* 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
This was achieved by having the hash in the node-info file to be just of the node's X.500 name. This also solves existing duplicate node-info file issues that we've been having.
Also updated the docsite.
* CORDA-986 and CORDA-985 CompositeKey and Signature verification performance fixes (#2467)
* CORDA-696: Create separate transaction types for contract upgrade transactions.
Add rationale around upgrade transactions
Move contract upgrade transaction resolution logic into internal until it's stabilised.
Throw a better exception when contract attachment not found
Default legacy contract constraint to always accepting - needs to be changed to whitelist constraint before merging
Introduce a new upgraded contract interface that allows specifying the legacy constraint.
Remove StateLoader, make all tx resolution functions take in ServicesForResolution
Contract upgrade transactions can handle whitelist by zone constraints
When creating a contract upgrade transaction, make sure the attachment of the old cordapp gets attached when using hash constraints.
Attachment lookup for a given contract class name only scans currently loaded cordapps, and we don't load old versions of cordapps.
CORDA-696: Update upgrade docs
* ENT-1443 Add cert role to CSR and doorman issue cert according to the cert role (#431)
* Doorman and HSM create certificate base on requested cert role specified in the certificate signing request.
(cherry picked from commit 94f7392)
* remove R3 corda code
CORDA-1010: Notary flow - clients now send a signature over a notarisation
request in addition to the transaction. This will be logged by the notary
to be able to prove that a particular party has requested the consumption
of a particular state.
* Jolokia agents are loaded dynamically if configured
* Renamed exportJmxTo (never used) to jmxMonitoringHttpPort and take it from config
* Updated documentation and tests
