(Both old and new style commands)

After a run is aborted, all previous entries in the "running" log must
be changed to false.

re #17924

The extractToEOL Kernal namespace method has been moved to the Kernal::Strings namespace where it makes more sense to be alongside other string and ascii stream methods

The change was made because of the difficulties i was having with the binary files stream provided by the FileDescriptor.

This is required as Qt4 is not completely C++11 compliant.  I think that these will no longer be needed when we move to Qt5.
Should only be required for files up to and including API.
Refs #7284

Refs #9059

Introduced a helper class to perform this stuff and tidy up a lot
of copied code.

Ensures that clone can return the concrete type.

Refs #3157 Sort our System.h. It was becoming a dumping ground. It should only be touched when absolutely necessary as it affects every file in Mantid. Also combined this with Refs #2345 to sort out DLLExport/DLLImport usage. It's done for Kernel, Geometry and API but stuff in the plugins could do with updating as well.

Rename Framework code directory to just that. Also delete Main and VS & Eclipse project file. Re #1881.

Move the Instrument and Instrument interface classes down to Geometry. The new raytracing framework needs instrument access and it should all be in geometry. Also, given that everything else was defined in geometry it seems to make more sense to have it all in one place. Re #1212