Packages re-jig was meant to reduce the size of the jars that are being produced by the
node driver. E.g. previously `MessageState` was in package `net.corda` which resulted in jar file
of around 2MB to be created. Same for `NodeStatePersistenceTests` which was in `net.corda.node`
* Making Corda's JPA classes non-final and Serializable.
* Making Corda's JPA classes non-final and Serializable.
* Making Corda's JPA classes non-final and Serializable.
* Making Corda's JPA classes non-final and Serializable.
* CORDA-1208: Notary service should persist the notarisation request signature along with the committed input states.
This required modifying the uniqueness provider interface to accept the signature in addition to input states.
Until now the committed state log used to be stored as a map of (state reference -> (tranasction id, consuming party)).
Adding the serialized signature would mean inflating each state entry by around 700 bytes, which would be grossly inefficient.
Instead, two tables are now used: one for storing (state referece -> transaction id) map, and another for storing the notarisation
request details (transaction id, consuming party, date, signature).
* Update api - all of these changes are only related to custom notaries
Old code failed with:
```
11:34:01.536 [main] ERROR net.corda.node.internal.Node - Exception during node startup
java.nio.file.InvalidPathException: Illegal char <:> at index 2: /C:/Program%20Files/JetBrains/IntelliJ%20IDEA%20Community%20Edition%202017.3.1/lib/idea_rt.jar
at sun.nio.fs.WindowsPathParser.normalize(WindowsPathParser.java:182) ~[?:1.8.0_144]
at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:153) ~[?:1.8.0_144]
at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:77) ~[?:1.8.0_144]
at sun.nio.fs.WindowsPath.parse(WindowsPath.java:94) ~[?:1.8.0_144]
at sun.nio.fs.WindowsFileSystem.getPath(WindowsFileSystem.java:255) ~[?:1.8.0_144]
at java.nio.file.Paths.get(Paths.java:84) ~[?:1.8.0_144]
at net.corda.node.utilities.JVMAgentRegistry.resolveAgentJar(JVMAgentRegistry.kt:46) ~[classes/:?]
at net.corda.node.internal.AbstractNode.initialiseJVMAgents(AbstractNode.kt:785) ~[classes/:?]
at net.corda.node.internal.AbstractNode.start(AbstractNode.kt:199) ~[classes/:?]
at net.corda.node.internal.Node.start(Node.kt:335) ~[classes/:?]
at net.corda.node.internal.NodeStartup.startNode(NodeStartup.kt:146) ~[classes/:?]
at net.corda.node.internal.NodeStartup.run(NodeStartup.kt:120) [classes/:?]
at net.corda.node.Corda.main(Corda.kt:16) [classes/:?]
```
- Existing embedded Shell connects via RPC including checking RPC user credentials (before was a direct use of CordaRPCOps): in dev mode when console terminal is enabled, node created `shell` user.
- New Standalone Shell app with the same functionalities as Shell: connects to a node via RPC Client, can use SSL and run SSH server.
* Fix another non-serializable exception, add docs, fix a possible security issue.
* Update API definition to reflect methods added to make more exceptions serializable
