Make structural tests pass

The fixes look correct to me, but I'm not 100% sure. However, better
than failing a set of tests.

pom.xml

@@ -5,6 +5,10 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
+	<prerequisites>
+		<maven>3.0.5</maven>
+	</prerequisites>
+
 	<parent>
 		<groupId>org.sonatype.oss</groupId>
 		<artifactId>oss-parent</artifactId>
@@ -21,7 +25,7 @@
 
 	<groupId>net.sourceforge.owlapi</groupId>
 	<artifactId>org.semanticweb.hermit</artifactId>
-	<version>1.4.1.514-SNAPSHOT</version>
+	<version>1.4.3.517</version>
 	<packaging>bundle</packaging>
 
 	<name>HermiT</name>
@@ -52,10 +56,6 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 
-	<prerequisites>
-		<maven>2.2.1</maven>
-	</prerequisites>
-
 	<profiles>
 		<profile>
 			<id>release</id>
@@ -71,7 +71,7 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-gpg-plugin</artifactId>
-						<version>1.4</version>
+						<version>1.6</version>
 						<executions>
 							<execution>
 								<id>sign-artifacts</id>
@@ -85,7 +85,7 @@
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
 						<artifactId>maven-source-plugin</artifactId>
-						<version>2.1.2</version>
+						<version>3.0.1</version>
 						<executions>
 							<execution>
 								<id>attach-sources</id>
@@ -98,7 +98,7 @@
 					<plugin>
 						<groupId>org.sonatype.plugins</groupId>
 						<artifactId>nexus-staging-maven-plugin</artifactId>
-						<version>1.6.5</version>
+						<version>1.6.7</version>
 						<extensions>true</extensions>
 						<configuration>
 							<serverId>ossrh</serverId>
@@ -116,7 +116,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.3</version>
+				<version>3.6.0</version>
 				<configuration>
 					<source>1.8</source>
 					<target>1.8</target>
@@ -125,11 +125,9 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.6</version>
+				<version>2.19.1</version>
 				<configuration>
 					<excludes>
-						<!-- structural tests don't work and it's known -->
-						<exclude>**/structural/*java</exclude>
 						<exclude>**/BlockingValidatorTest.java</exclude>
 					</excludes>
 
@@ -138,12 +136,12 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-jar-plugin</artifactId>
-				<version>2.6</version>
+				<version>3.0.2</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-source-plugin</artifactId>
-				<version>2.2</version>
+				<version>3.0.1</version>
 				<executions>
 					<execution>
 						<id>attach-source</id>
@@ -156,7 +154,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
-				<version>3.0.0</version>
+				<version>3.0.1</version>
 				<configuration>
 					<show>public</show>
 				</configuration>
@@ -205,7 +203,9 @@
 						</Export-Package>
 						<Import-Package>
 							!org.apache.*,
+							!gnu.getopt,
 							!javax.*,
+							javax.xml.stream.*,
 							!org.codehaus.*,
 							!org.jaxen*,
 							org.protege.editor.owl.*;version="4.3",
@@ -236,7 +236,7 @@
 		<dependency>
 			<groupId>net.sourceforge.owlapi</groupId>
 			<artifactId>owlapi-distribution</artifactId>
-			<version>5.1.3</version>
+			<version>5.1.7</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.ws.commons.axiom</groupId>
@@ -293,6 +293,16 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
+		<dependency>
+			<groupId>gnu.getopt</groupId>
+			<artifactId>java-getopt</artifactId>
+			<version>1.0.13</version>
+		</dependency>
+		<dependency>
+			<groupId>net.sf.trove4j</groupId>
+			<artifactId>trove4j</artifactId>
+			<version>3.0.3</version>
+		</dependency>
 	</dependencies>
 
 	<developers>