Remote cluster submission from Flink Runner broken due to staging issues

The usual way to submit pipelines with the Flink Runner is to build a fat jar and use the `bin/flink` utility to submit the jar to a Flink cluster. This works fine.

Alternatively, the Flink Runner can use the `flinkMaster` pipeline option to specify a remote cluster. Upon submitting an example we get the following at Flink's JobManager.

```

Caused by: java.lang.IllegalAccessError: class sun.reflect.GeneratedSerializationConstructorAccessor70
cannot access its superclass sun.reflect.SerializationConstructorAccessorImpl
at sun.misc.Unsafe.defineClass(Native
Method)
at sun.reflect.ClassDefiner.defineClass(ClassDefiner.java:63)
at sun.reflect.MethodAccessorGenerator$1.run(MethodAccessorGenerator.java:399)
at
sun.reflect.MethodAccessorGenerator$1.run(MethodAccessorGenerator.java:394)
at java.security.AccessController.doPrivileged(Native
Method)
at sun.reflect.MethodAccessorGenerator.generate(MethodAccessorGenerator.java:393)
at sun.reflect.MethodAccessorGenerator.generateSerializationConstructor(MethodAccessorGenerator.java:112)
at
sun.reflect.ReflectionFactory.newConstructorForSerialization(ReflectionFactory.java:340)
at java.io.ObjectStreamClass.getSerializableConstructor(ObjectStreamClass.java:1420)
at
java.io.ObjectStreamClass.access$1500(ObjectStreamClass.java:72)
at java.io.ObjectStreamClass$2.run(ObjectStreamClass.java:497)
at
java.io.ObjectStreamClass$2.run(ObjectStreamClass.java:472)
at java.security.AccessController.doPrivileged(Native
Method)
at java.io.ObjectStreamClass.(ObjectStreamClass.java:472)
at java.io.ObjectStreamClass.lookup(ObjectStreamClass.java:369)
at
java.io.ObjectStreamClass.initNonProxy(ObjectStreamClass.java:598)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1630)
at
java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1521)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1781)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2018)
at
java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:1942)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1808)
at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1353)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:373)
at
org.apache.flink.util.InstantiationUtil.deserializeObject(InstantiationUtil.java:502)
at org.apache.flink.util.InstantiationUtil.deserializeObject(InstantiationUtil.java:489)
at
org.apache.flink.util.InstantiationUtil.deserializeObject(InstantiationUtil.java:477)
at org.apache.flink.util.InstantiationUtil.readObjectFromConfig(InstantiationUtil.java:438)
at
org.apache.flink.runtime.operators.util.TaskConfig.getStubWrapper(TaskConfig.java:288)
at org.apache.flink.runtime.jobgraph.InputFormatVertex.initializeOnMaster(InputFormatVertex.java:63)
...
32 more

```

It appears there is an issue with the staging via `PipelineResources`.

Imported from Jira [BEAM-7478](https://issues.apache.org/jira/browse/BEAM-7478). Original Jira may contain additional context.
Reported by: mxm.