+mockito = "5.15.2"
+plexus = "3.3.0"
+shadow = "8.3.5"
+versions = "0.51.0"
 
 [libraries]
 agrona = { group = "org.agrona", name = "agrona", version.ref = "agrona" }
-mockito = { group = "org.mockito", name = "mockito-core", version = "5.15.2" }
-hamcrest = { group = "org.hamcrest", name = "hamcrest", version = "3.0" }
-jqwik = { group = "net.jqwik", name = "jqwik", version = "1.9.2" }
-json = { group = "org.json", name = "json", version = "20250107" }
+commons-codec = { group = "commons-codec", name = "commons-codec", version.ref = "commons-codec" }
+commons-lang3 = { group = "org.apache.commons", name = "commons-lang3", version.ref = "commons-lang3" }
+hamcrest = { group = "org.hamcrest", name = "hamcrest", version.ref = "hamcrest" }
+httpcore = { group = "org.apache.httpcomponents", name = "httpcore", version.ref = "httpcore" }
+jqwik = { group = "net.jqwik", name = "jqwik", version.ref = "jqwik" }
+json = { group = "org.json", name = "json", version.ref = "json" }
 jmh-core = { group = "org.openjdk.jmh", name = "jmh-core", version.ref = "jmh" }
 jmh-generator-annprocess = { group = "org.openjdk.jmh", name = "jmh-generator-annprocess", version.ref = "jmh" }
+junit-bom = { group = "org.junit", name = "junit-bom", version.ref = "junit" }
+mockito = { group = "org.mockito", name = "mockito-core", version.ref = "mockito" }
+plexus-utils = { group = "org.codehaus.plexus", name = "plexus-utils", version.ref = "plexus" }
 
 [plugins]
-versions = { id = "com.github.ben-manes.versions", version = "0.51.0" }
-shadow = { id = "com.gradleup.shadow", version = "8.3.5" }
+shadow = { id = "com.gradleup.shadow", version.ref = "shadow" }
+versions = { id = "com.github.ben-manes.versions", version.ref = "versions" }