fix links & formatting in help; remove old workflow that triggers help build for GSAS-II sources

Author: briantoby

.github/workflows/helpxfer.yml .github/workflows/helpxfer.yml.inactive.github/workflows/helpxfer.yml renamed to .github/workflows/helpxfer.yml.inactive

@@ -14,7 +14,7 @@ Some GSAS-II operations (*e.g.*, structure refinement, Fourier map calculation &
 * The "Set filters" button allows you to select which type of entries are shown, as are selected on a list. Note that older Notebook entries were not recorded with tags that allow filtering to work. 
 
 * The "Plot" button allows plotting the progression of the overall Rw or reduced \(\chi^2\) in the refinement, or logged variables (to log a parameter see **View LS parms** in the 
-[Calculate menu](./mainmenu.md#Calculate) or the `LogAllVars` setting in the 
+[Calculate menu](./mainmenu.md#Calculate_menu) or the `LogAllVars` setting in the 
 [Configuration variables](./others.md#config)).
 
 * The "Save" button writes the contents of the Notebook as a text file named <project>-notebook.txt. 

MDhelp/docs/commontreeitems.md

@@ -65,26 +65,30 @@ Finally, move to the atoms tab where atoms can be inserted or imported. Note tha
 
     Clicking on a row of the table brings up a window where **parameter limits** may be set. One may set a lower limit value, an upper limit value or both. When a parameter value refines to value outside the limit, the parameter is set to that limit value and the refinement flag for the parameter is subsequently ignored. 
 
-Also, one can set here parameters that will be logged into the [Notebook](./commontreeitems.md#Notebook), so the values can be tracked and plotted across a refinement. 
-Right-click to toggle the log setting. Note that individual log
-settings will override the the `LogAllVars` preference setting (see  [Configuration variables](./others.md#config)).
-
-
     !!! Note
         Note that for atom positions, the variables associated with coordinate values (named as `p::Aw:n`, where p is the phase number, n is the atom number and w is x, y or z) is not a refinable parameter, but the shift in the value is. The refined parameters are 'p::dAw:n'. The reason this is done is that by treating an atom position as (Ax+dAx,Ay+dAy,Az+dAz) where the “d” values indicate shifts from the starting position. Shifts are refined rather than the x, y, or z values as this this simplifies symmetry constraints. As an example, suppose we have an atom on a symmetry constrained site, `x,1/2-x,z`. The process needed to enforce this symmetry constraint, so that if x moves positively y has to move negatively by the same amount would be messy. With refinement of shifts, all we need to do is constrain the dAy to be equal to the negative of dAx (`0::dAy:n = -1 * 0::dAx:n` ).
 
+    Also, one can set here parameters that will be logged into the [Notebook](./commontreeitems.md#Notebook), so the values can be tracked and plotted across a refinement. Right-click to toggle the log setting. Note that individual log settings will override the the `LogAllVars` preference setting (see  [Configuration variables](./others.md#config)).
+
 * **Refine (Sequential refine)** - This performs the refinement (Pawley/Rietveld/LeBail or single crystal) fit according to the controls set in the Controls data tree item. This menu item name will be "Refine" unless the datasets to be used in a sequential refinement have been selected in the [Controls data tree](./commontreeitems.md#Controls) item, at which point the name will appear as "Sequential refine".
 
     When a PWDR histogram item is selected in the data tree, or a child tree item of a PDWR histogram is selected in the tree when Refine is used, the plot of that histogram will be updated after each cycle of refinement.
 
     Once the refinement is completed, you will be offered the chance to load the results of the fit or to reject the fit,in which case no parameters will be changed, so it is possible to change settings or refinement flags and try different options. After the refinement results are reloaded, plots will be updated to reflect the new refinement values if the plot has a defined update process or will be closed as the plot contents are presumed to be obsolete and need to be manually recreated to be valid.
+    
 * **Compute partials** - 
 The term "phase partial intensities" is used to designate keeping separate track of the intensity contribution from each phase separately. When this is used, a zero-cycle refinement (meaning no parameters values are changed) where the contributions from each phase (phase partial intensities) are written for each histogram and each phase in that histogram into a single file named <project>`.partials` where <project> is the GSAS-II project (.gpx) name. This file is intended for internal use in GSAS-II and will be deleted if additional refinements are performed (as the information in them is then obsolete; use this menu command to recreate them if needed.) When the .partials file is created, the user can then choose to export the intensity information in a series of ASCII files named <project>_part_N.csv, which can be read by spreadsheets and most scientific software.
+
 * **Parameter impact** - This shows the parameters that will have the greatest improvement to the reduced \(\chi^2\) for the fit if refined. See [Toby, JAC 57, 175-180 (2024).](https://doi.org/10.1107/S1600576723011032)
+
 * **Evaluate Expression and s.u.** - This allows an expression to be entered based on multiple GSAS-II parameters that computes a value and its standard uncertainty. The uncertainty computation will use the covariance matrix and thus accounts for correlation or anti-correlation in the parameters. An example for how this might be used would be for computing the total amount along with uncertainty for an element that occurs with several refined occupancies. 
+
 * **Setup Cluster Analysis** - Uses unsupervised machine learning to group PWDR entries into groups (clusters) that share the most similarity. See the [tutorial on this](https://advancedphotonsource.github.io/GSAS-II-tutorials/ClusterAnalysis/Cluster%20and%20Outlier%20Analysis.htm) for more information. 
-* **Run Fprime** - This run the utility routine Fprime, which displays real and imaginary components of the x-ray form factors for user-selected elements, as a function of wavelength/energy. Allows for an informed choice of wavelength for resonant x-ray scattering experiments
+
+* **Run Fprime** - This run the utility routine Fprime, which displays real and imaginary components of the x-ray form factors for user-selected elements, as a function of wavelength/energy. Allows for an informed choice of wavelength for resonant x-ray scattering experiments.
+
 * **Run Absorb** - This runs the utility routine Absorb that displays the x-ray absorption for a user selected sample composition as a function of wavelength/energy. Allows determination of the maximum sample size before absorption corrections are needed or where diffraction intensities will be severely reduced by x-ray absorption. 
+
 * **Run PlotXNFF** - This runs the utility routine PlotXNFF which displays the x-ray, neutron, electron and magnetic form factors for a selected element. This imcludes
 resonant (if any) neutron scattering lengths for all isotopes of a selected element. It also displays the x-ray and magnetic neutron form factors for all valences (if any) for this element.