Retrofit Batch 1 & 2 docs: Required Input Sources + MyST links

- Add "Required Input Sources" section to filters with non-obvious upstream
  dependencies, naming the specific filter that produces each required input.
- Convert inline filter name mentions to MyST markdown links
  ([Filter Name](FilterFile.md)) so they render as clickable cross-references
  in the Sphinx-generated documentation.
- Remove redundant "Outputs" listing in ComputeFeatureNeighborCAxisMisalignments
  (auto-generated parameter table already covers it).
- Replace existing {ref} directive in ComputeGBPDMetricBased with a simpler
  MyST link.

Author: imikejackson

src/Plugins/OrientationAnalysis/docs/AlignSectionsMisorientationFilter.md

@@ -10,7 +10,7 @@ This **Filter** aligns serial sections (2D slices stacked along the Z-direction)
 
 ### When to Use This Method
 
-Use this method when your data contains crystal orientation measurements (quaternions or Euler angles) and you want to align sections based on the actual crystallographic content. This works well for most EBSD datasets. For data without orientation information, consider the **Align Sections (Feature Centroid)** or **Align Sections (Mutual Information)** methods instead.
+Use this method when your data contains crystal orientation measurements (quaternions or Euler angles) and you want to align sections based on the actual crystallographic content. This works well for most EBSD datasets. For data without orientation information, consider the [Align Sections (Feature Centroid)](../SimplnxCore/AlignSectionsFeatureCentroidFilter.md) or [Align Sections (Mutual Information)](AlignSectionsMutualInformationFilter.md) methods instead.
 
 ### How This Filter Works
 
@@ -25,7 +25,7 @@ The filter uses an iterative grid search to find the optimal alignment for each
 
 ### Local Minima Warning
 
-This iterative grid search is similar to a downhill simplex optimization and **can get caught in a local minimum**. If alignment results look incorrect, try adjusting the misorientation tolerance or consider using the **Align Sections (Feature Centroid)** method, which does not have this limitation.
+This iterative grid search is similar to a downhill simplex optimization and **can get caught in a local minimum**. If alignment results look incorrect, try adjusting the misorientation tolerance or consider using the [Align Sections (Feature Centroid)](../SimplnxCore/AlignSectionsFeatureCentroidFilter.md) method, which does not have this limitation.
 
 ### Masking
 
@@ -58,6 +58,12 @@ In this new structure, what follows is what the created structures represent:
 
 In previous versions a file would have been produced instead. If you wish to recreate this, you can write the Attribute Matrix as a CSV/Text file.
 
+### Required Input Sources
+
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+- **Mask** (optional) -- a boolean array marking valid cells, typically produced by a threshold operation such as [Multi-Threshold Objects](../SimplnxCore/MultiThresholdObjectsFilter.md).
 
 % Auto generated parameter table will be inserted here
 

src/Plugins/OrientationAnalysis/docs/AlignSectionsMutualInformationFilter.md

@@ -6,7 +6,7 @@ Reconstruction (Alignment)
 
 ## Description
 
-This **Filter** aligns serial sections (2D slices stacked along the Z-direction) by maximizing the *mutual information* between the feature patterns on neighboring slices. Rather than comparing individual cell orientations (as in **Align Sections (Misorientation)**), this method first groups cells into temporary features on each slice, then finds the shift that best aligns those feature patterns between slices.
+This **Filter** aligns serial sections (2D slices stacked along the Z-direction) by maximizing the *mutual information* between the feature patterns on neighboring slices. Rather than comparing individual cell orientations (as in [Align Sections (Misorientation)](AlignSectionsMisorientationFilter.md)), this method first groups cells into temporary features on each slice, then finds the shift that best aligns those feature patterns between slices.
 
 ### When to Use This Method
 
@@ -18,7 +18,7 @@ Mutual information is a statistical measure of how much information one variable
 
 ### How This Filter Works
 
-1. **Segment features on each slice:** Neighboring cells on each 2D slice are grouped into temporary features using a misorientation tolerance (the same algorithm as **Segment Features (Misorientation)**, applied in 2D). These feature IDs are internal to this filter and are not stored.
+1. **Segment features on each slice:** Neighboring cells on each 2D slice are grouped into temporary features using a misorientation tolerance (the same algorithm as [Segment Features (Misorientation)](EBSDSegmentFeaturesFilter.md), applied in 2D). These feature IDs are internal to this filter and are not stored.
 2. **Calculate mutual information:** For a given relative position of two slices, compute the mutual information between the feature ID patterns on the two slices.
 3. **Grid search:** Evaluate the mutual information at all 49 positions in a 7x7 grid (shifting the upper slice from -3 to +3 cells in both X and Y). Select the position with the highest mutual information.
 4. **Iterate:** Re-center the 7x7 grid on the best position and repeat until the best position no longer changes.
@@ -30,7 +30,7 @@ The *misorientation tolerance* parameter controls how cells are grouped into tem
 
 ### Local Minima Warning
 
-This iterative grid search is similar to a downhill simplex optimization and **can get caught in a local minimum**. If alignment results look incorrect, try adjusting the misorientation tolerance or consider using the **Align Sections (Feature Centroid)** method, which does not have this limitation.
+This iterative grid search is similar to a downhill simplex optimization and **can get caught in a local minimum**. If alignment results look incorrect, try adjusting the misorientation tolerance or consider using the [Align Sections (Feature Centroid)](../SimplnxCore/AlignSectionsFeatureCentroidFilter.md) method, which does not have this limitation.
 
 ### Masking
 
@@ -59,6 +59,13 @@ In this new structure, what follows is what the created structures represent:
 
 In previous versions a file would have been produced instead. If you wish to recreate this, you can write the Attribute Matrix as a CSV/Text file.
 
+### Required Input Sources
+
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+- **Mask** (optional) -- a boolean array marking valid cells, typically produced by a threshold operation such as [Multi-Threshold Objects](../SimplnxCore/MultiThresholdObjectsFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## References

src/Plugins/OrientationAnalysis/docs/ComputeAvgCAxesFilter.md

@@ -30,6 +30,15 @@ In cubic materials, the [001], [010], and [100] directions are all crystallograp
 
 The filter will produce an error if no hexagonal phases are present in the data.
 
+### Required Input Sources
+
+This filter operates on previously segmented data and requires that several prior operations have already been run:
+
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md); can also be produced from Euler angles by [Convert Orientations](ConvertOrientationsFilter.md).
+- **Cell Feature Ids** -- produced by a segmentation filter such as [Segment Features (Misorientation)](EBSDSegmentFeaturesFilter.md) or [Segment Features (C-Axis Misalignment)](CAxisSegmentFeaturesFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeAvgOrientationsFilter.md

@@ -72,6 +72,13 @@ These values may be exposed as user-configurable parameters in a future release.
 - **Features with zero elements:** Features with no elements (phase <= 0 for all voxels) will have their output arrays initialized to NaN (for vMF/Watson) or identity quaternion / zero Euler angles (for Rodrigues).
 - **Phase indexing:** The filter requires that phase values be > 0 for elements to be included in the averaging. Phase index 0 is reserved for "Unknown" in the Crystal Structures array and is always skipped.
 
+### Required Input Sources
+
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md); can also be produced from Euler angles by [Convert Orientations](ConvertOrientationsFilter.md).
+- **Cell Feature Ids** -- produced by a segmentation filter such as [Segment Features (Misorientation)](EBSDSegmentFeaturesFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeBoundaryStrengthsFilter.md

@@ -8,9 +8,9 @@ Statistics (Crystallography)
 
 This **Filter** computes slip transmission metrics for each **Face** (triangle) on a grain boundary mesh. These metrics quantify how easily plastic deformation can transfer across a grain boundary, based on the geometric alignment of slip systems in the two grains on either side.
 
-This filter computes the same metrics as the **Compute Neighbor Slip Transmission Metrics** filter, but stores results per boundary **Face** rather than per **Feature**. This makes it suitable for visualization and analysis on a **Triangle Geometry** surface mesh.
+This filter computes the same metrics as the [Compute Neighbor Slip Transmission Metrics](ComputeSlipTransmissionMetricsFilter.md) filter, but stores results per boundary **Face** rather than per **Feature**. This makes it suitable for visualization and analysis on a **Triangle Geometry** surface mesh.
 
-For a detailed explanation of the slip transmission concept and the individual metrics, see the **Compute Neighbor Slip Transmission Metrics** documentation.
+For a detailed explanation of the slip transmission concept and the individual metrics, see the [Compute Neighbor Slip Transmission Metrics](ComputeSlipTransmissionMetricsFilter.md) documentation.
 
 ### Cubic Materials Only
 
@@ -43,6 +43,15 @@ Three fracture initiation parameter values are computed per **Face**, as defined
 
 [2] [D. Kumar, T. R. Bieler, P. Eisenlohr, D. E. Mason, M. A. Crimp, F. Roters, and D. Raabe. On Predicting Nucleation of Microcracks Due to Slip Twin Interactions at Grain Boundaries in Duplex Near γ-TiAl. Journal of Engineering Materials and Technology, 130(2):021012–12, 2008. doi:10.1115/1.2841620.](https://doi.org/10.1115/1.2841620)
 
+### Required Input Sources
+
+This filter operates on a grain-boundary surface mesh and requires the following upstream steps:
+
+- **Triangle Geometry** and **Face Labels** -- produced by a surface meshing filter such as [Quick Surface Mesh](../SimplnxCore/QuickSurfaceMeshFilter.md).
+- **Average Quaternions** -- the per-feature average orientation produced by [Compute Average Orientations](ComputeAvgOrientationsFilter.md).
+- **Feature Phases** -- produced by [Compute Feature Phases](../SimplnxCore/ComputeFeaturePhasesFilter.md).
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeCAxisLocationsFilter.md

@@ -28,7 +28,13 @@ In cubic materials, the [001], [010], and [100] directions are all crystallograp
 
 ### Comparison with Compute Average C-Axis Orientations
 
-This filter computes the C-axis direction for each individual **Cell**. If you need the average C-axis direction for each **Feature** (grain) instead, use the **Compute Average C-Axis Orientations** filter.
+This filter computes the C-axis direction for each individual **Cell**. If you need the average C-axis direction for each **Feature** (grain) instead, use the [Compute Average C-Axis Orientations](ComputeAvgCAxesFilter.md) filter.
+
+### Required Input Sources
+
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md); can also be produced from Euler angles by [Convert Orientations](ConvertOrientationsFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
 
 % Auto generated parameter table will be inserted here
 

src/Plugins/OrientationAnalysis/docs/ComputeFeatureNeighborCAxisMisalignmentsFilter.md

@@ -13,23 +13,27 @@ This is distinct from a full misorientation, which considers the complete rotati
 ### Flexible Neighbor Definition
 
 The neighbor list is supplied by the user and can come from any filter that produces neighbor relationships. For example:
-- **Find Feature Neighbors** -- neighbors that physically share a boundary
-- **Compute Feature Neighborhoods** -- neighbors within a specified radius
+- [Compute Feature Neighbors](../SimplnxCore/ComputeFeatureNeighborsFilter.md) -- neighbors that physically share a boundary
+- [Compute Feature Neighborhoods](../SimplnxCore/ComputeNeighborhoodsFilter.md) -- neighbors within a specified radius
 - Any other custom filter that generates a neighbor list
 
-### Outputs
-
-- A list of C-axis misalignment angles (in degrees) for each **Feature**, one per neighbor
-- Optionally, the average misalignment across all neighbors
+The filter also optionally computes the average misalignment across all of a feature's neighbors.
 
 ### Hexagonal Materials Only
 
-Only **Features** with identical phase values and a crystal structure of **Hexagonal_High** (6/mmm) or **Hexagonal_Low** (Hexagonal 6/m (C6h)) are compared. If two **Features** have different phases or a non-hexagonal crystal structure, a value of NaN is stored for the misalignment. See the **Compute Average C-Axis Orientations** documentation for an explanation of why C-axis calculations are restricted to hexagonal materials.
+Only **Features** with identical phase values and a crystal structure of **Hexagonal_High** (6/mmm) or **Hexagonal_Low** (Hexagonal 6/m (C6h)) are compared. If two **Features** have different phases or a non-hexagonal crystal structure, a value of NaN is stored for the misalignment. See the [Compute Average C-Axis Orientations](ComputeAvgCAxesFilter.md) documentation for an explanation of why C-axis calculations are restricted to hexagonal materials.
 
 ### Note
 
 Results from this filter may differ from the original DREAM.3D 6.5 version by approximately 0.0001 degrees due to the use of double precision and Eigen for matrix operations.
 
+### Required Input Sources
+
+- **Neighbor List** -- produced by [Compute Feature Neighbors](../SimplnxCore/ComputeFeatureNeighborsFilter.md) or [Compute Feature Neighborhoods](../SimplnxCore/ComputeNeighborhoodsFilter.md).
+- **Average Quaternions** -- produced by [Compute Average Orientations](ComputeAvgOrientationsFilter.md).
+- **Feature Phases** -- produced by [Compute Feature Phases](../SimplnxCore/ComputeFeaturePhasesFilter.md).
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeFeatureNeighborMisorientationsFilter.md

@@ -16,6 +16,13 @@ Optionally, the filter can also compute the average misorientation between a **F
 
 Only **Features** with identical crystal structures are compared. If two neighboring **Features** have different crystal structures, a value of NaN is stored for their misorientation, since misorientation between different crystal systems is not physically meaningful.
 
+### Required Input Sources
+
+- **Neighbor List** -- produced by [Compute Feature Neighbors](../SimplnxCore/ComputeFeatureNeighborsFilter.md) or [Compute Feature Neighborhoods](../SimplnxCore/ComputeNeighborhoodsFilter.md).
+- **Average Quaternions** -- produced by [Compute Average Orientations](ComputeAvgOrientationsFilter.md).
+- **Feature Phases** -- produced by [Compute Feature Phases](../SimplnxCore/ComputeFeaturePhasesFilter.md).
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeFeatureReferenceCAxisMisorientationsFilter.md

@@ -21,12 +21,20 @@ A low average misalignment indicates a grain with a uniform C-axis orientation.
 
 ### Hexagonal Materials Only
 
-This filter requires at least one hexagonal crystal structure phase (6/m or 6/mmm). Non-hexagonal phases are skipped. See the **Compute Average C-Axis Orientations** documentation for an explanation of why C-axis calculations are restricted to hexagonal materials.
+This filter requires at least one hexagonal crystal structure phase (6/m or 6/mmm). Non-hexagonal phases are skipped. See the [Compute Average C-Axis Orientations](ComputeAvgCAxesFilter.md) documentation for an explanation of why C-axis calculations are restricted to hexagonal materials.
 
 ### Note
 
 Results may differ from the DREAM3D 6.6 version by approximately 0.0001 degrees due to improved double-precision calculations for cross-platform accuracy.
 
+### Required Input Sources
+
+- **Cell Feature Ids** -- produced by a segmentation filter such as [Segment Features (Misorientation)](EBSDSegmentFeaturesFilter.md) or [Segment Features (C-Axis Misalignment)](CAxisSegmentFeaturesFilter.md).
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Average C-Axes** -- produced by [Compute Average C-Axis Orientations](ComputeAvgCAxesFilter.md).
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines

src/Plugins/OrientationAnalysis/docs/ComputeFeatureReferenceMisorientationsFilter.md

@@ -45,6 +45,15 @@ feature boundary, and use that voxel's orientation as the **reference orientatio
 
 ![ComputeFeatureReferenceMisorientations_1.png](Images/ComputeFeatureReferenceMisorientations_1.png)
 
+### Required Input Sources
+
+- **Cell Feature Ids** -- produced by a segmentation filter such as [Segment Features (Misorientation)](EBSDSegmentFeaturesFilter.md).
+- **Cell Quaternions** -- typically read from EBSD data via [Read H5EBSD](ReadH5EbsdFilter.md), [Read CTF Data](ReadCtfDataFilter.md), or [Read ANG Data](ReadAngDataFilter.md).
+- **Cell Phases** -- typically read from EBSD data alongside the quaternions.
+- **Average Quaternions** (for Average Feature Orientation mode) -- produced by [Compute Average Orientations](ComputeAvgOrientationsFilter.md).
+- **Boundary Euclidean Distances** (for Orientation Farthest from Feature Boundary mode) -- produced by [Compute Euclidean Distance Map](../SimplnxCore/ComputeEuclideanDistMapFilter.md).
+- **Crystal Structures** -- ensemble-level array read from EBSD data or created by [Create Ensemble Info](CreateEnsembleInfoFilter.md).
+
 % Auto generated parameter table will be inserted here
 
 ## Example Pipelines