re-enabling the MatrixMultiplicationSpec

It passes ok with the latest sbt version (0.12.0-RC4).

Fixes #102
Enable logs by default for a ScoobiApp

Fixes #111

also added () to the 'run' method in the examples and the guide
fixed the link for the latest api documentation on the site page
ScoobiApp.run should have parenthesis

Add parenthesis, to avoid errors about side-effecting nullary methods being discouraged
added a simple pom file for Sonar metrics
fixed the argument passing for Specifications

test-only *WordCountSpec* -- scoobi verbose.info

was not showing INFO logs appropriately (whereas verbose only works ok)
A DList can now be created with Text elements (or anything Writable)

Note that the io.seq package has been renamed "io.sequence" and "io.seq" now holds code for i/o of scala collections.
Fixes #99
Throwing a more descriptive error message when the reduce operation is called on an empty DList

Fixes #104
Remove unused code.
Don't mutate Configuration objects, clone them.

When creating new Configuration objects from an existing Configuration
object, be sure to use 'new' to ensure that a deep-copy occurs. If not,
depeding on the version of Hadoop, the new Configuration object will
simply mutate the old object.
Make changes to compile with CDH4.

- Change Hadoop dependencies:
  * "hadoop-client" % "2.0.0-mr1-cdh4.0.0"
  * "hadoop-core" % "2.0.0-mr1-cdh4.0.0"
- TaskAttemptContext - now an interface, not a class
- JobContext - now an interface, not a class
- filesStatus and globStatus throw an exception if path doesn't exist
- SequenceFile.Reader API change
- isDir deprecated in favor of isDirectory

Note that Avro I/O does not yet work.
fixed the keepFile argument usage in HadoopExamples
updated to specs2-1.12
fixed the simple groupByKey.groupBarrier.groupByKey example

When persisting traversables, we persist 1000 elements by 1000 elements.
The bug in the previous code was partially related to iterating a first time to get the size of the iterator,
then to iterate a second time to access the elements (when the iterator is actually consumed).

The code has been refactored so that one implementation covers Traversable, Maps and Arrays
Fixes issue #117. Fixed the reference counting of BridgeStore usages during the execution

The fix consists in creating a proper equals method on a BridgeStore to get the map holding the references count right.
Not having this count right meant that intermediary output files were deleted while they were still useful for some jobs.

Refactorings:

 - created a CommandLineScoobiUserArgs trait to control Scoobi args from the command line
 - created a CommandLineHadoopLogFactory trait to control the logs in any Specification
made the SecondarySortSpec example more robust
Simplify the build process
Simplified the SimpleJobs trait

it is possible to call "run" on DLists or DObjects. Also, fromInput returns a DList directly.
added a missing method definition for tests: fromKeyValues

to create a DList from a list of "key,value"
Fixed issue #113: taking the minimum and the maximum of a list

The issue was in the Persister class were the relationship between DComp nodes and their optimised version was not properly tracked.
More specifically, a DComp nodes were associated to its sinks and sinks to their optimised nodes. However in the case of materialised values
there were no sinks so when looking for the result for a particular DComp, we ended up getting the result for another one.

This whole issue indicates that we should find a better way to track the DComp <-> optimised nodes relationship.