Also cleared some warnings. Re #1416

more doxygen warning hunting

Added new class MaskedProperty to mask some of the properties of ICat algorithms
Added ICat download directory to Build/Tests/Mantid.Properties file

Add a curve fitting page to the MantidPlot settings dialog to allow setting the AutoBackground property. Also fixed a minor issue in the Config service saveConfig that was overly zealous with adding new line endings to the saved file. Re #1310

Fix for problems with saving property files that contain line continuation characters. Also added a test for this. Re #1248.

Fix for Windows when ConfigService saving causes a crash if it encounters a blank line in the original file. Re #1248

Allow property values within the ConfigService to be changed at run time. Added a function to save the current configuration to a file. Re #1248

Re-jig the ConfigService so that the logging doesn't start up until after the Mantid.user.properties file has been dealt with. Re #1161.

Downgrade some of the logging messages in the ConfigService - they weren't necessarily errors and could be confusing. Re #1161.

Update SANS script and interface to include options to specify the range over which the transmission curve should be fitted. Re #1153.
Minor update to ConfigService to correctly handle non-existant directories in the properties file. Re #1152

Improved the handling of scripts paths in the ConfigService so that there are two separate keys for the Python scripts: those required by Mantid and those specified by users.
Updated SANS interface so that it better handles being unable to find the reduction script. Re #1152 

Change DiffractionFocussing2 to use rebin instead of rebinNonDispersive in the same way as Q1D. Tests show that it makes no difference to the result (well < 10^-11 anyway). Re #438.

handles this for algorithm file properties. The algorithms don't use this yet. Also added
ignore properties for the generated object files of the new Geometry directories. Re #767

The script to find badly performing detectors is complete, including examination of the background of experimental runs.  There's also a custom dialog box for entering parameters to the script. refs #769 closes #602

In the Matlab API fixed a problem with compilation against a new version of Matlab and finding property files.  Improvements to the documentation of some diagnostic routines fixes #590

Loggers should not leak now and can be disabled by calling setEnabledfalse)

Outputting files now differs under Windows and Linux. Linux now uses a directory under the user's home directory, $HOME/.mantid, to store things such as mantidsimple, logs, managed workspace files. This is basically so that the 
installation via the RPM can work properly. Windows behaviour should be unchanged. Re #587  

Log the offending statement and then ignores the property. Fixes #553.

Changed FindPeaks algorithms to use WorkspaceFactory to create their TableWorkspace properties (and not to do it in the constructor). Removed statics from ConfigService. Re #470.

Mantid.user.properties is now written by mantid if it cannot be found - so there is no need to deliver this in the installer.
Also logging levels set higher for files to alleviate speed problem on encrypted hard drives.

missed a file

Changes to Properties files

Mantid now tries to load TWO properties files
Mantid.Properties as before
and now a Mantid.user.properties

Any entries in the user.properties file overides those on the main file.  The intention is that on reinstalls we will not overwrite the user file, but are free to replace the original .properties file to add new keys etc.

IMPORTANT:
The release properties files are now in the Properties subdirectory, the ones in the release directory have been removed.

The Python API now adds both the current directory and the scripts directory to its search path. There is a new property in Mantid.properties that indicates the location of the scripts directory. The default is set to the path 
for the installed layout on Windows machines. Re #506

Temporary fix for the fact that we aren't dealing with unphysical bins correctly when converting units to DeltaE. Am now setting the boundaries in this case to +/-DBL_MAX, which should at least mean that Rebin can be run on the output. Re #499.

Changed handling of working directory so that if we are running through Python then the initial working directory is that set by Python. Closes #434. 

Altered ConfigService so that relative path names are converted to absolute ones. Note that the original value is not actually altered but the call for a key is intercepted and a locally stored value is returned. Re #404

New classes added: SignalChannel to Mantid and MantidLog to QtiPlot. 

FrameworkManager's initialization is moved to the constructor.

FilterChannel added to the logging to allow filtering of individual logging channels based on a priority level.

This allows you to send debug messages to the log while only sending information level messages and above to the console.