diff --git a/Code/Mantid/docs/source/algorithms/AbortRemoteJob-v1.rst b/Code/Mantid/docs/source/algorithms/AbortRemoteJob-v1.rst
index 093496d0937d52675db7fb7e9b764e2185d72050..b0a08b346b6681053d46f231d6c6334ca180a207 100644
--- a/Code/Mantid/docs/source/algorithms/AbortRemoteJob-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst b/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst
index cb1a9924296915cb9657085f6e8b846ddc54728e..a2124ea1f6b83c5f15df6a2d44510db45cd0eba6 100644
--- a/Code/Mantid/docs/source/algorithms/AbsorptionCorrection-v1.rst
+++ b/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
diff --git a/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst b/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
index 7c75def3e47433d24eacd7aff674f2d704ca3bf5..684c742aee489b34f832aa3ee3fd31e839d57267 100644
--- a/Code/Mantid/docs/source/algorithms/AppendSpectra-v1.rst
+++ b/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:
diff --git a/Code/Mantid/docs/source/algorithms/ApplyCalibration-v1.rst b/Code/Mantid/docs/source/algorithms/ApplyCalibration-v1.rst
index 9a7fd3a15e7f56ffe85990c446c85093aafe6954..ae20e21840163aafdbd93f3f00889dae8e281a4c 100644
--- a/Code/Mantid/docs/source/algorithms/ApplyCalibration-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/Authenticate-v1.rst b/Code/Mantid/docs/source/algorithms/Authenticate-v1.rst
index a010f4b95f0b130e04a7e5d06907c14073e2e55e..b90a5bcc7b1fcd520afc3bf8e171b8410aa69db3 100644
--- a/Code/Mantid/docs/source/algorithms/Authenticate-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst b/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst
index e3a40212b0c451ef415df8f33b4610e170a7e47a..0d52ebaa304b41238243bc93f4ac13fac83d515e 100644
--- a/Code/Mantid/docs/source/algorithms/CalculateTransmission-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst b/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst
index de2b445787b558d46cae5dec569ba329fc3525b7..8aa5b8d7868a488afcd0cb9bc5ad54bee7104e39 100644
--- a/Code/Mantid/docs/source/algorithms/CheckWorkspacesMatch-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst b/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
index ec6ac6f10e0339e94c846f672db1e6b7c04861d2..1dfc639a69ac98d746804b549e27604e2ed77c6d 100644
--- a/Code/Mantid/docs/source/algorithms/ClearUB-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
index 0bdffabd6606f34139c352e17a4d5428004af493..a94d18b7491deb30a621d56af94138924d7da78d 100644
--- a/Code/Mantid/docs/source/algorithms/CloneMDWorkspace-v1.rst
+++ b/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
diff --git a/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
index 8751a4e2008e5358723ed3e3a0387f469b35a16e..43f797bbd36d694490335f1238db7e5eb3c23b50 100644
--- a/Code/Mantid/docs/source/algorithms/CloneWorkspace-v1.rst
+++ b/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::
diff --git a/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst b/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst
index 71767070b6ec9f89818c83459bdb23b2dbda825c..6a2393ec4affad9142076dc2db64e0a68ff03a40 100644
--- a/Code/Mantid/docs/source/algorithms/CompareMDWorkspaces-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst b/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
index f4588a561cf80c299b5de9a7d47e0ad0c0e98202..ba7024eaf863421c09ba1ee2433108467eae02f9 100644
--- a/Code/Mantid/docs/source/algorithms/ConvertToMD-v1.rst
+++ b/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
diff --git a/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst b/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
index a8eee956a0e60ec76ae19a16570be0015afffdbf..502fd37acb0938177a3f376ad0777a2d420ca736 100644
--- a/Code/Mantid/docs/source/algorithms/CorrectToFile-v1.rst
+++ b/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
diff --git a/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst b/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst
index 593936fa0ed84aa804fa9582315d602252c87803..493884bf9d1140df794f5a8faf37b2fcf020ccc4 100644
--- a/Code/Mantid/docs/source/algorithms/CreateCalFileByNames-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst b/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst
index 5d346bcb070e03753e95f980f8024c9c42473a6b..5f4d653b7bb2d8856e2929311f8883b7aeb67844 100644
--- a/Code/Mantid/docs/source/algorithms/CreateDummyCalFile-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst
index c2c2fe864e195b47742badeb1a423bd26a995622..a76d2016665d09af16435d5fa100dadd9aaa0aae 100644
--- a/Code/Mantid/docs/source/algorithms/CreateGroupingWorkspace-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/CreatePeaksWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/CreatePeaksWorkspace-v1.rst
index 6a12e4658094fa027eb352b58f5d75bc95dfe2fe..9749bacfed0fa26da72a6082a6bf792e7b82fbb3 100644
--- a/Code/Mantid/docs/source/algorithms/CreatePeaksWorkspace-v1.rst
+++ b/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
diff --git a/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst b/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst
index bd12300dddd6bf73f59fa2601582350528912ce3..50223df96eaa77dc3b1f359a6660217e12d9fa53 100644
--- a/Code/Mantid/docs/source/algorithms/CreateSampleShape-v1.rst
+++ b/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
-----
diff --git a/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst b/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst
index cdc14f02fc2af6a8a9f2d5cf430f78c94d0e4086..34fbdfeeb2d3187114b28df808a8653e2ab915c9 100644
--- a/Code/Mantid/docs/source/algorithms/DetectorEfficiencyCor-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst b/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst
index 21000ca8236195f421babeb5093db6e0e39b7b5d..6ffd784802d3e6e8fd8ccc9e94b605283e396f30 100644
--- a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v1.rst
+++ b/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.
diff --git a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v2.rst b/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v2.rst
index ab00b693af9bc9eabb292f0ee44e778f74fb545c..8d7efb3281f39bb145e5a64e6096ab5e0e9d29a2 100644
--- a/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/DiffractionFocussing-v2.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.
diff --git a/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst b/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
index 239425dd531987842bd57d607829ae0c0f08204d..8b796bb3254bf745c460ae8868da8c034ad6d26b 100644
--- a/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DivideMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Divide two `MDHistoWorkspace <MDHistoWorkspace>`__'s or a
+Divide two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
MDHistoWorkspace and a scalar.
The error of :math:`f = a / b` is propagated with
@@ -27,7 +27,7 @@ The error of :math:`f = a / b` is propagated with
- This is not allowed.
-- **`MDEventWorkspace <MDEventWorkspace>`__'s**
+- **`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_'s**
- This operation is not supported, as it is not clear what its
meaning would be.
diff --git a/Code/Mantid/docs/source/algorithms/DownloadRemoteFile-v1.rst b/Code/Mantid/docs/source/algorithms/DownloadRemoteFile-v1.rst
index 225acbacec0c54e49a95326009f7d8c0df596e88..024e71402e81b8d283a5ba5cdbcefdf2a206517c 100644
--- a/Code/Mantid/docs/source/algorithms/DownloadRemoteFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/DownloadRemoteFile-v1.rst
@@ -12,6 +12,6 @@ Description
Download a file from 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::
diff --git a/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst b/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
index 4b99688fe99623f44cf16fb4423dbb9928b2ff5e..d58e7378cfa0d4b524864c693fd37909e5c92da2 100644
--- a/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ExtractSingleSpectrum-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Extracts a single spectrum from a `Workspace2D <Workspace2D>`__ and
+Extracts a single spectrum from a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ and
stores it in a new workspace.
Usage
diff --git a/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst b/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
index 1069c2625902dbb72375a8788caea81116e519dc..b8152747da152098e0adffda48514dfd29138ec4 100644
--- a/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FilterEvents-v1.rst
@@ -10,10 +10,10 @@ Description
-----------
This algorithm filters events from an
-`EventWorkspace <EventWorkspace>`__ to one or multiple
-`EventWorkspaces <EventWorkspace>`__ according to an input
-`SplittersWorkspace <SplittersWorkspace>`__ containing a series of
-splitters (i.e., `SplittingIntervals <SplittingInterval>`__).
+`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_ to one or multiple
+`EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_ according to an input
+`SplittersWorkspace <http://www.mantidproject.org/SplittersWorkspace>`_ containing a series of
+splitters (i.e., `SplittingIntervals <http://www.mantidproject.org/SplittingInterval>`_).
Output
######
@@ -63,7 +63,7 @@ Therefore, FilterByLogValue is not suitable for fast log filtering.
Comparing with other event filtering algorithms
###############################################
-Wiki page `EventFiltering <EventFiltering>`__ has a detailed
+Wiki page `EventFiltering <http://www.mantidproject.org/EventFiltering>`_ has a detailed
introduction on event filtering in MantidPlot.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst b/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
index ce91f92202a17b660722c8dcfda131a1c6ae6581..f77b7d42fb04092f3162e1b9527be53208262cb0 100644
--- a/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/FilterEventsByLogValuePreNexus-v2.rst
@@ -10,10 +10,10 @@ Description
-----------
The LoadEventPreNeXus algorithm stores data from the pre-nexus neutron
-event data file in an `EventWorkspace <EventWorkspace>`__. The default
+event data file in an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default
histogram bin boundaries consist of a single bin able to hold all events
-(in all pixels), and will have their `units <units>`__ set to
-time-of-flight. Since it is an `EventWorkspace <EventWorkspace>`__, it
+(in all pixels), and will have their `units <http://www.mantidproject.org/units>`_ set to
+time-of-flight. Since it is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, it
can be rebinned to finer bins with no loss of data.
Optional properties
diff --git a/Code/Mantid/docs/source/algorithms/FindClusterFaces-v1.rst b/Code/Mantid/docs/source/algorithms/FindClusterFaces-v1.rst
index a658287ab29ead057f61f1520049f17d59b33590..51028b3910ebdd5bb3ba45157445e27cc4fcd491 100644
--- a/Code/Mantid/docs/source/algorithms/FindClusterFaces-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FindClusterFaces-v1.rst
@@ -10,16 +10,16 @@ Description
-----------
Algorithm takes an image workspace (a.k.a
-`IMDHistoWorkspace <IMDHistoWorkspace>`__) and determines the faces of
+`IMDHistoWorkspace <http://www.mantidproject.org/IMDHistoWorkspace>`_) and determines the faces of
the clusters contained within the image. The image is expected to be a
labeled image workspace outputted from
:ref:`algm-IntegratePeaksUsingClusters`. The
-algorithm generates a `TableWorkspace <TableWorkspace>`__ as output,
+algorithm generates a `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ as output,
which contains all the cluster edge faces required to draw the outer
edge of all clusters within the workspace.
You may optionally provide a FilterWorkspace, which is a
-`PeaksWorkspace <PeaksWorkspace>`__. If provided, the Peak locations are
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. If provided, the Peak locations are
projected onto the InputWorkspace and the center locations are used to
restrict the output to only include the clusters that are the union
between the peak locations and the image clusters.
diff --git a/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst b/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
index 3b87b79f4ae21df8e3e0c9685b5b1393a2cb81b0..cb1dc9415defbc003a8de6ca30a4cf965dbedd70 100644
--- a/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FindPeaks-v1.rst
@@ -17,7 +17,7 @@ is then searched for patterns consistent with the presence of a peak.
The list of candidate peaks found is passed to a fitting routine and
those that are successfully fitted are kept and returned in the output
workspace (and logged at information level). The output
-`TableWorkspace <TableWorkspace>`__ contains the following columns,
+`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ contains the following columns,
which reflect the fact that the peak has been fitted to a Gaussian atop
a linear background: spectrum, centre, width, height,
backgroundintercept & backgroundslope.
diff --git a/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst b/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
index f30672b31504c41ec40a585db3545bf3a336bb36..0a22d1e068299d386cd41305a59ed58f20af7f8c 100644
--- a/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FindPeaksMD-v1.rst
@@ -10,8 +10,8 @@ Description
-----------
This algorithm is used to find single-crystal peaks in a
-multi-dimensional workspace (`MDEventWorkspace <MDEventWorkspace>`__ or
-`MDHistoWorkspace <MDHistoWorkspace>`__). It looks for high signal
+multi-dimensional workspace (`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ or
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_). It looks for high signal
density areas, and is based on an algorithm designed by Dennis Mikkelson
for ISAW.
@@ -34,14 +34,14 @@ The algorithm proceeds in this way:
- This is repeated until we find up to MaxPeaks peaks.
Each peak created is placed in the output
-`PeaksWorkspace <PeaksWorkspace>`__, which can be a new workspace or
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_, which can be a new workspace or
replace the old one.
-This algorithm works on a `MDHistoWorkspace <MDHistoWorkspace>`__
+This algorithm works on a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_
resulting from the :ref:`algm-BinMD` algorithm also. It works in the
same way, except that the center of each bin is used since the centroid
is not accessible. It may give better results on
-`Workspace2D <Workspace2D>`__'s that were converted to
-`MDWorkspaces <MDWorkspace>`__.
+`Workspace2D <http://www.mantidproject.org/Workspace2D>`_'s that were converted to
+`MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/Fit-v1.rst b/Code/Mantid/docs/source/algorithms/Fit-v1.rst
index 5d1787757f7d5d3441748545b38840f40d0f7bbc..51a86574f4e4f835d89f82cf722103774b24482f 100644
--- a/Code/Mantid/docs/source/algorithms/Fit-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Fit-v1.rst
@@ -13,7 +13,7 @@ Additional properties for a 1D function and a MatrixWorkspace
#############################################################
If Function defines a one-dimensional function and InputWorkspace is a
-`MatrixWorkspace <MatrixWorkspace>`__ the algorithm will have these
+`MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ the algorithm will have these
additional properties:
+------------------+-------------+-----------+-------------------------+---------------------------------------------------------------------+
@@ -31,10 +31,10 @@ Overview
This is a generic algorithm for fitting data in a Workspace with a
function. The workspace must have the type supported by the algorithm.
-Currently supported types are: `MatrixWorkspace <MatrixWorkspace>`__ for
-fitting with a `IFunction1D <IFunction1D>`__ and
-`IMDWorkspace <IMDWorkspace>`__ for fitting with
-`IFunctionMD <IFunctionMD>`__. After Function and InputWorkspace
+Currently supported types are: `MatrixWorkspace <http://www.mantidproject.org/MatrixWorkspace>`_ for
+fitting with a `IFunction1D <http://www.mantidproject.org/IFunction1D>`_ and
+`IMDWorkspace <http://www.mantidproject.org/IMDWorkspace>`_ for fitting with
+`IFunctionMD <http://www.mantidproject.org/IFunctionMD>`_. After Function and InputWorkspace
properties are set the algorithm may decide that it needs more
information from the caller to locate the fitting data. For example, if
a spectrum in a MatrixWorkspace is to be fit with a 1D function it will
@@ -151,7 +151,7 @@ Parameters can be constrained to be above a lower boundary and/or below
an upper boundary. If a constraint is violated a penalty to the fit is
applied which should result the parameters satisfying the constraint.
The penalty applied is described in more detail
-`here <FitConstraint>`__. Use Constraints property to set any
+`here <http://www.mantidproject.org/FitConstraint>`_. Use Constraints property to set any
constraints. In case of a simple function the parameter names are used
as variables in the constraint expressions. For example
@@ -184,9 +184,9 @@ Output
######
Setting the Output property defines the names of the two output
-workspaces. One of them is a `TableWorkspace <TableWorkspace>`__ with
+workspaces. One of them is a `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ with
the fitted parameter values. The other is a
-`Workspace2D <Workspace2D>`__ which compares the fit with the original
+`Workspace2D <http://www.mantidproject.org/Workspace2D>`_ which compares the fit with the original
data. It has three spectra. The first (index 0) contains the original
data, the second one the data simulated with the fitting function and
the third spectrum is the difference between the first two. For example,
diff --git a/Code/Mantid/docs/source/algorithms/FitPeak-v1.rst b/Code/Mantid/docs/source/algorithms/FitPeak-v1.rst
index 45f57b679ee28b42f0ed9cffd0f393656d61c9a5..d3847ba8e9a6de9548afcb1b85a8b5d067c3c4a2 100644
--- a/Code/Mantid/docs/source/algorithms/FitPeak-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FitPeak-v1.rst
@@ -12,7 +12,7 @@ Description
This algorithm is used to fit a single peak with some checking mechanism
to ensure its fitting result is physical.
-The output `TableWorkspace <TableWorkspace>`__ contains the following
+The output `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ contains the following
columns...
Peak profile
diff --git a/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
index 75bcc56352d2046aea736b6f9fca04b56e21ba16..46f9764380f771838cd66b47d6857477d9c1040d 100644
--- a/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/FlatPlateAbsorption-v1.rst
@@ -27,7 +27,7 @@ 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.
diff --git a/Code/Mantid/docs/source/algorithms/GeneratePeaks-v1.rst b/Code/Mantid/docs/source/algorithms/GeneratePeaks-v1.rst
index a2ae001cd752921d159549b2fae4822bf1a992d8..0d761120123bc96fe41f8cd49ac7ad361af26ec6 100644
--- a/Code/Mantid/docs/source/algorithms/GeneratePeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/GeneratePeaks-v1.rst
@@ -10,13 +10,13 @@ Description
-----------
Generate a workspace by summing over the peak functions. The peaks'
-parameters are given in a `TableWorkspace <TableWorkspace>`__.
+parameters are given in a `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_.
Peak Parameters
###############
Peak parameters must have the following parameters, which are case
-sensitive in input `TableWorkspace <TableWorkspace>`__
+sensitive in input `TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_
| ``1. spectrum``
| ``2. centre``
diff --git a/Code/Mantid/docs/source/algorithms/IntegratePeakTimeSlices-v1.rst b/Code/Mantid/docs/source/algorithms/IntegratePeakTimeSlices-v1.rst
index a18b641125f736126ef34850a2e1a7363cf28c61..cc164445b109547f01135ad171db86cd1e71358c 100644
--- a/Code/Mantid/docs/source/algorithms/IntegratePeakTimeSlices-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegratePeakTimeSlices-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm fits a bivariate normal distribution( plus background) to
the data on each time slice. The Fit program uses
-`BivariateNormal <BivariateNormal>`__ for the Fit Function.
+`BivariateNormal <http://www.mantidproject.org/BivariateNormal>`_ for the Fit Function.
The area used for the fitting is calculated based on the dQ parameter. A
good value for dQ is 1/largest unit cell length. This parameter dictates
diff --git a/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst b/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
index cc16432a58975c4ac84c8898c848bb173aa73cc6..74aa957cdc8eed319c2f155686925fbccab93314 100644
--- a/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegratePeaksHybrid-v1.rst
@@ -13,10 +13,10 @@ This is a hybrid between :ref:`algm-IntegratePeaksMD` and :ref:`algm-IntegratePe
The NumberOfBins and BackgroundOuterRadius are global to all Peaks. The actual background threshold is calculated independently for each peak based on NumberOfBins, BackgroundOuterRadius and the signal values in that region. This algorithm is in general faster than :ref:`algm-IntegratePeaksUsingClusters` and has a better ability to distinguish peaks from the background because each peak is treated independently.
Integrates arbitary shaped single crystal peaks defined on an
-`MDHistoWorkspace <MDHistoWorkspace>`__ using connected component
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ using connected component
analysis to determine regions of interest around each peak of the
-`PeaksWorkspace <PeaksWorkspace>`__. The output is an integrated
-`PeaksWorkspace <PeaksWorkspace>`__ as well as a group of images `WorkspaceGroup <WorkspaceGroup>`__ of `MDWorkspaces <MDWorkspace>`__ containing the
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. The output is an integrated
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ as well as a group of images `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ of `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ containing the
labels assigned to each cluster for diagnostic and visualisation
purposes.
@@ -48,10 +48,10 @@ the detector/TOF space is no longer accessible.
No Cluster Corresponding to Peak
################################
-This is because the input `PeaksWorkspace <PeaksWorkspace>`__ has peaks
+This is because the input `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ has peaks
that do not align with peaks in the image. The error could either be on
the side of the input PeaksWorkspace (spurious peaks), or of the
-`MDHistoWorkspace <MDHistoWorkspace>`__ generated as part of processing.
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ generated as part of processing.
One thing to verify is that the combination of Threshold and
Normalization input parameters are not so low that they are treating
genuine peaks in the image as background.
diff --git a/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst b/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
index 54100d3cd32e549b590ca2af51550a02ccb9b3f9..f4ae300277f71eb3879cf8e6b259f7bf5b772e8c 100644
--- a/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/IntegratePeaksUsingClusters-v1.rst
@@ -10,10 +10,10 @@ Description
-----------
Integrates arbitary shaped single crystal peaks defined on an
-`MDHistoWorkspace <MDHistoWorkspace>`__ using connected component
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ using connected component
analysis to determine regions of interest around each peak of the
-`PeaksWorkspace <PeaksWorkspace>`__. The output is an integrated
-`PeaksWorkspace <PeaksWorkspace>`__ as well as an image containing the
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_. The output is an integrated
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ as well as an image containing the
labels assigned to each cluster for diagnostic and visualisation
purposes.
@@ -69,10 +69,10 @@ the detector/TOF space is no longer accessible.
No Cluster Corresponding to Peak
################################
-This is because the input `PeaksWorkspace <PeaksWorkspace>`__ has peaks
+This is because the input `PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ has peaks
that do not align with peaks in the image. The error could either be on
the side of the input PeaksWorkspace (spurious peaks), or of the
-`MDHistoWorkspace <MDHistoWorkspace>`__ generated as part of processing.
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ generated as part of processing.
One thing to verify is that the combination of Threshold and
Normalization input parameters are not so low that they are treating
genuine peaks in the image as background.
diff --git a/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst b/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
index 16ed08ba4f12d20af2ba97cdf5ac272bafe21562..e37b44bbb6f0120997a10b26c94fd4649db91134 100644
--- a/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadAscii-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
The LoadAscii algorithm reads in spectra data from a text file and
-stores it in a `Workspace2D <Workspace2D>`__ as data points. The data in
+stores it in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ as data points. The data in
the file must be organized in columns separated by commas, tabs, spaces,
colons or semicolons. Only one separator type can be used throughout the
file; use the "Separator" property to tell the algorithm which to use.
diff --git a/Code/Mantid/docs/source/algorithms/LoadAscii-v2.rst b/Code/Mantid/docs/source/algorithms/LoadAscii-v2.rst
index 6e3e98ecd1876dfb37c8e1137fd20c08853e491b..5168a6df0da9741bd6b1a246924920293f4ccd86 100644
--- a/Code/Mantid/docs/source/algorithms/LoadAscii-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadAscii-v2.rst
@@ -10,11 +10,11 @@ Description
-----------
The LoadAscii2 algorithm reads in spectra data from a text file and
-stores it in a `Workspace2D <Workspace2D>`__ as data points. The data in
+stores it in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ as data points. The data in
the file must be organized in columns separated by commas, tabs, spaces,
colons or semicolons. Only one separator type can be used throughout the
file; use the "Separator" property to tell the algorithm which to use.
-The algorithm `SaveAscii2 <SaveAscii2>`__ is normally able to produce
+The algorithm `SaveAscii2 <http://www.mantidproject.org/SaveAscii2>`_ is normally able to produce
such a file.
The format must be:
diff --git a/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
index f4e0fd145c897307b6152013d04c008c85655fe9..d2444a17abef32b4940af14d4f57b073f3cf382c 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEmptyInstrument-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm is to enable you to look at an instrument without having
to load a full data file. Instead of loading a data file, it loads the
-`InstrumentDefinitionFile <InstrumentDefinitionFile>`__ for the
+`InstrumentDefinitionFile <http://www.mantidproject.org/InstrumentDefinitionFile>`_ for the
instrument, which has information about the instrument. The instrument
is referred to as being empty because there is no data associated with
it.
diff --git a/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
index 5c0612667b39cf718baf83b48af80d9d125f20f6..2fa8a0150998dde628065c16b52233758684d6e0 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEventNexus-v1.rst
@@ -10,10 +10,10 @@ Description
-----------
The LoadEventNeXus algorithm loads data from an EventNexus file into an
-`EventWorkspace <EventWorkspace>`__. The default histogram bin
+`EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default histogram bin
boundaries consist of a single bin able to hold all events (in all
-pixels), and will have their `units <units>`__ set to time-of-flight.
-Since it is an `EventWorkspace <EventWorkspace>`__, it can be rebinned
+pixels), and will have their `units <http://www.mantidproject.org/units>`_ set to time-of-flight.
+Since it is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, it can be rebinned
to finer bins with no loss of data.
Sample logs, such as motor positions or e.g. temperature vs time, are
diff --git a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
index 097ff5b2d00366dbf94e5b4877a304a0789e491d..ff1b35aa72fab08601f0d215a7b4acae4651d890 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v1.rst
@@ -10,10 +10,10 @@ Description
-----------
The LoadEventPreNeXus algorithm stores data from the pre-nexus neutron
-event data file in an `EventWorkspace <EventWorkspace>`__. The default
+event data file in an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default
histogram bin boundaries consist of a single bin able to hold all events
-(in all pixels), and will have their `units <units>`__ set to
-time-of-flight. Since it is an `EventWorkspace <EventWorkspace>`__, it
+(in all pixels), and will have their `units <http://www.mantidproject.org/units>`_ set to
+time-of-flight. Since it is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, it
can be rebinned to finer bins with no loss of data.
Optional properties
diff --git a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v2.rst b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v2.rst
index ce91f92202a17b660722c8dcfda131a1c6ae6581..f77b7d42fb04092f3162e1b9527be53208262cb0 100644
--- a/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadEventPreNexus-v2.rst
@@ -10,10 +10,10 @@ Description
-----------
The LoadEventPreNeXus algorithm stores data from the pre-nexus neutron
-event data file in an `EventWorkspace <EventWorkspace>`__. The default
+event data file in an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_. The default
histogram bin boundaries consist of a single bin able to hold all events
-(in all pixels), and will have their `units <units>`__ set to
-time-of-flight. Since it is an `EventWorkspace <EventWorkspace>`__, it
+(in all pixels), and will have their `units <http://www.mantidproject.org/units>`_ set to
+time-of-flight. Since it is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, it
can be rebinned to finer bins with no loss of data.
Optional properties
diff --git a/Code/Mantid/docs/source/algorithms/LoadFullprofResolution-v1.rst b/Code/Mantid/docs/source/algorithms/LoadFullprofResolution-v1.rst
index 597fbaf168f879de4db632dfeedd23da71ff441b..8858870817eab04fe6de743e994d0d4e5a774372 100644
--- a/Code/Mantid/docs/source/algorithms/LoadFullprofResolution-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadFullprofResolution-v1.rst
@@ -19,11 +19,11 @@ resolution parameters into the workspace for subsequent fitting is
limitted to Fullprof:
- NPROF=13, Ikeda-Carpender pseudo-Voigt translated into
- `IkedaCarpenterPV <IkedaCarpenterPV>`__ according to
- `CreateIkedaCarpenterParameters <CreateIkedaCarpenterParameters>`__
+ `IkedaCarpenterPV <http://www.mantidproject.org/IkedaCarpenterPV>`_ according to
+ `CreateIkedaCarpenterParameters <http://www.mantidproject.org/CreateIkedaCarpenterParameters>`_
- NPROF=9, back-to-back-exponential pseudo-Voigt translated into
- `BackToBackExponential <BackToBackExponential>`__ according to
- `CreateBackToBackParameters <CreateBackToBackParameters>`__
+ `BackToBackExponential <http://www.mantidproject.org/BackToBackExponential>`_ according to
+ `CreateBackToBackParameters <http://www.mantidproject.org/CreateBackToBackParameters>`_
Note for NPROF=9 the translation is currently ignoring the Lorentzian
part of the pseudo-Voigt.
diff --git a/Code/Mantid/docs/source/algorithms/LoadGSASInstrumentFile-v1.rst b/Code/Mantid/docs/source/algorithms/LoadGSASInstrumentFile-v1.rst
index ef735d1c318da8107988d52bd9f893f02a3979cb..bd1a9836f2de186a678cac353df53afeb708e048 100644
--- a/Code/Mantid/docs/source/algorithms/LoadGSASInstrumentFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadGSASInstrumentFile-v1.rst
@@ -13,8 +13,8 @@ Load parameters from a GSAS instrument file into a table workspace
Later developments of this algorithm will enable these parameters to be
put into the instrument of a wotrkspace for either Ikeda-Carpender
-pseudo-Voigt translated into `IkedaCarpenterPV <IkedaCarpenterPV>`__ or
+pseudo-Voigt translated into `IkedaCarpenterPV <http://www.mantidproject.org/IkedaCarpenterPV>`_ or
back-to-back-exponential pseudo-Voigt translated into
-`BackToBackExponential <BackToBackExponential>`__.
+`BackToBackExponential <http://www.mantidproject.org/BackToBackExponential>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
index 5c354cafcd9a2569c8c4d9735e56d72ead426cb7..441d2c7130d6ac374c1cf79ea24830fe2b5d5017 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILL-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL TOF NeXus file into a `Workspace2D <Workspace2D>`__ with
+Loads an ILL TOF NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
the given name.
This loader calculates the elastic peak position (EPP) on the fly. In
diff --git a/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
index 01f225a01daf2c6ba2323ba3a8f2bdae4d56a93c..0f887cdd567192e2f79ef4223aee49fadd93cbab 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILLIndirect-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL Back Scattering NeXus file into a `Workspace2D <Workspace2D>`__ with
+Loads an ILL Back Scattering NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
the given name.
The Units axis is defined with *empty* units. The main purpose of this loader is to be used with the **Indirect Load** interface.
diff --git a/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst b/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
index 0e4f7ffd17b9e88cbd33e355924ae06230a909d0..d2cccc197c02ae1cb27c9a69ff9ec86fb5693e33 100644
--- a/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadILLSANS-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an ILL D33 nexus file into a `Workspace2D <Workspace2D>`__ with
+Loads an ILL D33 nexus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
the given name.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst b/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
index 9ff225c18d65d5abe83b08ab35fe4b54ef280ee2..93ecc1f018693f8bff68602b4a530a13eaec7339 100644
--- a/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadInstrument-v1.rst
@@ -9,11 +9,11 @@
Description
-----------
-Loads an instrument definition file (`IDF <InstrumentDefinitionFile>`__)
+Loads an instrument definition file (`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_)
into a workspace, which contains information about detector positions,
their geometric shape, slit properties, links between values stored in
ISIS log-files and components of the instrument and so on. For more on
-IDFs see: `InstrumentDefinitionFile <InstrumentDefinitionFile>`__.
+IDFs see: `InstrumentDefinitionFile <http://www.mantidproject.org/InstrumentDefinitionFile>`_.
By default the algorithm will write a 1:1 map between the spectrum
number and detector ID. Any custom loading algorithm that calls this as
diff --git a/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst b/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
index b637d49353d575406ee1647f95a996bf18519358..320f0206029594ff2b2bd83e955f4dc58a02e92a 100644
--- a/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadLLB-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads an LLB MIBEMOL TOF NeXus file into a `Workspace2D <Workspace2D>`__
+Loads an LLB MIBEMOL TOF NeXus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_
with the given name.
This loader calculates the elastic peak position (EPP) on the fly.
diff --git a/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst b/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
index 72f3d192af329cb240b8f2c8a5d35fc332135861..ff520ef735e1b8d470103547466a7a28d7f351a5 100644
--- a/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadLiveData-v1.rst
@@ -22,10 +22,10 @@ Data Processing
###############
- Each time LoadLiveData is called, a chunk of data is loaded from the
- `LiveListener <LiveListener>`__.
+ `LiveListener <http://www.mantidproject.org/LiveListener>`_.
- This consists of all the data collected since the previous call.
- - The data is saved in a temporary `workspace <workspace>`__.
+ - The data is saved in a temporary `workspace <http://www.mantidproject.org/workspace>`_.
- You have two options on how to process this workspace:
@@ -76,7 +76,7 @@ A Warning About Events
######################
Beware! If you select *PreserveEvents* and your processing keeps the
-data as `EventWorkspaces <EventWorkspace>`__, you may end up creating
+data as `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, you may end up creating
**very large** EventWorkspaces in long runs. Most plots require
re-sorting the events, which is an operation that gets much slower as
the list gets bigger (Order of N\*log(N)). This could cause Mantid to
diff --git a/Code/Mantid/docs/source/algorithms/LoadMD-v1.rst b/Code/Mantid/docs/source/algorithms/LoadMD-v1.rst
index 446bad4ea38f558ce2724db615824908059a9144..ff226cb1c527e6d813f542f26e13008a473ca472 100644
--- a/Code/Mantid/docs/source/algorithms/LoadMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-This algorithm loads a `MDEventWorkspace <MDEventWorkspace>`__ that was
+This algorithm loads a `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ that was
previously saved using the :ref:`algm-SaveMD` algorithm to a .nxs file
format.
diff --git a/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
index 45d70d7017a462b53c86acb6f0606a5c090d7d0a..169522064cbe5e4565b8ddb35e11a96c4ca111ae 100644
--- a/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadMcStasNexus-v1.rst
@@ -11,7 +11,7 @@ Description
Reads a McStas NeXus file into a Mantid WorkspaceGroup with a
user-supplied name. Data generated by McStas monitor components are
-stored in workspaces of type `Workspace2D <Workspace2D>`__. All data
+stored in workspaces of type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_. All data
sets are numbered and nested within the WorkspaceGroup. This algorithm
is under development. To date it has been tested with the following
instrument files from the McStas 2.0 instrument suite: templateDIFF,
diff --git a/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst b/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
index e90a82b8f76d3626ae316557f23584e915c9a5e1..dc5417360d7cc16cefd40f8219410a218cb18b4f 100644
--- a/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadRKH-v1.rst
@@ -11,7 +11,7 @@ Description
Loads the given file in the RKH text format, which can be a file with
three columns of numbers. If the FirstColumnValue is a recognised
-`Mantid unit <Unit_Factory>`__ the workspace is created with just one
+`Mantid unit <http://www.mantidproject.org/Unit_Factory>`_ the workspace is created with just one
spectrum. Alteratively if FirstColumnValue is set to 'SpectrumNumber'
then the workspace can have many spectra with the spectrum ID's equal to
the first column in the file.
diff --git a/Code/Mantid/docs/source/algorithms/LoadRawBin0-v1.rst b/Code/Mantid/docs/source/algorithms/LoadRawBin0-v1.rst
index e345c3ebb2ae9b4aa68962b71fae400599b6ef36..e1e0cb93f33eae706cc5cf5ad49b0e2a92193ea8 100644
--- a/Code/Mantid/docs/source/algorithms/LoadRawBin0-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadRawBin0-v1.rst
@@ -10,6 +10,6 @@ Description
-----------
The LoadRawBin0 algorithm stores bin 0 data from the selected
-`RAW <RAW_File>`__ file in a `Workspace2D <Workspace2D>`__.
+`RAW <http://www.mantidproject.org/RAW_File>`_ file in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst b/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
index 649e7d07cecd42300bf60a478c51a5cff4836b22..d0b0059e8c888bfe751b6b2100770727c26602df 100644
--- a/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadRawSpectrum0-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
The LoadRawSpectrum0 algorithm stores spectrum zero data from the
-selected `RAW <RAW_File>`__ file in a `Workspace2D <Workspace2D>`__.
+selected `RAW <http://www.mantidproject.org/RAW_File>`_ file in a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_.
Usage
-----
diff --git a/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
index 27273535d56b76b0f6516dbe08c8cc1b2b5cda8f..b4568ab145ea59be8d360d01aba6bd2d4cafa05c 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSINQFocus-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads a SINQ (PSI) nexus file into a `Workspace2D <Workspace2D>`__ with
+Loads a SINQ (PSI) nexus file into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with
the given name.
To date this algorithm only supports: FOCUS
diff --git a/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
index b2e7bd3fe6cd1889817411a67721b71d31d0471e..3a9a203af328cdcbf8b34889e3c925f6e01f29f9 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSPE-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Loads the file given into a `Workspace2D <Workspace2D>`__ with the given name. The file should be in the SPE format, which is described `here <Media:Spe_file_format.pdf>`__. The workspace will have X units of `Energy transfer <Unit_Factory>`__. The other axis will be binned and have units of either `Momentum transfer / Q <Unit_Factory>`__ or degrees, depending on the label in the input file. The workspace will be flagged as a distribution.
+Loads the file given into a `Workspace2D <http://www.mantidproject.org/Workspace2D>`_ with the given name. The file should be in the SPE format, which is described `here <Media:Spe_file_format.pdf>`__. The workspace will have X units of `Energy transfer <http://www.mantidproject.org/Unit_Factory>`_. The other axis will be binned and have units of either `Momentum transfer / Q <Unit_Factory>`__ or degrees, depending on the label in the input file. The workspace will be flagged as a distribution.
File Format
###########
diff --git a/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
index 7e8ba572cf76cfdc04bc8936354874771c8463f8..4fdae35008c8ef06753678fa64f37915fbd224d0 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSQW-v1.rst
@@ -19,7 +19,7 @@ recalculated to the Crystal? frame, without HKL transformation).
U matrix is set to unity but the B-matrix is read from the SQW and
attached to the workspace which may confuse the algorithms which work
-with `MDEventWorkspace <MDEventWorkspace>`__ produced by Mantid
+with `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ produced by Mantid
algorithms.
Notes on Horace SQW files
diff --git a/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst b/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
index bdd66208a94e8dce07c05d606b2fe9daa0e96015..f3a12706e2c6354a5227813152cee69b95c3ba0c 100644
--- a/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/LoadSassena-v1.rst
@@ -12,8 +12,8 @@ Description
The Sassena application `1 <http://sassena.org>`__ generates
intermediate scattering factors from molecular dynamics trajectories.
This algorithm reads Sassena output and stores all data in workspaces of
-type `Workspace2D <Workspace2D>`__, grouped under a single
-`WorkspaceGroup <WorkspaceGroup>`__.
+type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_, grouped under a single
+`WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_.
Sassena ouput files are in HDF5 format
`2 <http://www.hdfgroup.org/HDF5>`__, and can be made up of the
diff --git a/Code/Mantid/docs/source/algorithms/MergeLogs-v1.rst b/Code/Mantid/docs/source/algorithms/MergeLogs-v1.rst
index 3345b658a6b083e1698583ce44b3d894c4b4069a..fd1f2ad4578e78ca09bebe1cfda76944962f5eaf 100644
--- a/Code/Mantid/docs/source/algorithms/MergeLogs-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MergeLogs-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Two `TimeSeriesProperty <TimeSeriesProperty>`__ logs are merged together
+Two `TimeSeriesProperty <http://www.mantidproject.org/TimeSeriesProperty>`_ logs are merged together
by the time stamps.
Output
diff --git a/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst b/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
index 2e2deb70d9e0a4d8c895a53d32e31a649ac4e65a..5c7633717d11be8f3e1d2ea544ac30e9a9b349dc 100644
--- a/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MergeMD-v1.rst
@@ -9,11 +9,11 @@
Description
-----------
-This algorithm merges several `MDWorkspaces <MDWorkspace>`__ together
+This algorithm merges several `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ together
into one by adding their events together.
The algorithm starts by going through the list of
-`MDWorkspaces <MDWorkspace>`__ to find the extents that fully encompass
+`MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_ to find the extents that fully encompass
all input workspaces in each dimension. The number and names of
dimensions must match for all input workspaces.
diff --git a/Code/Mantid/docs/source/algorithms/MergeRuns-v1.rst b/Code/Mantid/docs/source/algorithms/MergeRuns-v1.rst
index c4f4f2ab7d7bcda18d25a86ef164beda93813e6d..144cfe7fac97a351864b480139eb9bdabb3235c9 100644
--- a/Code/Mantid/docs/source/algorithms/MergeRuns-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MergeRuns-v1.rst
@@ -21,15 +21,15 @@ The input workspaces must contain histogram data with the same number of
spectra and matching units and instrument name in order for the
algorithm to succeed.
-**For `Workspace2Ds <Workspace2D>`__**: Each input workspace must have
+**For `Workspace2Ds <http://www.mantidproject.org/Workspace2D>`_**: Each input workspace must have
common binning for all its spectra.
-**For `EventWorkspaces <EventWorkspace>`__**: This algorithm is
+**For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_**: This algorithm is
Event-aware; it will append event lists from common spectra. Binning
parameters need not be compatible; the output workspace will use the
first workspaces' X bin boundaries.
-**For `WorkspaceGroups <WorkspaceGroup>`__**: Each nested has to be one
+**For `WorkspaceGroups <http://www.mantidproject.org/WorkspaceGroup>`_**: Each nested has to be one
of the above.
Other than this it is currently left to the user to ensure that the
diff --git a/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst b/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
index df7ffb08a3424e7c666cf7da6e1294c422c88f41..71830673666001045ee73acfa994ff0859317096 100644
--- a/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MinusMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Subtract two `MDHistoWorkspace <MDHistoWorkspace>`__'s or a
+Subtract two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
MDHistoWorkspace and a scalar.
- **MDHistoWorkspace - MDHistoWorkspace**
@@ -25,15 +25,15 @@ MDHistoWorkspace and a scalar.
- This is not allowed.
-- **`MDEventWorkspace <MDEventWorkspace>`__ -
- `MDEventWorkspace <MDEventWorkspace>`__**
+- **`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ -
+ `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_**
- The signal of each event on the right-hand-side is multiplied by
-1 before the events are summed.
- The number of events in the output MDEventWorkspace is that of the
LHS and RHS workspaces put together.
-- **`MDEventWorkspace <MDEventWorkspace>`__ - Scalar or
+- **`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ - Scalar or
MDHistoWorkspace**
- This is not possible.
diff --git a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
index 00c7a90ef59cf0547e73423a61d1f529982598c6..57dce38cdd82f9b48b76e92a71f81d80f9c912f9 100644
--- a/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MonteCarloAbsorption-v1.rst
@@ -36,7 +36,7 @@ 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.
At a minimum, the input workspace must have a sample shape defined.
diff --git a/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst b/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
index 87ca39b550c4d98bf3a6d09bc88ccaf3783105b0..f48bcbe024b70058bd91ea2754046c10a106bc06 100644
--- a/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/MultiplyMD-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Multiply two `MDHistoWorkspace <MDHistoWorkspace>`__'s or a
+Multiply two `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_'s or a
MDHistoWorkspace and a scalar.
The error of :math:`f = a * b` is propagated with
@@ -23,7 +23,7 @@ The error of :math:`f = a * b` is propagated with
- Every element of the MDHistoWorkspace is multiplied by the scalar.
-- **`MDEventWorkspace <MDEventWorkspace>`__'s**
+- **`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_'s**
- This operation is not supported, as it is not clear what its
meaning would be.
diff --git a/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst b/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
index 85f1e9e07aa55a3752ecb8ddeb20583e8a0aca11..cc32b76ddd4649a976aa3df6088c249340a5f561 100644
--- a/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/NormaliseByCurrent-v1.rst
@@ -11,7 +11,7 @@ Description
Normalises a workspace according to the good proton charge figure taken
from the Input Workspace log data, which is stored in the workspace's
-`Sample <Sample>`__ object). Every data point (and its error) is divided
+`Sample <http://www.mantidproject.org/Sample>`_ object). Every data point (and its error) is divided
by that number.
ISIS Calculation Details
@@ -29,7 +29,7 @@ property.
EventWorkspaces
###############
-If the input workspace is an `EventWorkspace <EventWorkspace>`__, then
+If the input workspace is an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, then
the output will be as well. Weighted events are used to scale by the
current (see the :ref:`algm-Divide` algorithm, which is a child
algorithm being used).
diff --git a/Code/Mantid/docs/source/algorithms/NormaliseByDetector-v1.rst b/Code/Mantid/docs/source/algorithms/NormaliseByDetector-v1.rst
index 404b546905261e9671e7bc35c89c7066308b7ed8..89fbc14b991b748baa33af38bdd65c7c9c6ae89b 100644
--- a/Code/Mantid/docs/source/algorithms/NormaliseByDetector-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/NormaliseByDetector-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm is designed to normalise a workspace via detector
efficiency functions. **For this algorithm to work, the Instrument
-Defintion File `IDF <IDF>`__ must have fitting functions on the
+Defintion File `IDF <http://www.mantidproject.org/IDF>`_ must have fitting functions on the
component tree**. The setup information for this, as well as some
examples, are provided below.
@@ -45,7 +45,7 @@ Background
In brief, the components in the IDF file form a tree structure.
Detectors and Instruments are both types of component. Detectors are
ultimately children of Instruments in the tree structure. For a more
-complete description see `IDF <IDF>`__. The tree structure of the
+complete description see `IDF <http://www.mantidproject.org/IDF>`_. The tree structure of the
components, mean that fitting functions do not necessarily have to be
assigned on a detector-by-detector basis. Applying a fit function to the
instrument, will ensure that all subcomponents (including detectors),
diff --git a/Code/Mantid/docs/source/algorithms/NotMD-v1.rst b/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
index 0fdb33fced7d10338d7045a326622527d8cb2050..f85a197efdfff7bfec908800ed6731090d58c8d0 100644
--- a/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/NotMD-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
Perform the Not (negation) boolean operation on a
-`MDHistoWorkspace <MDHistoWorkspace>`__. The not operation is performed
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. The not operation is performed
element-by-element. Any 0.0 signal is changed to 1.0 (meaning true). Any
non-zero signal is changed to 0.0 (meaning false).
diff --git a/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst b/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
index eafaa01b0ce5d1f4ae98505377d49f10dcd3217a..c9b4b768c4b7375b45d3f053b1e33020acfef4c3 100644
--- a/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/OneStepMDEW-v1.rst
@@ -11,13 +11,13 @@ Description
This algorithm is used in the Paraview event nexus loader to both load
an event nexus file and convert it into a
-`MDEventWorkspace <MDEventWorkspace>`__ for use in visualization.
+`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ for use in visualization.
The :ref:`algm-LoadEventNexus` algorithm is called with default
-parameters to load into an `EventWorkspace <EventWorkspace>`__.
+parameters to load into an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_.
After, the
-`MakeDiffractionMDEventWorkspace <MakeDiffractionMDEventWorkspace>`__
+`MakeDiffractionMDEventWorkspace <http://www.mantidproject.org/MakeDiffractionMDEventWorkspace>`_
algorithm is called with the new EventWorkspace as input. The parameters
are set to convert to Q in the lab frame, with Lorentz correction, and
default size/splitting behavior parameters.
diff --git a/Code/Mantid/docs/source/algorithms/PDLoadCharacterizations-v1.rst b/Code/Mantid/docs/source/algorithms/PDLoadCharacterizations-v1.rst
index 3b8850d903c6743df0df57e560c0015560d860d6..d29e17ce3758894b8fa52e2d8420cb5167e50bed 100644
--- a/Code/Mantid/docs/source/algorithms/PDLoadCharacterizations-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PDLoadCharacterizations-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
This algorithm loads information into a
-`TableWorkspace <TableWorkspace>`__ for the characterization information
+`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ for the characterization information
and a collection of output parameters for the focus positions to be used
in :ref:`algm-EditInstrumentGeometry`. If a section is
missing then those parameters will be empty. This includes an empty
diff --git a/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst b/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
index cf491c8336d1f0602095d2b0b8211622be77fa82..5c221be6cac07fab5da1bae045594a3d5518d455 100644
--- a/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PlotPeakByLogValue-v1.rst
@@ -16,7 +16,7 @@ defined in the Input property. The Input property expects a list of
spectra identifiers separated by semicolons (;). An identifier is itself
a comma-separated list of values. The first value is the name of the
source. It can be either a workspace name or a name of a file (RAW or
-Nexus). If it is a name of a `WorkspaceGroup <WorkspaceGroup>`__ all its
+Nexus). If it is a name of a `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ all its
members will be included in the fit. The second value selects a spectrum
within the workspace or file. It is an integer number with a prefix
defining the meaning of the number: "sp" for a spectrum number, "i" for
@@ -55,7 +55,7 @@ Output workspace format
PlotPeakByLogValue\_Output.png
In this example a group of three Matrix workspaces were fitted with a
-`Gaussian <Gaussian>`__ on a linear background.
+`Gaussian <http://www.mantidproject.org/Gaussian>`_ on a linear background.
The output workspace is a table in which rows correspond to the spectra
in the order they (spectra) appear in the Input property. The first
diff --git a/Code/Mantid/docs/source/algorithms/Plus-v1.rst b/Code/Mantid/docs/source/algorithms/Plus-v1.rst
index 24f6d85bf03b4b96fd0702151174ccd903fc6f6e..394b74a279dfc9fd0dee1def7e39e71fae29e067 100644
--- a/Code/Mantid/docs/source/algorithms/Plus-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Plus-v1.rst
@@ -20,7 +20,7 @@ Description
EventWorkspace note
###################
-For `EventWorkspaces <EventWorkspace>`__, the event lists at each
+For `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_, the event lists at each
workspace index are concatenated to create the output event list at the
same workspace index. Note that in some (rare :sup:`\*`) cases, these
event lists might be from different detectors; this is not checked
diff --git a/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst b/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
index 1a507830dc2852f894c48e53989810f4e303153b..7c19cb1c465d87f7c0c01f8563711bb842733c17 100644
--- a/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PlusMD-v1.rst
@@ -9,8 +9,8 @@
Description
-----------
-This algorithm sums two `MDHistoWorkspaces <MDHistoWorkspace>`__ or
-merges two `MDEventWorkspaces <MDEventWorkspace>`__ together.
+This algorithm sums two `MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ or
+merges two `MDEventWorkspaces <http://www.mantidproject.org/MDEventWorkspace>`_ together.
MDHistoWorkspaces
#################
@@ -28,7 +28,7 @@ MDEventWorkspaces
#################
This algorithm operates similary to calling Plus on two
-`EventWorkspaces <EventWorkspace>`__: it combines the events from the
+`EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_: it combines the events from the
two workspaces together to form one large workspace.
Note for file-backed workspaces
@@ -37,7 +37,7 @@ Note for file-backed workspaces
The algorithm uses :ref:`algm-CloneMDWorkspace` to create the
output workspace, except when adding in place (e.g. :math:`A = A + B` ).
See :ref:`algm-CloneMDWorkspace` for details, but note that a
-file-backed `MDEventWorkspace <MDEventWorkspace>`__ will have its file
+file-backed `MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ will have its file
copied.
- If A is in memory and B is file-backed, the operation
diff --git a/Code/Mantid/docs/source/algorithms/PredictPeaks-v1.rst b/Code/Mantid/docs/source/algorithms/PredictPeaks-v1.rst
index 2c9ea69422bb05243edb57163467a3f478b5c5b8..53ca34696a7c96f8c74ed10324f85fdec9d6244e 100644
--- a/Code/Mantid/docs/source/algorithms/PredictPeaks-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/PredictPeaks-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm will predict the position of single-crystal diffraction
peaks (both in detector position/TOF and Q-space) and create an output
-`PeaksWorkspace <PeaksWorkspace>`__ containing the result.
+`PeaksWorkspace <http://www.mantidproject.org/PeaksWorkspace>`_ containing the result.
This algorithm uses the InputWorkspace to determine the instrument in
use, as well as the UB Matrix and Unit Cell of the sample used. You can
diff --git a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
index ec1f06d8570991f0d8df86251b32fe677ebd6b48..4bc467f4deab1e1e3a176f27fbe2f543d9fd01e8 100644
--- a/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/Q1D-v2.rst
@@ -37,8 +37,8 @@ neutrons are all travelling in horizontal at sample, and that
Normalized Intensity
####################
-This `algorithm <Algorithm>`__ takes a workspace of number of neutron
-counts against `wavelength <Units>`__ and creates a workspace of cross
+This `algorithm <http://www.mantidproject.org/Algorithm>`_ takes a workspace of number of neutron
+counts against `wavelength <http://www.mantidproject.org/Units>`_ and creates a workspace of cross
section against Q. The output Q bins boundaries are defined by setting
the property OutputBinning.
@@ -54,7 +54,7 @@ of many, one, or no wavelength bins\|centre|
In the equation the number of counts in the input spectrum number is
denoted by :math:`S(n)`, :math:`N(n)` is the wavelength dependent
-correction and :math:`\Omega` is the `solid angle <SolidAngle>`__ of the
+correction and :math:`\Omega` is the `solid angle <http://www.mantidproject.org/SolidAngle>`_ of the
detector
.. math:: P_I(Q) = \frac{ \sum_{n \supset I} S(n)}{\Omega\sum_{n \supset I}N(n)}
@@ -85,11 +85,11 @@ where :math:`F` is the detector dependent (e.g. flood) scaling specified
by the PixelAdj property, and where a :math:`\lambda` bin :math:`n`
spans more than one :math:`Q` bin :math:`I`, it is split assuming a
uniform distribution of the counts in :math:`\lambda`. The normalization
-takes any `bin masking <MaskBins>`__ into account.
+takes any `bin masking <http://www.mantidproject.org/MaskBins>`_ into account.
Although the units on the y-axis of the output workspace space are
quoted in 1/cm note that conversion to a cross section requires scaling
-by an `instrument <instrument>`__ dependent absolute units constant.
+by an `instrument <http://www.mantidproject.org/instrument>`_ dependent absolute units constant.
Resolution and Cutoffs
######################
diff --git a/Code/Mantid/docs/source/algorithms/QueryAllRemoteJobs-v1.rst b/Code/Mantid/docs/source/algorithms/QueryAllRemoteJobs-v1.rst
index 36aac90dc0566f269f51845cc10be15ee079fe66..7032130a21ee733cf1c5efd15b137299794fa398 100644
--- a/Code/Mantid/docs/source/algorithms/QueryAllRemoteJobs-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/QueryAllRemoteJobs-v1.rst
@@ -14,6 +14,6 @@ Note that the output properties are all arrays. There will be one
element for each job that was found.
For more details, see the `remote job submission API
-docs <Remote_Job_Submission_API>`__.
+docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/QueryRemoteFile-v1.rst b/Code/Mantid/docs/source/algorithms/QueryRemoteFile-v1.rst
index dd59d0696e7dbaaed51f6c9d10fba056d4062f5d..ff8c27470d70d6b5480fe98062943159e97c1c45 100644
--- a/Code/Mantid/docs/source/algorithms/QueryRemoteFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/QueryRemoteFile-v1.rst
@@ -13,6 +13,6 @@ Retrieve a list of the files associated with the specified transaction
from 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::
diff --git a/Code/Mantid/docs/source/algorithms/QueryRemoteJob-v1.rst b/Code/Mantid/docs/source/algorithms/QueryRemoteJob-v1.rst
index 1b6af39b801a871dbd50ade30cf4126e758fabee..c43635621566c9f5c7762f40234316610a79b0e5 100644
--- a/Code/Mantid/docs/source/algorithms/QueryRemoteJob-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/QueryRemoteJob-v1.rst
@@ -13,6 +13,6 @@ Query a remote compute resource for a specific job the user has
submitted.
For more details, see the `remote job submission API
-docs <Remote_Job_Submission_API>`__.
+docs <http://www.mantidproject.org/Remote_Job_Submission_API>`_.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
index 50cd71ab9f466a9701992b9cd24d7d545b89e805..737e72f74d4549bd186fb1b44f1fbeebdd828ec8 100644
--- a/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RadiusSum-v1.rst
@@ -31,7 +31,7 @@ one with :math:`width = BinSize` for
:math:`BinSize=\frac{MaxRadius-MinRadius}{NumBins}`.
The algorithm applies a rudimentary calculation to define the bin for
-each that each pixel or detector in the `Workspace2D <Workspace2D>`__,
+each that each pixel or detector in the `Workspace2D <http://www.mantidproject.org/Workspace2D>`_,
but taking its center point. If the center point belongs to one bin, it
is considered that the whole pixel belongs to the bin. The picture
below, shows what does this means. An ideal solution for RadiusSum is
@@ -42,7 +42,7 @@ the left image, while the right image is what is current implemented.
300px
Although the images were applied to an image
-`Workspace2D <Workspace2D>`__, the image below shows that it is possible
+`Workspace2D <http://www.mantidproject.org/Workspace2D>`_, the image below shows that it is possible
to apply this algorithm to Workspaces attached to instruments.
.. figure:: /images/RadiusSumInstrument.png
diff --git a/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst b/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
index 0f6b172689ea77f67d5634c6d689f82b907112d4..b95e398f8f57e48aa09d8c100daf1eaf5f10c098 100644
--- a/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RawFileInfo-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Extracts run parameters from the `RAW <RAW_File>`__ file given as an
+Extracts run parameters from the `RAW <http://www.mantidproject.org/RAW_File>`_ file given as an
input property. If the *GetRunParameters* argument is *True* then a
TableWorkspace is created that contains a column for each value of the
RPB\_STRUCT, i.e. column names such as r\_dur, r\_goodfrm etc. This is
diff --git a/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst b/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
index 26559bca88a89935c90f9f67d63faf565d4c23c4..64c87ac20fe418257de5fe1c64524569a9f43347 100644
--- a/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/ResizeRectangularDetector-v1.rst
@@ -10,17 +10,17 @@ Description
-----------
This algorithm will resize a
-`RectangularDetector <RectangularDetector>`__ by applying X and Y
+`RectangularDetector <http://www.mantidproject.org/RectangularDetector>`_ by applying X and Y
scaling factors. Each pixel's position will be modifed relative to the
0,0 point of the detector by these factors. Typically, a
RectangularDetector is constructed around its center, so this would
scale the detector around its center.
-This only works on `RectangularDetectors <RectangularDetector>`__. Banks
+This only works on `RectangularDetectors <http://www.mantidproject.org/RectangularDetector>`_. Banks
formed by e.g. tubes cannot be scaled in this way.
Internally, this sets the "scalex" and "scaley" parameters on the
-`RectangularDetector <RectangularDetector>`__. Note that the scaling is
+`RectangularDetector <http://www.mantidproject.org/RectangularDetector>`_. Note that the scaling is
relative to the original size, and is not cumulative: that is, if you
Resize \* 2 and again \* 3, your final detector is 3 times larger than
the original, not 6 times.
diff --git a/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst b/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
index 8ab1d3cfc569444064c377905da4b7a34151ca4d..5a2d9b52f9048837a6dbca79dc76a093bac33e5c 100644
--- a/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/RingProfile-v1.rst
@@ -12,7 +12,7 @@ Description
RingProfile sums the counts against a ring.
Below, there is an example of the execution of the RingProfile to a
-`Workspace2D <Workspace2D>`__ where the position of the pixels are not
+`Workspace2D <http://www.mantidproject.org/Workspace2D>`_ where the position of the pixels are not
associated to detector positions, but it is derived from the
`Axes <Interacting_with_Matrix_Workspaces#Axes>`__.
diff --git a/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst b/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
index bc10703199e0c0a2fc935639320cf6976312e111..019682e40bae55ec1a0a5c84ee85f7ee06343542 100644
--- a/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SassenaFFT-v1.rst
@@ -12,8 +12,8 @@ Description
The Sassena application `1 <http://sassena.org>`__ generates
intermediate scattering factors from molecular dynamics trajectories.
This algorithm reads Sassena output and stores all data in workspaces of
-type `Workspace2D <Workspace2D>`__, grouped under a single
-`WorkspaceGroup <WorkspaceGroup>`__. It is implied that the time unit is
+type `Workspace2D <http://www.mantidproject.org/Workspace2D>`_, grouped under a single
+`WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_. It is implied that the time unit is
one **picosecond**.
Sassena ouput files are in HDF5 format
diff --git a/Code/Mantid/docs/source/algorithms/SaveAscii-v2.rst b/Code/Mantid/docs/source/algorithms/SaveAscii-v2.rst
index 22329b1c732724f54125c259f99fcadf2bc5b7fe..d81ef033833d87c067d834ce98ce91de9918284e 100644
--- a/Code/Mantid/docs/source/algorithms/SaveAscii-v2.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveAscii-v2.rst
@@ -9,7 +9,7 @@
Description
-----------
-The workspace data are stored in the file in columns: the first column contains the X-values, followed by pairs of Y and E values. Columns are separated by commas. The resulting file can normally be loaded into a workspace by the `LoadAscii2 <LoadAscii2>`__ algorithm.
+The workspace data are stored in the file in columns: the first column contains the X-values, followed by pairs of Y and E values. Columns are separated by commas. The resulting file can normally be loaded into a workspace by the `LoadAscii2 <http://www.mantidproject.org/LoadAscii2>`_ algorithm.
Limitations
###########
diff --git a/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst b/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
index ed31f1c75987601561ed9c1e65f5dfeb81b486f7..51718572c8556aa4886f672ac9178d61ab3320e8 100644
--- a/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SaveNexusProcessed-v1.rst
@@ -36,7 +36,7 @@ loaded at present.
EventWorkspaces
###############
-This algorithm will save `EventWorkspaces <EventWorkspace>`__ with full
+This algorithm will save `EventWorkspaces <http://www.mantidproject.org/EventWorkspace>`_ with full
event data, unless you uncheck *PreserveEvents*, in which case the
histogram version of the workspace is saved.
diff --git a/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst b/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
index 770a2efc4ffe9c6c15e47e681881a49608e26dac..2d1f41b14ac8da04bbb3f5dceccf827e71e18637 100644
--- a/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SetMDUsingMask-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
This algorithm is used to replace values in a
-`MDHistoWorkspace <MDHistoWorkspace>`__ but only at particular points.
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_ but only at particular points.
A mask MDHistoWorkspace is provided, where non-zero values indicate
'true'. At these points, the corresponding value in the ValueWorkspace
diff --git a/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst b/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
index 2994848801510f4cb2f3443483e2af90a4e3698b..998506051fa6c207967feb00de869ba48beb5319 100644
--- a/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SetSpecialCoordinates-v1.rst
@@ -9,10 +9,10 @@
Description
-----------
-`MDEventWorkspaces <MDEventWorkspace>`__ and
-`MDHistoWorkspaces <MDHistoWorkspace>`__ can be used with any type of
+`MDEventWorkspaces <http://www.mantidproject.org/MDEventWorkspace>`_ and
+`MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ can be used with any type of
coordinate system. On the other hand
-`PeaksWorkspaces <PeaksWorkspace>`__ may be plotted either in QLab,
+`PeaksWorkspaces <http://www.mantidproject.org/PeaksWorkspace>`_ may be plotted either in QLab,
QSample or HKL. There is an inherent link between a PeaksWorkspace and a
MDWorkspace in that an MDWorkspace may utilise the same coordinate
systems as the PeaksWorkspaces. For example, workspaces created via
diff --git a/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst b/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
index d42cf541aa13861509b7305ba99dd5cb19fef7b9..38066391d7607dc59831b62bc99ba852dd33a4b7 100644
--- a/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SliceMD-v1.rst
@@ -10,7 +10,7 @@ Description
-----------
Algorithm that can take a slice out of an original
-`MDEventWorkspace <MDEventWorkspace>`__ while preserving all the events
+`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ while preserving all the events
contained therein.
It uses the same parameters as :ref:`algm-BinMD` to determine a
@@ -48,9 +48,9 @@ in every other dimension - that way, boxes will only be split along the
Slicing a MDHistoWorkspace
##########################
-It is possible to slice a `MDHistoWorkspace <MDHistoWorkspace>`__. Each
+It is possible to slice a `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. Each
MDHistoWorkspace holds a reference to the
-`MDEventWorkspace <MDEventWorkspace>`__ that created it, as well as the
+`MDEventWorkspace <http://www.mantidproject.org/MDEventWorkspace>`_ that created it, as well as the
coordinate transformation that was used.
In this case, the algorithm is executed on the original
diff --git a/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst b/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
index 01c7265780781c4114ff8aa5ad6b403de2a2b9ea..9bd498464229484c931f58482f4ced844077082f 100644
--- a/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SortEvents-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-In an `EventWorkspace <EventWorkspace>`__, event binning is performed on
+In an `EventWorkspace <http://www.mantidproject.org/EventWorkspace>`_, event binning is performed on
the fly. The algorithm for binning requires a list of events sorted by
time of flight, so it will perform a sort (once) on each pixel -
however, this is done on request and without using multiple CPUs). To
diff --git a/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst b/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
index 003e8e33124e0a5fb9e42c3be2409a3dc07704b3..4ed00ad71d915c851c30406f2eb169fe6c50b667 100644
--- a/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SortXAxis-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Clones the input `Matrix Workspaces <MatrixWorkspace>`__ and orders the
+Clones the input `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_ and orders the
x-axis in an ascending fashion. Ensures that the y-axis and error data
is sorted in a consistent way with the x-axis. All x-values of the input
workspace MUST be in either a descending or ascending fashion before
@@ -17,6 +17,6 @@ passing to this algorithm.
This algorithm is for use with small workspaces loaded. It is
particularly suitable for reformatting workspaces loaded via
-`LoadASCII <LoadASCII>`__. Input workspaces must be a distribution.
+`LoadASCII <http://www.mantidproject.org/LoadASCII>`_. Input workspaces must be a distribution.
.. categories::
diff --git a/Code/Mantid/docs/source/algorithms/StartRemoteTransaction-v1.rst b/Code/Mantid/docs/source/algorithms/StartRemoteTransaction-v1.rst
index 9b38917f41481d918b516c48161f10b4e1df570a..d8c0cac01d4b333d698ac81a515fdedba5283f57 100644
--- a/Code/Mantid/docs/source/algorithms/StartRemoteTransaction-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/StartRemoteTransaction-v1.rst
@@ -12,6 +12,6 @@ Description
Start a job transaction on 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::
diff --git a/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst b/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
index d8593dadf251c1b54122eb308089050445bfb2c0..c72bbb4ce755893b21039e118f7bb1c9c2f86d60 100644
--- a/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
+++ b/Code/Mantid/docs/source/algorithms/Stitch1D-v3.rst
@@ -9,7 +9,7 @@
Description
-----------
-Stitches single histogram `Matrix Workspaces <MatrixWorkspace>`__
+Stitches single histogram `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_
together outputting a stitched Matrix Workspace. Either the
right-hand-side or left-hand-side workspace can be chosen to be scaled.
Users must provide a Param step (single value), but the binning start
diff --git a/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst b/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
index b75536d2c01b756c851e48e50c0547dd90dd82de..8efe758f4b424c4fe3098656056f295aef1f0943 100644
--- a/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/Stitch1DMany-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Stitches single histogram `Matrix Workspaces <MatrixWorkspace>`__
+Stitches single histogram `Matrix Workspaces <http://www.mantidproject.org/MatrixWorkspace>`_
together outputting a stitched Matrix Workspace. This algorithm is a
wrapper over :ref:`algm-Stitch1D`.
diff --git a/Code/Mantid/docs/source/algorithms/StopRemoteTransaction-v1.rst b/Code/Mantid/docs/source/algorithms/StopRemoteTransaction-v1.rst
index 3ca2ef82bd325ab3c2b2d145f065fd40d202632d..b3bbe34c6bf793067f8cf3a51a74cdab56c80725 100644
--- a/Code/Mantid/docs/source/algorithms/StopRemoteTransaction-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/StopRemoteTransaction-v1.rst
@@ -12,6 +12,6 @@ Description
Stop a job transaction on 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::
diff --git a/Code/Mantid/docs/source/algorithms/SubmitRemoteJob-v1.rst b/Code/Mantid/docs/source/algorithms/SubmitRemoteJob-v1.rst
index 8647b662d196f12d8e29cac568cd06fc516bdbe6..3685be67e8b9a6ec77aee63e82a6e661f2d3d611 100644
--- a/Code/Mantid/docs/source/algorithms/SubmitRemoteJob-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SubmitRemoteJob-v1.rst
@@ -12,6 +12,6 @@ Description
Submit a job to be executed on the specified 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::
diff --git a/Code/Mantid/docs/source/algorithms/SumEventsByLogValue-v1.rst b/Code/Mantid/docs/source/algorithms/SumEventsByLogValue-v1.rst
index fe80aabad49dda9a698334a91a8b3e9a6ef7d67d..ae733b1f18c27ba157fbfb0b8eb54365c2a8154f 100644
--- a/Code/Mantid/docs/source/algorithms/SumEventsByLogValue-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/SumEventsByLogValue-v1.rst
@@ -11,7 +11,7 @@ Description
This algorithm counts up the events in a workspace against the values of
a log within the workspace. It will most commonly be used as a
-sub-algorithm of the `RockingCurve <RockingCurve>`__ algorithm.
+sub-algorithm of the `RockingCurve <http://www.mantidproject.org/RockingCurve>`_ algorithm.
The algorithm has two modes:
diff --git a/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst b/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
index b791d1c6f4f5d7ab0938c00468eb2cb313ad205b..9e56e6fd6cb6d6169abcb228b4e14853f81d17ec 100644
--- a/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/TransformMD-v1.rst
@@ -10,8 +10,8 @@ Description
-----------
This algorithm applies a simple linear transformation to a
-`MDWorkspace <MDWorkspace>`__ or
-`MDHistoWorkspace <MDHistoWorkspace>`__. This could be used, for
+`MDWorkspace <http://www.mantidproject.org/MDWorkspace>`_ or
+`MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_. This could be used, for
example, to scale the Energy dimension to different units.
Each coordinate is tranformed so that :math:`x'_d = (x_d * s_d) + o_d`
@@ -29,9 +29,9 @@ Notes
#####
The relationship between the workspace and the original
-`MDWorkspace <MDWorkspace>`__, for example when the MDHistoWorkspace is
+`MDWorkspace <http://www.mantidproject.org/MDWorkspace>`_, for example when the MDHistoWorkspace is
the result of :ref:`algm-BinMD`, is lost. This means that you cannot
-re-bin a transformed `MDHistoWorkspace <MDHistoWorkspace>`__.
+re-bin a transformed `MDHistoWorkspace <http://www.mantidproject.org/MDHistoWorkspace>`_.
No units are not modified by this algorithm.
@@ -41,12 +41,12 @@ Performance Notes
- Performing the operation in-place (input=output) is always faster
because the first step of the algorithm if NOT in-place is to clone
the original workspace.
-- For `MDHistoWorkspaces <MDHistoWorkspace>`__ done in-place,
+- For `MDHistoWorkspaces <http://www.mantidproject.org/MDHistoWorkspace>`_ done in-place,
TransformMD is very quick (no data is modified, just the
coordinates).
-- For `MDWorkspaces <MDWorkspace>`__, every event's coordinates gets
+- For `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_, every event's coordinates gets
modified, so this may take a while for large workspaces.
-- For file-backed `MDWorkspaces <MDWorkspace>`__, you will find much
+- For file-backed `MDWorkspaces <http://www.mantidproject.org/MDWorkspace>`_, you will find much
better performance if you perform the change in-place (input=output),
because the data gets written out to disk twice otherwise.
diff --git a/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst b/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
index cfd043303dc9f291b5a228588fe86decd35ca1f8..4726bcff117829499ebcad40412204271bcdd711 100644
--- a/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UnGroupWorkspace-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Takes a `WorkspaceGroup <WorkspaceGroup>`__ as input and ungroups it
+Takes a `WorkspaceGroup <http://www.mantidproject.org/WorkspaceGroup>`_ as input and ungroups it
into several workspaces. You can perform this from the MantidPlot GUI by
selecting the WorkspaceGroup and clicking "Ungroup".
diff --git a/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst b/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
index 987d379028108463b1706457b40861d4757de03a..036ea38184c9e6bea3a130b7c8d2290fe8d0d8d1 100644
--- a/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UpdateInstrumentFromFile-v1.rst
@@ -9,7 +9,7 @@
Description
-----------
-Some instrument definition file (`IDF <InstrumentDefinitionFile>`__)
+Some instrument definition file (`IDF <http://www.mantidproject.org/InstrumentDefinitionFile>`_)
positions are only approximately correct and the true positions are
located within data files. This algorithm reads the detector positioning
from the supplied file and updates the instrument accordingly. It
diff --git a/Code/Mantid/docs/source/algorithms/UploadRemoteFile-v1.rst b/Code/Mantid/docs/source/algorithms/UploadRemoteFile-v1.rst
index 4c2e7e10118612dfc1722a4581a00d2a282d8321..400f65c4bc87c8995d91403bf0701d599319ba6d 100644
--- a/Code/Mantid/docs/source/algorithms/UploadRemoteFile-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UploadRemoteFile-v1.rst
@@ -14,6 +14,6 @@ is a python script or input data necessary to run a Mantid algorithm on
the 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::
diff --git a/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst b/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
index 16c5b23c5b531ae8aef2c958db480bc338f2042e..3121153c0e88092fce3886c339957a2f12a47da7 100644
--- a/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
+++ b/Code/Mantid/docs/source/algorithms/UserFunction1D-v1.rst
@@ -82,7 +82,7 @@ with 0.0. If some of the parameters should be fixed in the fit list them
in the *Fix* property in any order, e.g. "a,c".
The resulting parameters are returned in a
-`TableWorkspace <TableWorkspace>`__ set in *OutputParameters* property.
+`TableWorkspace <http://www.mantidproject.org/TableWorkspace>`_ set in *OutputParameters* property.
Also for displaying purposes *OutputWorkspace* is returned. It contains
the initial spectrum, the fitted spectrum and their difference.