Refs #9447.  Removed unused property PeakHeightTolerance.

And the variables related to this property.
Re #9588 Minimal changes. This is probably be deprecated in the future
Refs #9568. PlotAsymmetryByLogValue
Refs #9568. ConvertAxisByFormula
Refs #9568. MuonGroupDetectors
Refs #9568. RenameWorkspaces
Refs #9568. Removed clean up sections

Workspaces should be cleaned up automatically now
Refs #9568. AsymmetryCalc
Refs #9568. RemoveExpDecay
Refs #9568. ApplyDeadTimeCorr
Refs #9568. CalculateFlatBackground
Refs #9568. AlphaCalc
Refs #9568. SaveDetectorsGrouping
Refs #9568. Create workspaces instead of loading files
Update documentation & add usage for UpdateScriptRepository

Refs #9574
Implement usage for NormaliseByPeakArea

Also clarify a property description
Refs #9574
Remove unrequired testcleanup sections

Refs #9574
Add hidden toctree to index.rst

This squashes all of the warnings about most documents not in a toctree.
Refs #9574
Add usage examples to DeleteWorkspace.

Refs #9574
Add reference to t0 parameter in NormaliseByPeakArea.

Refs #9574