swtiched to maven shade plugin

I was having problems with unpredictable class loading behavior when building the project using maven command line.  Switching from the maven-assembly-plugin to maven-shade-plugin (like in minerva-cli) seems to have resolved the issue.

.gitignore

@@ -1,9 +1,9 @@
 target/
-/.DS_Store
+*.DS_Store
 .project
 .settings
 .classpath
 minerva-server/blazegraph.jnl
 /bin/
 *.icloud
-minerva-server/.DS_Store
+minerva-cli/bin/reactome-entities-blazegraph.jnl

.gitignore~

@@ -0,0 +1,11 @@
+target/
+/.DS_Store
+.project
+.settings
+.classpath
+minerva-server/blazegraph.jnl
+/bin/
+*.icloud
+minerva-server/.DS_Store
+minerva-cli/bin/reactome-entities-blazegraph.jnl
+minerva-core/.DS_Store

minerva-server/pom.xml

@@ -22,7 +22,7 @@
 					</excludes>
 				</configuration>
 			</plugin>
-			<plugin>
+		<!--  	<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-assembly-plugin</artifactId>
 				<configuration>
@@ -50,16 +50,49 @@
 					</execution>
 				</executions>
 			</plugin>
+			-->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-shade-plugin</artifactId>
+				<executions>
+					<execution>
+						<phase>package</phase>
+						<goals>
+							<goal>shade</goal>
+						</goals>
+						<configuration>
+						 <filters>
+        					<filter>
+            					<artifact>*:*</artifact>
+            					<excludes>
+                					<exclude>META-INF/*.SF</exclude>
+               					 	<exclude>META-INF/*.DSA</exclude>
+                					<exclude>META-INF/*.RSA</exclude>
+            					</excludes>
+        					</filter>
+    					</filters>
+							<outputFile>bin/minerva-server.jar</outputFile>
+							<createDependencyReducedPom>false</createDependencyReducedPom>
+							<transformers>
+								<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
+								<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+									<manifestEntries>
+										<Main-Class>org.geneontology.minerva.server.StartUpTool</Main-Class>
+										<git-revision-sha1>${git.commit.id}</git-revision-sha1>
+										<git-revision-url>https://github.com/geneontology/minerva/commit/${git.commit.id}</git-revision-url>
+										<git-branch>${git.branch}</git-branch>
+										<git-dirty>${git.dirty}</git-dirty>
+									</manifestEntries>
+								</transformer>
+							</transformers>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
 		</plugins>
 	</build>
 
 	<dependencies>
-	<!-- https://mvnrepository.com/artifact/org.apache.httpcomponents/httpclient -->
-<dependency>
-    <groupId>org.apache.httpcomponents</groupId>
-    <artifactId>httpclient</artifactId>
-    <version>4.5.9</version>
-</dependency>
 		<dependency>
 			<groupId>org.geneontology</groupId>
 			<artifactId>minerva-core</artifactId>

pom.xml

@@ -16,7 +16,8 @@
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<owltools.version>0.3.0-SNAPSHOT</owltools.version>
-		<owlapi.version>4.2.8</owlapi.version>
+		<!--  <owlapi.version>4.2.8</owlapi.version>-->
+		<owlapi.version>4.5.7</owlapi.version>
 	</properties>
 
 	<build>
@@ -240,7 +241,8 @@
 			<dependency>
 				<groupId>org.apache.httpcomponents</groupId>
 				<artifactId>httpclient</artifactId>
-				<version>4.2.5</version>
+				<!-- <version>4.2.5</version>-->
+				<version>4.5.9</version>
 			</dependency>
 			<dependency>
 				<groupId>net.sourceforge.owlapi</groupId>