Some of your dependency JARs is a signed JAR, so when you combine then all in one JAR and run that JAR then signature of the signed JAR doesn't match up and hence you get the security exception about signature mis-match.
To fix this you need to first identify which all dependency JARs are signed JARs and then exclude them. Depending upon whether you are using MAVEN or ANT, you have to take appropriate solution. Below are but you can read more here, here and here.
Maven:
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.6</version>
<executions>
<execution>
<id>unpack-dependencies</id>
<phase>package</phase>
<goals>
<goal>unpack-dependencies</goal>
</goals>
<configuration>
<excludeScope>system</excludeScope>
<excludes>META-INF/*.SF</excludes>
<excludes>META-INF/*.DSA</excludes>
<excludes>META-INF/*.RSA</excludes>
<excludeGroupIds>junit,org.mockito,org.hamcrest</excludeGroupIds>
<outputDirectory>${project.build.directory}/classes</outputDirectory>
</configuration>
</execution>
</executions>
</plugin>
ANT:
<jar destfile="app.jar" basedir="${classes.dir}">
<zipfileset excludes="META-INF/**/*" src="${lib.dir}/bcprov-jdk16-145.jar"></zipfileset>
<manifest>
<attribute name="Main-Class" value="app.Main"/>
</manifest>
</jar>
Update based on OP's comment:
"sqljdbc4.jar" was the signed JAR in OP's external libraries. So, following above approach to systematically exclude the signature related files like .SF, .RSA or .DES or other algorithms files is the right way to move forward.
If these signature files are not excluded then security exception will occur because of signature mismatch.
How to know if a JAR is signed or not?: If a JAR contains files like files like .SF, .RSA or .DES or other algorithms files, then it is a signed JAR. Or run jarsigner -verify jarname.jar and see if it outputs "verified"
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