Merge pull request #1 from FreekDB/master

Fixed ReportReaderTest
Merge pull request #2 from FreekDB/master

Getting ChartUnitTest class working again (with some refactoring)
Merge pull request #3 from FreekDB/master

Moved ChartUnit and ChartUnitTest classes from input to gui package
Fixed import of ChartUnit
Declared progressLogMonitor as private global
Added explanation about runningMSname
Added comments to AboutFrame.java, ChartUnit.java, DetailsFrame.java.
Replaced tabs by 4 spaces in AboutFrame.java, ChartUnit.java,
DetailsFrame.java.
Removed following classes corresponding to version 1 GUI (not in use
anymore) - ViewerPanel.java, MainTable.java, MainTableModel.java.
Removed ImageRenderer.java corresponding to version 1 GUI (not in use
anymore).
Removed MainSelectionListener corresponding to version 1 GUI (not in use
anymore)
Added comments in various classes.
Replaced tabs with 4 spaces in various classes.
Moved DataEntryForm.java from input package to gui package. 
Updated corresponding references.
Added/updated documentation for several functions in corresponding
classes. 
Removed unnecessary System.out statements.
Removed unused constructor from ReportUnit.java
Removed code related to setting preferred server. 
Since QC Pipeline does not depend on Apache webserver, the preferred
server setting is not required.
Removed unit tests corresponding to version 1 GUI.
Updated remaining 12 unit tests.
Updated user and installation manual.
Added comments, processing suggestions from the Eclipse toolkit for code
readability
Removed ProteomicsQCReportViewer.jar
Minor changes in comments 
Minor changes following suggestions from Eclipse
Removed doc folder from ProteomicsQCReportViewer
Generated and updated JavaDoc for ProteomicsQCReportViewer
Create README.md
Update README.md