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 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 ;-)

- Improvements on the performance of communication system
- big clean up of the code (many old methods deleted)
- corrected bug in out of context (now, a consensus is only started if a propose is received)
Note: still need to verify if state transfer and leader change works right

In this commit, I have submitted the code for the leader change. Unfortunately there is some kind of conflict between the code I developed for an older version of smart, and the most recent code available on the svn. Such conflict renders the leader change protocol faulty. Further debugging is necessary. The normal operating remains good, though.

Fixed a bug in ExecutionManager.java where not all stoppedMsgs would be removed from the List upon restart

Removed out of context thread. The processing out of context messages is now made at the delivery thread and Server CS thread
Removed paxos internal timers.  From now on, the external timers from the total ordering layer shall trigger the leader change
Added a few debugging messages for delivering messages
Fixed a bug related to signatures of forwarded messages from replicas to the leader
Fixed a bug on the TTP that would make it crash in some cases
Fixed 2 bugs on the state transfer protocol responsable for not letting the old leader fetch the state once it recovered

In this commit, it was added a new feature to SMaRt. It now supports dynamic views. Some bugs from the previous commit were also fixed. This was a fairly extensive update to SMaRt.

Nonces are now generated for each TOMMessage in a Batch with a single seed that is sent along with the batch instead of a fixed number of nonces per Batch.
Decided notification in Consensus.java now is done via a sync monitor instead of busy waiting on the decided value to be set. Because of the Java MemoryModel the former mechanism was problematic and could theoretically lead to the DeliveryThread never learning the new value - which is very unlikely though.

In this commit I made an optimization to the state transfer protocol that consists on the sending of hash's of the state. Only one replica will send the actual state. I also worked towards fixing some bugs.

In this commit I started to clean up the code that I wrote. I also added some debug messages which are produced with the Logger object.

In this commit, I continued to work on the state transfer protocol .I finally managed to correctly implement the optimization for the revived replica to request the state sooner than the paxos highmark.

In this commit, I continued to work on the state transfer protocol.I finally tested the protocol in the case of a crash of a replica. I was able to make the replica recover the state on those circunstances.  However, the replica will still only requests the state after it passes the highmark value. I started working on an optimization to request the state before it reaches that highmark, but its still not completed.

In this commit, I continued to work on the state transfer protocol. It is already capable of transfering leader information, and supply it to the delayed replica. This means the code is no longer hacked to always assume replica 0 is the leader. It also does garbage collection again.

I also made some minor adjustements to some debbuging messages and the new demo

In this commit, i've continued to try to find and fix more errors related to the updating of delayed replicas. I have managed to fix three of them, but the code is merely "patched". If there is a leader change, SMaRt will go haywire. This version o the code should not be used for other purpose then testing.

I added more debug messages, and I will keep looking at the code during the weekend. I expect to fix some more bugs that i found during that period. I will also produce more debug logs so i can try to find more bugs.

I this commit, I continued the work on the state transfer protocol. I implemented the modifications discussed. However, the protocol remains faulty. Further debugging is required.

In this commit, i've only added some debug messages.But I committed it anyway, so I can work on SMaRt during the weekend at home

In this commit, i've continued my task of debuging the code.I finally managed to get the replica to update itself. However, when the clients finish to send requests, that same replica still remains a little behind, even though it sucessfully updates itself during previous executions of the state transfer protocol.

In this commit, i've continued my task of debuging the code. I believe the protocol itself is functioning correctly, but I still have to set the replicas to actually enforce the received state upon the application. The commited code is tested, and SMaRt seems to work properly according to the counter demo.

In this commit, i've continued my task of debuging the code. I made sure that the checkpoints are indeed working properly, so i re-activated the code which implements it.  Part of the state transfer protocol is also working, but I committed it de-activated. I'll resume the debugging tomorrow.

I've resumed my work on the state transfer protocol. However, I'm having trouble getting it to work right. I've de-activated the protocol, in order to safely commit the changes.

I have completed the coding of the state transfer protocol. However, I'm still yet to test the changes made in this commit. Therefore, this is likely to be an unstable version of SMaRt

Previous changes to the message handler were not intended. It were really meant in the execution manager. Fixed.