Update the APE version and dependencies

Author: vedran-kasalica

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>io.github.sanctuuary</groupId>
 	<artifactId>APE</artifactId>
-	<version>2.2.6</version>
+	<version>2.3.0</version>
 	<packaging>jar</packaging>
 	<name>io.github.sanctuuary:APE</name>
 	<description>APE is a command line tool and an API for the automated exploration of possible computational pipelines (workflows) from large collections of computational tools.</description>
@@ -164,12 +164,12 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.13.0</version>
+			<version>3.14.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.20.0</version>
+			<version>2.22.1</version>
 		</dependency>
 		<dependency>
 			<groupId>guru.nidi</groupId>
@@ -180,7 +180,7 @@
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20231013</version>
+			<version>20240205</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
 		<dependency>
@@ -192,12 +192,12 @@
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
-			<version>2.0.9</version>
+			<version>2.0.12</version>
 		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-simple</artifactId>
-			<version>2.0.9</version>
+			<version>2.0.12</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/org.antlr/antlr4-runtime -->
 		<dependency>
@@ -214,7 +214,7 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.14.0</version>
+			<version>2.15.1</version>
 		</dependency>
 		<!-- https://mvnrepository.com/artifact/com.squareup.okhttp3/okhttp -->
 		<dependency>