re #9734 3rd pass of the links

Code/Mantid/docs/source/algorithms/AbortRemoteJob-v1.rst

@@ -12,6 +12,6 @@ Description
 Abort a job that has been submitted to a remote compute resource.
 
 For more details, see the `remote job submission API
-docs <Remote_Job_Submission_API>`__.
+docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
 
 .. categories::

Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst

@@ -51,7 +51,7 @@ This algorithm assumes that the (parallel) beam illuminates the entire
 sample **unless** a 'gauge volume' has been defined using the
 :ref:`algm-DefineGaugeVolume` algorithm (or by otherwise
 adding a valid XML string `defining a
-shape <HowToDefineGeometricShape>`__ to a `Run <Run>`__ property called
+shape <http://www.mantidproject.org/HowToDefineGeometricShape>`_ to a `Run <http://www.mantidproject.org/Run>`_ property called
 "GaugeVolume"). In this latter case only scattering within this volume
 (and the sample) is integrated, because this is all the detector can
 'see'. The full sample is still used for the neutron paths. (**N.B.** If
@@ -64,7 +64,7 @@ Restrictions on the input workspace
 ###################################
 
 The input workspace must have units of wavelength. The
-`instrument <instrument>`__ associated with the workspace must be fully
+`instrument <http://www.mantidproject.org/instrument>`_ associated with the workspace must be fully
 defined because detector, source & sample position are needed.
 
 .. |AbsorptionFlow.png| image:: /images/AbsorptionFlow.png

Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst

@@ -22,10 +22,10 @@ anyway, then you probably shouldn't be using this algorithm!).
 Restrictions on the input workspace
 ###################################
 
-For `EventWorkspaces <EventWorkspace>`__, there are no restrictions on
+For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, there are no restrictions on
 the input workspaces if ValidateInputs=false.
 
-For `Workspace2Ds <Workspace2D>`__, the number of bins must be the same
+For `Workspace2Ds <http://www.mantidproject.org/Workspace2D>`_, the number of bins must be the same
 in both inputs.
 
 If ValidateInputs is selected, then the input workspaces must also:

Code/Mantid/docs/source/algorithms/ApplyCalibration-v1.rst

@@ -15,7 +15,7 @@ updated as absolute positions and so this update can be repeated.
 The PositionTable must have columns *Detector ID* and *Detector
 Position*. The entries of the *Detector ID* column are integer referring
 to the Detector ID and the enties of the *Detector Position* are
-`V3Ds <V3D>`__ referring to the position of the detector whose ID is in
+`V3Ds <http://www.mantidproject.org/V3D>`_ referring to the position of the detector whose ID is in
 same row.
 
 .. categories::

Code/Mantid/docs/source/algorithms/Authenticate-v1.rst

@@ -13,6 +13,6 @@ Authenticate to the remote compute resource. This must be executed
 before calling any other remote algorithms.
 
 For more details, see the `remote job submission API
-docs <Remote_Job_Submission_API>`__.
+docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
 
 .. categories::

Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst

@@ -12,7 +12,7 @@ Description
 Calculates the probability of a neutron being transmitted through the
 sample using detected counts from two monitors, one in front and one
 behind the sample. A data workspace can be corrected for transmission by
-`dividing <Divide>`__ by the output of this algorithm.
+`dividing <http://www.mantidproject.org/Divide>`_ by the output of this algorithm.
 
 | Because the detection efficiency of the monitors can be different the
 transmission calculation is done using two runs, one run with the sample
@@ -36,7 +36,7 @@ the data to be corrected.
 ChildAlgorithms used
 ####################
 
-Uses the algorithm `linear <linear>`__ to fit to the calculated
+Uses the algorithm `linear <http://www.mantidproject.org/linear>`_ to fit to the calculated
 transmission fraction.
 
 .. categories::

Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst

@@ -17,7 +17,7 @@ also optionally check the axes (this includes the units), the
 spectra-detector map, the instrument (the name and parameter map) and
 any bin masking.
 
-In the case of `EventWorkspaces <EventWorkspace>`__, they are checked to
+In the case of `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, they are checked to
 hold identical event lists. Comparisons between an EventList and a
 Workspace2D always fail.
 

Code/Mantid/docs/source/algorithms/ClearUB-v1.rst

@@ -10,7 +10,7 @@ Description
 -----------
 
 Clears the OrientedLattice of each ExperimentInfo attached to the intput
-`Workspace <Workspace>`__. Works with both single ExperimentInfos and
+`Workspace <http://www.mantidproject.org/Workspace>`_. Works with both single ExperimentInfos and
 MultipleExperimentInfo instances.
 
 .. categories::

Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst

@@ -10,8 +10,8 @@ Description
 -----------
 
 This algorithm will clones an existing
-`MDEventWorkspace <MDEventWorkspace>`__ or
-`MDHistoWorkspace <MDHistoWorkspace>`__ into a new one.
+`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ into a new one.
 
 If the InputWorkspace is a file-backed MDEventWorkspace, then the
 algorithm will copy the original file into a new one with the suffix

Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst

@@ -11,9 +11,9 @@ Description
 
 This algorithm performs a deep copy of all of the information in the
 workspace. It maintains events if the input is an
-`EventWorkspace <EventWorkspace>`__. It will call CloneMDWorkspace for a
-`MDEventWorkspace <MDEventWorkspace>`__ or a
-`MDHistoWorkspace <MDHistoWorkspace>`__. It can also clone a
-`PeaksWorkspace <PeaksWorkspace>`__.
+`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. It will call CloneMDWorkspace for a
+`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or a
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. It can also clone a
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_.
 
 .. categories::

Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst

@@ -9,14 +9,14 @@
 Description
 -----------
 
-Compare two MDWorkspaces (`MDEventWorkspace <MDEventWorkspace>`__ or
-`MDHistoWorkspace <MDHistoWorkspace>`__) to see if they are the same.
+Compare two MDWorkspaces (`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_) to see if they are the same.
 This is mostly meant for testing/debugging use by developers.
 
 **What is compared**: The dimensions, as well as the signal and error
 for each bin of each workspace will be compared.
 
-**`MDEventWorkspace <MDEventWorkspace>`__**: the events in each box will
+**`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_**: the events in each box will
 be compared if the *CheckEvents* option is checked. The events would
 need to be in the same order to match.
 

Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst

@@ -12,7 +12,7 @@ Description
 Used Subalgorithms
 ------------------
 
-The algorithm uses `Unit Factory <Unit_Factory>`__ and existing unit
+The algorithm uses `Unit Factory <http://www.mantidproject.org/Unit_Factory>`_ and existing unit
 conversion procedures from input Workspace Units to the Units, necessary
 for transformation into correspondent MD Event workspace. It also uses
 :ref:`algm-PreprocessDetectorsToMD` algorithm to help
@@ -29,7 +29,7 @@ Notes
 -----
 
 #. For elastic analysis (:math:`dEAnalysisMode=Elastic`) the target
-   `unit <units>`__ is momentum :math:`k`.
+   `unit <http://www.mantidproject.org/units>`_ is momentum :math:`k`.
 #. For no analysis (CopyToMD) mode, the units remain the one, previously
    defined along the workspace's axes.
 #. When units of input Matrix 2D workspace (Histogram workspace) are not
@@ -45,7 +45,7 @@ Notes
    when one tries to process the results of inelastic scattering
    experiment in elastic mode. This message is generated by units
    conversion routine, which finds out that one of the workspace axis is
-   in `unit <units>`__ of DeltaE. These units can not be directly
+   in `unit <http://www.mantidproject.org/units>`_ of DeltaE. These units can not be directly
    converted into momentum or energy, necessary for elastic mode. Select
    Direct or Indirect mode and integrate over whole energy transfer
    range to obtain MD workspace, which would correspond to an Elastic

Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst

@@ -11,11 +11,11 @@ Description
 
 Use data from the supplied file, written in the RKH format, to correct
 the input data. The operations allowed for the correction are
-`multiply <multiply>`__ and `divide <divide>`__.
+`multiply <http://www.mantidproject.org/multiply>`_ and `divide <http://www.mantidproject.org/divide>`_.
 
 Allowed correction files may contain one spectrum with many bins or many
 spectra each with one bin. If the are many bins then the
-FirstColumnValue must match the `units <Unit_Factory>`__ of the
+FirstColumnValue must match the `units <http://www.mantidproject.org/Unit_Factory>`_ of the
 (X-values on the) workspace on the InputWorkspace. When there are many
 spectra (e.g. flood correction files) FirstColumnValue must be set to
 "SpectrumNumber" and the number of spectra in the file and workspace

Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst

@@ -13,12 +13,12 @@ Description
    :alt: Instrument Tree
 
    Instrument Tree
-Create a `calibration file <CalFile>`__ for diffraction focusing based
+Create a `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing based
 on list of names of the instrument tree.
 
 If a new file name is specified then offsets in the file are all sets to
 zero and all detectors are selected. If a valid calibration file already
-exists at the location specified by the `GroupingFileName <CalFile>`__
+exists at the location specified by the `GroupingFileName <http://www.mantidproject.org/CalFile>`_
 then any existing offsets and selection values will be maintained and
 only the grouping values changed.
 

Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst

@@ -13,7 +13,7 @@ Description
    :alt: Instrument Tree
 
    Instrument Tree
-Create a dummy `calibration file <CalFile>`__ for diffraction focusing
+Create a dummy `calibration file <http://www.mantidproject.org/CalFile>`_ for diffraction focusing
 with one group.
 
 Offsets in the file are all sets to zero and all detectors are selected.

Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst

@@ -9,7 +9,7 @@
 Description
 -----------
 
-A `GroupingWorkspace <GroupingWorkspace>`__ is a simple workspace with
+A `GroupingWorkspace <http://www.mantidproject.org/GroupingWorkspace>`_ is a simple workspace with
 one value per detector pixel; this value corresponds to the group number
 that will be used when focussing or summing another workspace.
 

Code/Mantid/docs/source/algorithms/CreatePeaksWorkspace-v1.rst

@@ -9,12 +9,12 @@
 Description
 -----------
 
-Create an empty `PeaksWorkspace <PeaksWorkspace>`__. Use
+Create an empty `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. Use
 :ref:`algm-LoadIsawPeaks` or :ref:`algm-FindPeaksMD` to
 create a peaks workspace with peaks.
 
 This workspace can serve as a starting point for modifying the
-`PeaksWorkspace <PeaksWorkspace>`__, using the GUI or python scripting,
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_, using the GUI or python scripting,
 for example.
 
 Usage

Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst

@@ -11,7 +11,7 @@ Description
 
 Creates a shape object that defines the sample and sets the sample for
 the given workspace. Shapes are defined using XML descriptions that can
-be found `here <HowToDefineGeometricShape>`__.
+be found `here <http://www.mantidproject.org/HowToDefineGeometricShape>`_.
 
 Usage
 -----

Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst

@@ -10,13 +10,13 @@ Description
 -----------
 
 The probability of neutron detection by each detector in the
-`workspace <workspace>`__ is calculated from the neutrons' kinetic
+`workspace <http://www.mantidproject.org/workspace>`_ is calculated from the neutrons' kinetic
 energy, angle between their path and the detector axis, detector gas
 pressure, radius and wall thickness. The detectors must be cylindrical
 and their :sup:`3`\ He partial pressure, wall thickness and radius
 stored in the input workspace, the first in atmospheres and the last two
 in metres. That workspace then needs to be converted so that its
-X-values are in `units <Unit_Factory>`__ of energy transfer, e.g. using
+X-values are in `units <http://www.mantidproject.org/Unit_Factory>`_ of energy transfer, e.g. using
 the :ref:`algm-ConvertUnits` algorithm.
 
 To estimate the true number of neutrons that entered the detector the
@@ -35,7 +35,7 @@ detector and energy bin). They're calculated, in angstrom\ :sup:`-1`, as
 where :math:`E_i` and :math:`\Delta E` are energies in meV, the inital
 neutron kinetic energy and the energy lost to the sample respectively.
 
-Note: it is not possible to use this `algorithm <algorithm>`__ to
+Note: it is not possible to use this `algorithm <http://www.mantidproject.org/algorithm>`_ to
 correct for the detector efficiency alone. One solution to this is to
 divide the output algorithm by :math:`k_i/k_f` calculated as above.
 

Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst

@@ -22,7 +22,7 @@ following:
 #. All histograms are read and rebinned to the new grid for their group.
 #. A new workspace with N histograms is created.
 
-Within the `CalFile <CalFile>`__ any detectors with the 'select' flag
+Within the `CalFile <http://www.mantidproject.org/CalFile>`_ any detectors with the 'select' flag
 can be set to zero or with a group number of 0 or -ve groups are not
 included in the analysis.
 
@@ -30,17 +30,17 @@ Since the new X boundaries depend on the group and not the entire
 workspace, this focusing algorithm does not create overestimated X
 ranges for multi-group instruments. However it is important to remember
 that this means that this algorithm outputs a `ragged
-workspace <Ragged_Workspace>`__. Some 2D and 3D plots will not display
+workspace <http://www.mantidproject.org/Ragged_Workspace>`_. Some 2D and 3D plots will not display
 the data correctly.
 
 The DiffractionFocussing algorithm uses GroupDetectors algorithm to
 combine data from several spectra according to GroupingFileName file
-which is a `CalFile <CalFile>`__.
+which is a `CalFile <http://www.mantidproject.org/CalFile>`_.
 
 For EventWorkspaces
 ###################
 
-The algorithm can be used with an `EventWorkspace <EventWorkspace>`__
+The algorithm can be used with an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_
 input, and will create an EventWorkspace output if a different workspace
 is specified.