Fixed a bug on the leader change protocol that would block all replicas if the delayed replica triggered again a leader change before the others finished the same protocol.

Identified a bug on the method "send" of class NettyClientServerCommunicationSystemServerSide, but its cause remains misterious: if invoked 2 times for the same message (why it sometimes is invoked 2 times for the same message is not known), the client may not receive a reply on its end, and if no sufficent replies are received, the client blocks. If locks are used in this method, the problem seems to disappear.

Removed various locks from the leader change protocol which were rendered useless in previous commits.

The Proposed thread now  unlocks by this order: I am the leader -> the consensus as finished  -> I have message to order 

Now Executable is the top class. It has the executeUnordered method, as all executables can process readonly messages.
There are two classes extending Executable.
SingleExecutable has the executeOrdered method to process a sigle command.
BatchExecutable has the executeBatch to process multiple commands.
BatchExecutable was also changed to have a matrix of bytes as parameter, corresponding to an array of commands, having an array of bytes.
Demo classes was changed to use the new Executable structure.
ServiceReplica was also changed.

- Added tests for killing leaders;
- Added Logger to log tests in console;
- Added ConsoleTest to execute tests in Console window instead of JUnit.

Fixed a bug on the state transfer protocol, that would render the leader change protocol from changing leader a second time. However, the leader change is still unstable when ciclying through replicas. I'm investigating the issue.

This commit as a lot of debugging message related to the leader change protocol.

Fixed a bug on the state transfer protocol. It will now longer abort if the replica which should send the complete state remains mute; instead, it will re-initialize the protocol. This way, the system will no longer freeze when trying to add a replica to the group while the original leader is down (because there are not enough replicas to have a quorum during the first phase of the consensus algorithm).

Also done a minor change in the implementation: upon a timeout, the computations will be passed to the CS thread, in a similar way in which is done with the leader change protocol.

Some refractoring was also done.

Fixed a small  bug that would render the state transfer protocol less efficient, although still functional. Found a small defect on the protocol, but not fixed yet (I want to discuss the issue first with Professor Bessani).

Also, substituted a printstack trace  by a system out, which would be displayed when the CS couldn't connect to another replica. Since this was very periodic, it would make difficult to do debugging with such an excpetion constantly appearing.

Small but important change in the leader change implementation: When a replica suspects the leader, such computations will be done by the CS thread isntead of the RequestTask Thread. This shall reduce the changes of concurrency and race conditions, thus, making  the code more resilient.

Small but important change in the communication system: when a connection to a replica is lost, the OutQueue is erased. This is meant to avoid gaps in the sequence of messages upon reconnection, and thus, avoid the "break" of upper protocols.

Also, small refractor in TomUtil.

- Changed ServiceReplica to implement TOMReceiver;
- Created interfaces Executable and Recoverable, so the replicas can choose which methods to implement;
- Changed replicas to use ServiceReplica instead of extend it.

Modified slightly the throughput client and server. You can now specify the size of the application state.

Moved executeOrdered method to the server implementation.
Added ant code to compile and export Jar of the project.
Added JUnit tests for the keyvalue demo.
Refactored keyvalue code.

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Huge update: merging corrections of Eduardo with current version of the repository. The reconfiguration protocol should work properly now!

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Fixed some bugs in the leader change (although it still needs plenty of work, specially when re-integrating the replica).

Fixed a bug related to read only requests. Moved RadomDemo to a dedicated package.

State transfer protocol can now notify the recovered replica about the most recente view. 

Added apache codecs do deal with base64 encode/decode.

Moved the code of the state transfer protocolo from class tomlayer to class statemanager. Also fixed the arrayindexoutofboud exception related to state transfer. Fixed a bug that wouldn't start the request timeout.

Cleanup on the TOMConfiguration. Removed several configuration parameters that do not make sense anymore. Besides that merged some packages and cleaned a bit more of code here and there.

Removed useless code. Classes RTInfo, RTCollect, RTLeaderChange and RTMessage are gone. Various methods that used these classes were also deleted.

In this commit, it was fixed a bug on leader change messages related to the serialization of messages contained in the STOP message. It was also added a method in the BatchBuilder class, that makes it easer to create a batch and is also used during the leader change.

Removed and refactored a lot of code, added new microbenchmarks and improved the parallelism between the delivery thread and server communication thread. Additionally, processing of out of context message changed a bit (done in the server communication thread, instead of the delivery thread).
IMPORTANT: Service replica API changed!!!
NOTE: currently achieving a zero-byte throughput of 151Kops/sec ;-)