From d28ff0c9086504f06611e529c590e704d4de69a2 Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 10:57:28 +1000
Subject: [PATCH 01/16] Create check-copilot-instructions.yml

---
 .../workflows/check-copilot-instructions.yml  | 118 ++++++++++++++++++
 1 file changed, 118 insertions(+)
 create mode 100644 .github/workflows/check-copilot-instructions.yml

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
new file mode 100644
index 0000000..9a06155
--- /dev/null
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -0,0 +1,118 @@
+name: Check Copilot Instructions Sync
+
+on:
+  push:
+    branches: '*'
+  pull_request:
+    branches: '*'
+
+jobs:
+  check-copilot-instructions:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout current repository
+      uses: actions/checkout@v4
+    
+    - name: Download copilot-instructions.md from flipDevTools
+      id: download-source
+      run: |
+        echo "Downloading copilot-instructions.md from flipDevTools..."
+        
+        # Try multiple possible paths for the copilot instructions
+        POSSIBLE_PATHS=(
+          ".github/copilot-instructions.md"
+          "copilot-instructions.md"
+          ".github/copilot_instructions.md"
+          "docs/copilot-instructions.md"
+        )
+        
+        DOWNLOADED=false
+        for path in "${POSSIBLE_PATHS[@]}"; do
+          echo "Trying path: $path"
+          if curl -s -H "Authorization: token ${{ secrets.TOKEN }}" \
+                  -H "Accept: application/vnd.github.v3.raw" \
+                  -o /tmp/source-copilot-instructions.md \
+                  "https://api.github.com/repos/Displayr/flipDevTools/contents/$path" 2>/dev/null; then
+            
+            # Check if we got actual content (not an error response)
+            if [ -f /tmp/source-copilot-instructions.md ] && [ -s /tmp/source-copilot-instructions.md ]; then
+              # Verify it's not a JSON error response
+              if ! grep -q '"message".*"Not Found"' /tmp/source-copilot-instructions.md; then
+                echo "✅ Successfully downloaded from: $path"
+                echo "source_path=$path" >> $GITHUB_OUTPUT
+                DOWNLOADED=true
+                break
+              fi
+            fi
+          fi
+        done
+        
+        if [ "$DOWNLOADED" = false ]; then
+          echo "❌ Could not find copilot-instructions.md in flipDevTools repo"
+          echo "This may indicate the file doesn't exist or has been moved."
+          echo "Please check the flipDevTools repository structure."
+          exit 1
+        fi
+    
+    - name: Check if local copilot-instructions.md exists
+      id: check-local
+      run: |
+        if [ ! -f .github/copilot-instructions.md ]; then
+          echo "❌ No copilot-instructions.md found in this repository"
+          echo "Expected location: .github/copilot-instructions.md"
+          echo "exists=false" >> $GITHUB_OUTPUT
+          exit 1
+        else
+          echo "✅ Found local copilot-instructions.md"
+          echo "exists=true" >> $GITHUB_OUTPUT
+        fi
+    
+    - name: Compare files
+      run: |
+        echo "Comparing copilot-instructions.md files..."
+        echo "Source: flipDevTools/${{ steps.download-source.outputs.source_path }}"
+        echo "Local: .github/copilot-instructions.md"
+        echo ""
+        
+        # Compare the files
+        if diff -u /tmp/source-copilot-instructions.md .github/copilot-instructions.md > /tmp/diff_output; then
+          echo "✅ Files match perfectly!"
+          echo "Your copilot-instructions.md is up to date with flipDevTools."
+        else
+          echo "❌ Files do not match!"
+          echo ""
+          echo "Differences found:"
+          echo "=================="
+          cat /tmp/diff_output
+          echo "=================="
+          echo ""
+          echo "To fix this issue:"
+          echo "1. Update your .github/copilot-instructions.md to match the source"
+          echo "2. Or run the update-copilot-instructions workflow"
+          echo "3. Or manually sync the files"
+          echo ""
+          echo "Source file location: flipDevTools/${{ steps.download-source.outputs.source_path }}"
+          exit 1
+        fi
+    
+    - name: Verify file integrity
+      run: |
+        echo "Verifying file integrity..."
+        
+        # Check that the local file is not empty
+        if [ ! -s .github/copilot-instructions.md ]; then
+          echo "❌ Local copilot-instructions.md is empty"
+          exit 1
+        fi
+        
+        # Check that it contains expected content patterns
+        if ! grep -q -i "copilot\|instruction\|coding\|standard" .github/copilot-instructions.md; then
+          echo "⚠️  Warning: File doesn't seem to contain typical copilot instruction content"
+          echo "Please verify the file contains the expected coding standards and instructions"
+        else
+          echo "✅ File appears to contain valid copilot instructions"
+        fi
+        
+        echo "File size: $(wc -c < .github/copilot-instructions.md) bytes"
+        echo "Line count: $(wc -l < .github/copilot-instructions.md) lines"
\ No newline at end of file

From 36df9de258d88374868b9b960e1420f97d8b3efd Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 11:03:30 +1000
Subject: [PATCH 02/16] Create copilot-instructions.md

---
 .github/copilot-instructions.md | 226 ++++++++++++++++++++++++++++++++
 1 file changed, 226 insertions(+)
 create mode 100644 .github/copilot-instructions.md

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
new file mode 100644
index 0000000..9a6a586
--- /dev/null
+++ b/.github/copilot-instructions.md
@@ -0,0 +1,226 @@
+# Copilot Instructions for flipData
+
+This document provides coding standards and best practices for the flipData R package development.
+
+## General R Coding Standards
+
+### Assignment Operators
+- **ALWAYS use `<-` for assignment, never `=`**
+- Function parameters should use `=` (this is correct R syntax)
+- Examples:
+  ```r
+  # Correct
+  my_variable <- some_function(param = value)
+  
+  # Incorrect
+  my_variable = some_function(param = value)
+  ```
+
+### String Quotes
+- **Use double quotes `"` for strings, avoid single quotes `'`**
+- Exception: Single quotes are acceptable within double-quoted strings
+- Examples:
+  ```r
+  # Correct
+  message <- "This is a string"
+  pattern <- "Can't use single quotes here"
+  
+  # Incorrect
+  message <- 'This is a string'
+  ```
+
+### Line Length
+- **Maximum line length: 120 characters**
+- Break long lines using appropriate indentation
+- Function calls with many parameters should be broken across lines:
+  ```r
+  # Correct
+  result <- some_long_function_name(
+      parameter_one = value1,
+      parameter_two = value2,
+      parameter_three = value3
+  )
+  
+  # Also correct for long expressions
+  long_message <- paste0("This is a very long message that exceeds ",
+                        "the line length limit and should be broken ",
+                        "across multiple lines")
+  ```
+
+### Naming Conventions
+- **Variables and functions**: Use `snake_case` or `dotted.case` (prefer `dotted.case` for parameters)
+- **Constants**: Use `UPPER_CASE`
+- **Private functions**: Prefix with `.` (e.g., `.private_function`)
+
+### Indentation and Spacing
+- **Use 4 spaces for indentation, never tabs**
+- Add spaces around operators (`<-`, `=`, `+`, `-`, etc.)
+- No trailing whitespace
+
+## flipData Package Specific Guidelines
+
+### Error Handling
+- **Use `flipU::StopForUserError()` for user-facing errors**
+- Include clear, actionable error messages
+- Example:
+  ```r
+  if (length(data) == 0) {
+      StopForUserError("No data provided. Please supply a valid dataset.")
+  }
+  ```
+
+### Dependencies
+- **Import functions explicitly using `@importFrom`**
+- Common imports for flipData:
+  ```r
+  #' @importFrom flipU StopForUserError
+  #' @importFrom flipAPI QLoadData
+  #' @importFrom haven read_sav
+  ```
+
+### Data Handling
+- **Preserve SPSS metadata** when working with .sav files
+- Use `attr()` to maintain variable labels and value labels
+- Handle missing data appropriately
+
+### Function Documentation
+- **All exported functions MUST have complete roxygen2 documentation**
+- Include `@param` for all parameters
+- Include `@return` describing the return value
+- Include `@export` for exported functions
+- Use `@noRd` for internal functions
+- Example:
+  ```r
+  #' Merge multiple SPSS data sets
+  #'
+  #' @param data.set.names A character vector of data set names
+  #' @param min.data.sets Minimum number of data sets required
+  #' @return A list of data frames
+  #' @export
+  #' @importFrom flipU StopForUserError
+  ```
+
+### SPSS Integration
+- **Variable names**: Ensure compatibility with SPSS naming restrictions
+- **Reserved keywords**: Handle SPSS reserved words appropriately
+- **File handling**: Use proper error handling for file I/O operations
+
+## Code Quality Standards
+
+### Functions
+- **Keep functions focused** - one responsibility per function
+- **Use descriptive names** that clearly indicate purpose
+- **Validate inputs** at the beginning of functions
+- **Return consistent types**
+
+### Comments
+- **Use `#` for single-line comments**
+- **Explain the "why", not the "what"**
+- **Document complex algorithms or business logic**
+- **Keep comments up-to-date with code changes**
+
+### Testing
+- **Write unit tests** for all exported functions
+- **Use `testthat` framework**
+- **Test edge cases and error conditions**
+- **Maintain high test coverage**
+
+## File Organization
+
+### R Files
+- **One main function per file** when possible
+- **Group related utility functions** together
+- **Use clear, descriptive file names**
+
+### Documentation
+- **Keep man/ directory up-to-date** with roxygen2
+- **Update NAMESPACE automatically** with roxygen2
+- **Maintain comprehensive vignettes** for complex functionality
+
+## Git and Version Control
+
+### Commit Messages
+- **Use descriptive commit messages**
+- **Start with verb in present tense** (e.g., "Add", "Fix", "Update")
+- **Reference issues when applicable**
+
+### Branching
+- **Use feature branches** for development
+- **Keep branches focused** on single features or fixes
+- **Delete merged branches** to keep repository clean
+
+## Performance Considerations
+
+### Memory Usage
+- **Avoid unnecessary data copying**
+- **Use appropriate data structures**
+- **Consider memory-efficient alternatives** for large datasets
+
+### Computational Efficiency
+- **Vectorize operations** when possible
+- **Avoid loops** when vectorized alternatives exist
+- **Profile code** for performance bottlenecks
+
+## Security and Privacy
+
+### Data Handling
+- **Never commit sensitive data** to version control
+- **Use appropriate file permissions**
+- **Handle user data responsibly**
+
+## Package Maintenance
+
+### Dependencies
+- **Minimize external dependencies**
+- **Pin version ranges** for critical dependencies
+- **Regularly update dependencies** for security patches
+
+### Documentation
+- **Keep README.md current**
+- **Update NEWS.md** for each release
+- **Maintain clear installation instructions**
+
+## Example Code Patterns
+
+### Typical Function Structure
+```r
+#' Function title
+#'
+#' @param data A data frame
+#' @param subset Optional subset condition
+#' @return Processed data frame
+#' @export
+#' @importFrom flipU StopForUserError
+myFunction <- function(data, subset = NULL) {
+    # Validate inputs
+    if (missing(data) || !is.data.frame(data)) {
+        StopForUserError("Data must be a data frame")
+    }
+    
+    # Process data
+    result <- processData(data, subset)
+    
+    # Return result
+    result
+}
+```
+
+### Error Handling Pattern
+```r
+# Check for required conditions
+if (condition_not_met) {
+    StopForUserError("Clear description of what went wrong and how to fix it")
+}
+```
+
+### SPSS Integration Pattern
+```r
+# Preserve SPSS attributes
+original_attrs <- attributes(data)
+data <- process_data(data)
+attributes(data) <- original_attrs
+```
+
+---
+
+These instructions ensure code quality, maintainability, and consistency across the flipData package. Always prioritize clarity and user experience in your implementations.
\ No newline at end of file

From 362af12edd26e2e5284e9ebcc2ea1876ad9ec116 Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 11:05:34 +1000
Subject: [PATCH 03/16] Only on PR

---
 .github/workflows/check-copilot-instructions.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index 9a06155..59fef5b 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -1,8 +1,6 @@
 name: Check Copilot Instructions Sync
 
 on:
-  push:
-    branches: '*'
   pull_request:
     branches: '*'
 

From fc4ee5b19802f4a03a77777e26f6ff51eea4f6af Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 11:22:49 +1000
Subject: [PATCH 04/16] Update check-copilot-instructions.yml

---
 .github/workflows/check-copilot-instructions.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index 59fef5b..1bc49cb 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -28,8 +28,7 @@ jobs:
         DOWNLOADED=false
         for path in "${POSSIBLE_PATHS[@]}"; do
           echo "Trying path: $path"
-          if curl -s -H "Authorization: token ${{ secrets.TOKEN }}" \
-                  -H "Accept: application/vnd.github.v3.raw" \
+          if curl -s -H "Accept: application/vnd.github.v3.raw" \
                   -o /tmp/source-copilot-instructions.md \
                   "https://api.github.com/repos/Displayr/flipDevTools/contents/$path" 2>/dev/null; then
             

From 0a0e4dc751e68143cf5aa1b8c7ea538230bbd806 Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 11:28:29 +1000
Subject: [PATCH 05/16] flipU

---
 .github/workflows/check-copilot-instructions.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index 1bc49cb..91859df 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -12,10 +12,10 @@ jobs:
     - name: Checkout current repository
       uses: actions/checkout@v4
     
-    - name: Download copilot-instructions.md from flipDevTools
+    - name: Download copilot-instructions.md from flipU
       id: download-source
       run: |
-        echo "Downloading copilot-instructions.md from flipDevTools..."
+        echo "Downloading copilot-instructions.md from flipU..."
         
         # Try multiple possible paths for the copilot instructions
         POSSIBLE_PATHS=(
@@ -30,7 +30,7 @@ jobs:
           echo "Trying path: $path"
           if curl -s -H "Accept: application/vnd.github.v3.raw" \
                   -o /tmp/source-copilot-instructions.md \
-                  "https://api.github.com/repos/Displayr/flipDevTools/contents/$path" 2>/dev/null; then
+                  "https://api.github.com/repos/Displayr/flipU/contents/$path" 2>/dev/null; then
             
             # Check if we got actual content (not an error response)
             if [ -f /tmp/source-copilot-instructions.md ] && [ -s /tmp/source-copilot-instructions.md ]; then
@@ -46,9 +46,9 @@ jobs:
         done
         
         if [ "$DOWNLOADED" = false ]; then
-          echo "❌ Could not find copilot-instructions.md in flipDevTools repo"
+          echo "❌ Could not find copilot-instructions.md in flipU repo"
           echo "This may indicate the file doesn't exist or has been moved."
-          echo "Please check the flipDevTools repository structure."
+          echo "Please check the flipU repository structure."
           exit 1
         fi
     
@@ -68,14 +68,14 @@ jobs:
     - name: Compare files
       run: |
         echo "Comparing copilot-instructions.md files..."
-        echo "Source: flipDevTools/${{ steps.download-source.outputs.source_path }}"
+        echo "Source: flipU/${{ steps.download-source.outputs.source_path }}"
         echo "Local: .github/copilot-instructions.md"
         echo ""
         
         # Compare the files
         if diff -u /tmp/source-copilot-instructions.md .github/copilot-instructions.md > /tmp/diff_output; then
           echo "✅ Files match perfectly!"
-          echo "Your copilot-instructions.md is up to date with flipDevTools."
+          echo "Your copilot-instructions.md is up to date with flipU."
         else
           echo "❌ Files do not match!"
           echo ""
@@ -89,7 +89,7 @@ jobs:
           echo "2. Or run the update-copilot-instructions workflow"
           echo "3. Or manually sync the files"
           echo ""
-          echo "Source file location: flipDevTools/${{ steps.download-source.outputs.source_path }}"
+          echo "Source file location: flipU/${{ steps.download-source.outputs.source_path }}"
           exit 1
         fi
     

From 4cbeb42ca3c316888509fe6f09e544764b58b6e6 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 11:42:08 +1000
Subject: [PATCH 06/16] Use flipU instructions for merge

---
 .github/copilot-instructions.md | 318 ++++++++++----------------------
 1 file changed, 93 insertions(+), 225 deletions(-)

diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
index 9a6a586..16819b3 100644
--- a/.github/copilot-instructions.md
+++ b/.github/copilot-instructions.md
@@ -1,226 +1,94 @@
-# Copilot Instructions for flipData
-
-This document provides coding standards and best practices for the flipData R package development.
-
-## General R Coding Standards
-
-### Assignment Operators
-- **ALWAYS use `<-` for assignment, never `=`**
-- Function parameters should use `=` (this is correct R syntax)
-- Examples:
-  ```r
-  # Correct
-  my_variable <- some_function(param = value)
-  
-  # Incorrect
-  my_variable = some_function(param = value)
-  ```
-
-### String Quotes
-- **Use double quotes `"` for strings, avoid single quotes `'`**
-- Exception: Single quotes are acceptable within double-quoted strings
-- Examples:
-  ```r
-  # Correct
-  message <- "This is a string"
-  pattern <- "Can't use single quotes here"
-  
-  # Incorrect
-  message <- 'This is a string'
-  ```
-
-### Line Length
-- **Maximum line length: 120 characters**
-- Break long lines using appropriate indentation
-- Function calls with many parameters should be broken across lines:
-  ```r
-  # Correct
-  result <- some_long_function_name(
-      parameter_one = value1,
-      parameter_two = value2,
-      parameter_three = value3
-  )
-  
-  # Also correct for long expressions
-  long_message <- paste0("This is a very long message that exceeds ",
-                        "the line length limit and should be broken ",
-                        "across multiple lines")
-  ```
-
-### Naming Conventions
-- **Variables and functions**: Use `snake_case` or `dotted.case` (prefer `dotted.case` for parameters)
-- **Constants**: Use `UPPER_CASE`
-- **Private functions**: Prefix with `.` (e.g., `.private_function`)
-
-### Indentation and Spacing
-- **Use 4 spaces for indentation, never tabs**
-- Add spaces around operators (`<-`, `=`, `+`, `-`, etc.)
-- No trailing whitespace
-
-## flipData Package Specific Guidelines
-
-### Error Handling
-- **Use `flipU::StopForUserError()` for user-facing errors**
-- Include clear, actionable error messages
-- Example:
-  ```r
-  if (length(data) == 0) {
-      StopForUserError("No data provided. Please supply a valid dataset.")
-  }
-  ```
-
-### Dependencies
-- **Import functions explicitly using `@importFrom`**
-- Common imports for flipData:
-  ```r
-  #' @importFrom flipU StopForUserError
-  #' @importFrom flipAPI QLoadData
-  #' @importFrom haven read_sav
-  ```
-
-### Data Handling
-- **Preserve SPSS metadata** when working with .sav files
-- Use `attr()` to maintain variable labels and value labels
-- Handle missing data appropriately
-
-### Function Documentation
-- **All exported functions MUST have complete roxygen2 documentation**
-- Include `@param` for all parameters
-- Include `@return` describing the return value
-- Include `@export` for exported functions
-- Use `@noRd` for internal functions
-- Example:
-  ```r
-  #' Merge multiple SPSS data sets
-  #'
-  #' @param data.set.names A character vector of data set names
-  #' @param min.data.sets Minimum number of data sets required
-  #' @return A list of data frames
-  #' @export
-  #' @importFrom flipU StopForUserError
-  ```
-
-### SPSS Integration
-- **Variable names**: Ensure compatibility with SPSS naming restrictions
-- **Reserved keywords**: Handle SPSS reserved words appropriately
-- **File handling**: Use proper error handling for file I/O operations
-
-## Code Quality Standards
-
-### Functions
-- **Keep functions focused** - one responsibility per function
-- **Use descriptive names** that clearly indicate purpose
-- **Validate inputs** at the beginning of functions
-- **Return consistent types**
-
-### Comments
-- **Use `#` for single-line comments**
-- **Explain the "why", not the "what"**
-- **Document complex algorithms or business logic**
-- **Keep comments up-to-date with code changes**
-
-### Testing
-- **Write unit tests** for all exported functions
-- **Use `testthat` framework**
-- **Test edge cases and error conditions**
-- **Maintain high test coverage**
-
-## File Organization
-
-### R Files
-- **One main function per file** when possible
-- **Group related utility functions** together
-- **Use clear, descriptive file names**
-
-### Documentation
-- **Keep man/ directory up-to-date** with roxygen2
-- **Update NAMESPACE automatically** with roxygen2
-- **Maintain comprehensive vignettes** for complex functionality
-
-## Git and Version Control
-
-### Commit Messages
-- **Use descriptive commit messages**
-- **Start with verb in present tense** (e.g., "Add", "Fix", "Update")
-- **Reference issues when applicable**
-
-### Branching
-- **Use feature branches** for development
-- **Keep branches focused** on single features or fixes
-- **Delete merged branches** to keep repository clean
-
-## Performance Considerations
-
-### Memory Usage
-- **Avoid unnecessary data copying**
-- **Use appropriate data structures**
-- **Consider memory-efficient alternatives** for large datasets
-
-### Computational Efficiency
-- **Vectorize operations** when possible
-- **Avoid loops** when vectorized alternatives exist
-- **Profile code** for performance bottlenecks
-
-## Security and Privacy
-
-### Data Handling
-- **Never commit sensitive data** to version control
-- **Use appropriate file permissions**
-- **Handle user data responsibly**
-
-## Package Maintenance
-
-### Dependencies
-- **Minimize external dependencies**
-- **Pin version ranges** for critical dependencies
-- **Regularly update dependencies** for security patches
-
-### Documentation
-- **Keep README.md current**
-- **Update NEWS.md** for each release
-- **Maintain clear installation instructions**
-
-## Example Code Patterns
-
-### Typical Function Structure
-```r
-#' Function title
-#'
-#' @param data A data frame
-#' @param subset Optional subset condition
-#' @return Processed data frame
-#' @export
-#' @importFrom flipU StopForUserError
-myFunction <- function(data, subset = NULL) {
-    # Validate inputs
-    if (missing(data) || !is.data.frame(data)) {
-        StopForUserError("Data must be a data frame")
+## Code Review Guidelines
+
+### R Package Standards
+- This is a standard R package - all changes must maintain CRAN-compatible structure
+- NAMESPACE is auto-generated by roxygen2 - never edit it directly
+- DESCRIPTION must be kept valid with proper versioning
+- All exported functions require complete roxygen2 documentation
+
+### Code Style Requirements
+- **Naming conventions**: Use `dotted.case`, `camelCase`, or `PascalCase` consistently
+  - Parameters/variables: `dotted.case` (e.g., `response.format`, `text.variables`, `api.key`)
+  - Functions: `camelCase` or `PascalCase` or `.camelCase` (e.g., `checkInputs`, `MakeOutput`, or `.nestedHelper`)
+    - Use `PascalCase` for exported functions (e.g., `AddFormulaBars`, `RegressionTable`)
+    - Use `camelCase` for internal/helper functions (e.g., `checkInputs`)
+    - Use `.camelCase` for internal nested functions
+    e.g., within an internal function
+    ```
+    addOneToAll <- function(x) {
+        .helpAdd <- function(y) {
+            y + 1
+        }
+        vapply(x, .helpAdd, numeric(1L)
     }
-    
-    # Process data
-    result <- processData(data, subset)
-    
-    # Return result
-    result
-}
-```
-
-### Error Handling Pattern
-```r
-# Check for required conditions
-if (condition_not_met) {
-    StopForUserError("Clear description of what went wrong and how to fix it")
-}
-```
-
-### SPSS Integration Pattern
-```r
-# Preserve SPSS attributes
-original_attrs <- attributes(data)
-data <- process_data(data)
-attributes(data) <- original_attrs
-```
-
----
-
-These instructions ensure code quality, maintainability, and consistency across the flipData package. Always prioritize clarity and user experience in your implementations.
\ No newline at end of file
+    ```
+- **Object name length**: Maximum 50 characters
+- **Assignment**: Always use `<-` for assignment, never `=`
+- **Pipes**: Use native pipe `|>` for chaining operations
+- **NULL coalescing**: Use `%||%` operator for NULL defaults
+- **Indentation**: 4 spaces
+- **Line length**: Maximum 120 characters
+- **No trailing whitespace**
+- **Consistent quotes**: Always use double quotes `"` for strings. It is ok for quotes within strings to be single quotes `'` but the parent string must use double quotes.
+- **Prefer full words over abbreviations**: e.g., `response.format` over `resp.fmt`
+- **Function names**: Use descriptive names that clearly indicate purpose: e.g. `createSummaryTableForRegressionResults()` rather than `make()`
+- **Braces**: Always use braces `{}` for functions, `if`, `else if` and `else` blocks. Except for the case of a single line statements. In particular, use Kernighan & Ritchie style braces.
+    - e.g. The following is acceptable:
+    ```
+    y <- if (x > 0) x else -x
+    w <- if (condition) {
+        z <- computeSomething(x)
+        foo(z)
+    } else {
+        z <- computeSomethingElse(x)
+        bar(z)
+    }
+    ```
+- **Redundant return**: Avoid using `return()` unless exiting early from a function. The last evaluated expression is returned by default.
+
+### Function Design Patterns
+- **Error handling**: Use `flipU::StopForUserError()` for user-facing errors with clear, actionable messages
+- **Return values**: Functions used for validation/side effects should explicitly return `NULL`
+- **Internal functions**: Internal or helper functions should not be exported; use `@noRd` in roxygen comments
+- **File organization**: Group related functions into logical files (e.g., check.inputs.R, tidy.inputs.R)
+- **Importing functions**: Use `@importFrom` in roxygen comments for all external package functions used and avoid usage of `:::`.
+- **Type checking**: Don't use `sapply`. Use `vapply` with a specified return type for type safety.
+- **Formatting numbers for printing**: Use `flipFormat::FormatAsReal()` and `flipFormat::FormatAsPercent()` instead of base R formatting functions
+- **Calculations**: Use the following functions where possible:
+    - `verbs::Average` instead of `mean`
+    - `verbs::Sum` instead of `sum`
+    - `verbs::Min` instead of `min`
+    - `verbs::Max` instead of `max`
+    - `verbs::Variance` instead of `var`
+    - `verbs::StandardDeviation` instead of `sd`
+
+### Documentation Requirements
+- All exported functions must have complete roxygen2 documentation
+- Required tags: `@param` (for each parameter), `@return`, `@export`
+- Include `@importFrom` for all external package functions used
+- Optional but recommended: `@details`, `@examples`
+
+### Testing Requirements
+- Use testthat v3 framework (edition 3)
+- Test files must be in `tests/testthat/` with `test-` prefix
+- Include snapshot tests where appropriate (`_snaps/` directory)
+
+### Security & Best Practices
+- **Never log or expose API keys or secrets**
+
+## PR Review Focus Areas
+1. **Breaking changes**: Flag any changes to exported function signatures
+2. **Documentation**: Ensure all new/modified exports have complete roxygen2 docs
+3. **Testing**: Verify new functionality has corresponding tests
+4. **Style consistency**: Check adherence to naming convetions, `<-`, `|>` patterns
+5. **Error messages**: Ensure user-facing errors are clear and helpful
+6. **Line length**: Flag lines exceeding 120 characters
+7. **Object names**: Ensure names don't exceed 50 characters
+
+## Common Issues to Flag
+- Using `=` instead of `<-` for assignment
+- Missing or incomplete roxygen2 documentation
+- Direct API key exposure or logging
+- Inconsistent naming conventions (mixing dotted.case/camelCase inappropriately)
+- New dependencies without justification
+- Error messages that don't guide users to solutions

From a012c1390c7bbbfcb76e0ff88da4a844899e67b9 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 11:49:17 +1000
Subject: [PATCH 07/16] Add .github to .Rbuildignore

---
 .Rbuildignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.Rbuildignore b/.Rbuildignore
index 7856c9b..5234e54 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 .*~
 ^\.circleci/config\.yml$
+.github

From aa2a138e40c6c92348e9131b086f7aa6d9e36926 Mon Sep 17 00:00:00 2001
From: Justin Yap <justin.yap@displayr.com>
Date: Fri, 3 Oct 2025 11:50:57 +1000
Subject: [PATCH 08/16] Add script

---
 scripts/update-copilot-instructions.sh | 130 +++++++++++++++++++++++++
 1 file changed, 130 insertions(+)
 create mode 100644 scripts/update-copilot-instructions.sh

diff --git a/scripts/update-copilot-instructions.sh b/scripts/update-copilot-instructions.sh
new file mode 100644
index 0000000..5a023dc
--- /dev/null
+++ b/scripts/update-copilot-instructions.sh
@@ -0,0 +1,130 @@
+#!/bin/bash
+
+# Script to update copilot-instructions.md from flipU repository
+# Usage: ./update-copilot-instructions.sh
+
+set -e  # Exit on any error
+
+# Colors for output
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+# Function to print colored output
+print_status() {
+    echo -e "${BLUE}[INFO]${NC} $1"
+}
+
+print_success() {
+    echo -e "${GREEN}[SUCCESS]${NC} $1"
+}
+
+print_warning() {
+    echo -e "${YELLOW}[WARNING]${NC} $1"
+}
+
+print_error() {
+    echo -e "${RED}[ERROR]${NC} $1"
+}
+
+# Check if we're in a git repository
+if [ ! -d ".git" ]; then
+    print_error "This script must be run from the root of a git repository"
+    exit 1
+fi
+
+# Create .github directory if it doesn't exist
+if [ ! -d ".github" ]; then
+    print_status "Creating .github directory..."
+    mkdir -p .github
+fi
+
+# Try multiple possible paths for the copilot instructions
+POSSIBLE_PATHS=(
+    ".github/copilot-instructions.md"
+    "copilot-instructions.md"
+    ".github/copilot_instructions.md"
+    "docs/copilot-instructions.md"
+    ".github/copilot-instructions.md"
+)
+
+print_status "Searching for copilot-instructions.md in flipU repository..."
+
+DOWNLOADED=false
+for path in "${POSSIBLE_PATHS[@]}"; do
+    print_status "Trying path: $path"
+    
+    HTTP_CODE=$(curl -s -w "%{http_code}" \
+                     -H "Accept: application/vnd.github.v3.raw" \
+                     -o "/tmp/copilot-instructions-temp.md" \
+                     "https://api.github.com/repos/Displayr/flipU/contents/$path" 2>/dev/null || echo "000")
+    
+    if [ "$HTTP_CODE" = "200" ]; then
+        # Check if we got actual content (not an error response)
+        if [ -f "/tmp/copilot-instructions-temp.md" ] && [ -s "/tmp/copilot-instructions-temp.md" ]; then
+            # Verify it's not a JSON error response
+            if ! grep -q '"message".*"Not Found"' "/tmp/copilot-instructions-temp.md" 2>/dev/null; then
+                print_success "Successfully downloaded from: $path"
+                mv "/tmp/copilot-instructions-temp.md" ".github/copilot-instructions.md"
+                DOWNLOADED=true
+                SOURCE_PATH=$path
+                break
+            fi
+        fi
+    elif [ "$HTTP_CODE" = "404" ]; then
+        print_status "File not found at: $path"
+    else
+        print_warning "HTTP $HTTP_CODE when accessing: $path"
+    fi
+done
+
+# Clean up temp file
+rm -f "/tmp/copilot-instructions-temp.md"
+
+if [ "$DOWNLOADED" = false ]; then
+    print_error "Could not find copilot-instructions.md in flipU repository"
+    print_error "Checked paths: ${POSSIBLE_PATHS[*]}"
+    
+    # Try to list available files for debugging
+    print_status "Attempting to list available files in flipU..."
+    curl -s "https://api.github.com/repos/Displayr/flipU/contents" | \
+         grep '"name"' | head -10 || print_warning "Could not list repository contents"
+    
+    exit 1
+fi
+
+# Verify the downloaded file
+if [ ! -s ".github/copilot-instructions.md" ]; then
+    print_error "Downloaded file is empty"
+    exit 1
+fi
+
+# Check if it looks like a valid copilot instructions file
+if ! grep -q -i "copilot\|instruction\|coding\|standard" ".github/copilot-instructions.md"; then
+    print_warning "Downloaded file may not contain typical copilot instruction content"
+    print_warning "Please verify the content manually"
+fi
+
+# Show file information
+FILE_SIZE=$(wc -c < ".github/copilot-instructions.md")
+LINE_COUNT=$(wc -l < ".github/copilot-instructions.md")
+
+print_success "File updated successfully!"
+print_status "Source: flipU/$SOURCE_PATH"
+print_status "Local: .github/copilot-instructions.md"
+print_status "Size: $FILE_SIZE bytes"
+print_status "Lines: $LINE_COUNT"
+
+# Check git status for informational purposes only
+if command -v git >/dev/null 2>&1; then
+    if git diff --quiet .github/copilot-instructions.md 2>/dev/null; then
+        print_status "No changes detected in copilot-instructions.md"
+    else
+        print_status "Changes detected in copilot-instructions.md"
+        print_status "File updated"
+    fi
+fi
+
+print_success "Update completed successfully!"
\ No newline at end of file

From 0ed23dfa1353f46a184e49873e50c3729c55ad09 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 12:04:57 +1000
Subject: [PATCH 09/16] Use variables to define filenames

---
 scripts/update-copilot-instructions.sh | 34 ++++++++++++++------------
 1 file changed, 18 insertions(+), 16 deletions(-)

diff --git a/scripts/update-copilot-instructions.sh b/scripts/update-copilot-instructions.sh
index 5a023dc..d091e30 100644
--- a/scripts/update-copilot-instructions.sh
+++ b/scripts/update-copilot-instructions.sh
@@ -47,27 +47,29 @@ POSSIBLE_PATHS=(
     "copilot-instructions.md"
     ".github/copilot_instructions.md"
     "docs/copilot-instructions.md"
-    ".github/copilot-instructions.md"
 )
 
+TEMP_FILE="/tmp/copilot-instructions-temp.md"
+DESIRED_FILE=".github/copilot-instructions.md"
+
 print_status "Searching for copilot-instructions.md in flipU repository..."
 
 DOWNLOADED=false
 for path in "${POSSIBLE_PATHS[@]}"; do
     print_status "Trying path: $path"
-    
+
     HTTP_CODE=$(curl -s -w "%{http_code}" \
                      -H "Accept: application/vnd.github.v3.raw" \
                      -o "/tmp/copilot-instructions-temp.md" \
                      "https://api.github.com/repos/Displayr/flipU/contents/$path" 2>/dev/null || echo "000")
-    
+
     if [ "$HTTP_CODE" = "200" ]; then
         # Check if we got actual content (not an error response)
         if [ -f "/tmp/copilot-instructions-temp.md" ] && [ -s "/tmp/copilot-instructions-temp.md" ]; then
             # Verify it's not a JSON error response
             if ! grep -q '"message".*"Not Found"' "/tmp/copilot-instructions-temp.md" 2>/dev/null; then
                 print_success "Successfully downloaded from: $path"
-                mv "/tmp/copilot-instructions-temp.md" ".github/copilot-instructions.md"
+                mv $TEMP_FILE $DESIRED_FILE
                 DOWNLOADED=true
                 SOURCE_PATH=$path
                 break
@@ -81,50 +83,50 @@ for path in "${POSSIBLE_PATHS[@]}"; do
 done
 
 # Clean up temp file
-rm -f "/tmp/copilot-instructions-temp.md"
+rm -f $TEMP_FILE
 
 if [ "$DOWNLOADED" = false ]; then
     print_error "Could not find copilot-instructions.md in flipU repository"
     print_error "Checked paths: ${POSSIBLE_PATHS[*]}"
-    
+
     # Try to list available files for debugging
     print_status "Attempting to list available files in flipU..."
     curl -s "https://api.github.com/repos/Displayr/flipU/contents" | \
          grep '"name"' | head -10 || print_warning "Could not list repository contents"
-    
+
     exit 1
 fi
 
 # Verify the downloaded file
-if [ ! -s ".github/copilot-instructions.md" ]; then
+if [ ! -s $DESIRED_FILE ]; then
     print_error "Downloaded file is empty"
     exit 1
 fi
 
 # Check if it looks like a valid copilot instructions file
-if ! grep -q -i "copilot\|instruction\|coding\|standard" ".github/copilot-instructions.md"; then
+if ! grep -q -i "copilot\|instruction\|coding\|standard" $DESIRED_FILE; then
     print_warning "Downloaded file may not contain typical copilot instruction content"
     print_warning "Please verify the content manually"
 fi
 
 # Show file information
-FILE_SIZE=$(wc -c < ".github/copilot-instructions.md")
-LINE_COUNT=$(wc -l < ".github/copilot-instructions.md")
+FILE_SIZE=$(wc -c < $DESIRED_FILE)
+LINE_COUNT=$(wc -l < $DESIRED_FILE)
 
 print_success "File updated successfully!"
 print_status "Source: flipU/$SOURCE_PATH"
-print_status "Local: .github/copilot-instructions.md"
+print_status "Local: $DESIRED_FILE"
 print_status "Size: $FILE_SIZE bytes"
 print_status "Lines: $LINE_COUNT"
 
 # Check git status for informational purposes only
 if command -v git >/dev/null 2>&1; then
-    if git diff --quiet .github/copilot-instructions.md 2>/dev/null; then
-        print_status "No changes detected in copilot-instructions.md"
+    if git diff --quiet $DESIRED_FILE 2>/dev/null; then
+        print_status "No changes detected in ${DESIRED_FILE}"
     else
-        print_status "Changes detected in copilot-instructions.md"
+        print_status "Changes detected in ${DESIRED_FILE}"
         print_status "File updated"
     fi
 fi
 
-print_success "Update completed successfully!"
\ No newline at end of file
+print_success "Update completed successfully!"

From fa3ef255023bdb38062987aea7af27c5a1f729b8 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 12:29:57 +1000
Subject: [PATCH 10/16] Update instructions to user for script

---
 scripts/update-copilot-instructions.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/update-copilot-instructions.sh b/scripts/update-copilot-instructions.sh
index d091e30..82273bf 100644
--- a/scripts/update-copilot-instructions.sh
+++ b/scripts/update-copilot-instructions.sh
@@ -1,7 +1,9 @@
 #!/bin/bash
 
 # Script to update copilot-instructions.md from flipU repository
-# Usage: ./update-copilot-instructions.sh
+# Usage: ./scripts/update-copilot-instructions.sh
+# Note: This script should be run from the root of this repository
+#      and requires internet access with curl installed.
 
 set -e  # Exit on any error
 

From c3a65999fb86897ed88756562c6f510e9e0bd842 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 12:31:45 +1000
Subject: [PATCH 11/16] Make script executable

---
 scripts/update-copilot-instructions.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 scripts/update-copilot-instructions.sh

diff --git a/scripts/update-copilot-instructions.sh b/scripts/update-copilot-instructions.sh
old mode 100644
new mode 100755

From 6d4452b13ca1f58805c8a03dcbb5e305d4af6a21 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 12:34:13 +1000
Subject: [PATCH 12/16] move script to .github directory and update feedback in
 workflow

---
 .../update-copilot-instructions.sh            |  0
 .../workflows/check-copilot-instructions.yml  | 30 +++++++++----------
 2 files changed, 15 insertions(+), 15 deletions(-)
 rename {scripts => .github}/update-copilot-instructions.sh (100%)

diff --git a/scripts/update-copilot-instructions.sh b/.github/update-copilot-instructions.sh
similarity index 100%
rename from scripts/update-copilot-instructions.sh
rename to .github/update-copilot-instructions.sh
diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index 91859df..ccdb9c0 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -7,16 +7,16 @@ on:
 jobs:
   check-copilot-instructions:
     runs-on: ubuntu-latest
-    
+
     steps:
     - name: Checkout current repository
       uses: actions/checkout@v4
-    
+
     - name: Download copilot-instructions.md from flipU
       id: download-source
       run: |
         echo "Downloading copilot-instructions.md from flipU..."
-        
+
         # Try multiple possible paths for the copilot instructions
         POSSIBLE_PATHS=(
           ".github/copilot-instructions.md"
@@ -24,14 +24,14 @@ jobs:
           ".github/copilot_instructions.md"
           "docs/copilot-instructions.md"
         )
-        
+
         DOWNLOADED=false
         for path in "${POSSIBLE_PATHS[@]}"; do
           echo "Trying path: $path"
           if curl -s -H "Accept: application/vnd.github.v3.raw" \
                   -o /tmp/source-copilot-instructions.md \
                   "https://api.github.com/repos/Displayr/flipU/contents/$path" 2>/dev/null; then
-            
+
             # Check if we got actual content (not an error response)
             if [ -f /tmp/source-copilot-instructions.md ] && [ -s /tmp/source-copilot-instructions.md ]; then
               # Verify it's not a JSON error response
@@ -44,14 +44,14 @@ jobs:
             fi
           fi
         done
-        
+
         if [ "$DOWNLOADED" = false ]; then
           echo "❌ Could not find copilot-instructions.md in flipU repo"
           echo "This may indicate the file doesn't exist or has been moved."
           echo "Please check the flipU repository structure."
           exit 1
         fi
-    
+
     - name: Check if local copilot-instructions.md exists
       id: check-local
       run: |
@@ -64,14 +64,14 @@ jobs:
           echo "✅ Found local copilot-instructions.md"
           echo "exists=true" >> $GITHUB_OUTPUT
         fi
-    
+
     - name: Compare files
       run: |
         echo "Comparing copilot-instructions.md files..."
         echo "Source: flipU/${{ steps.download-source.outputs.source_path }}"
         echo "Local: .github/copilot-instructions.md"
         echo ""
-        
+
         # Compare the files
         if diff -u /tmp/source-copilot-instructions.md .github/copilot-instructions.md > /tmp/diff_output; then
           echo "✅ Files match perfectly!"
@@ -86,23 +86,23 @@ jobs:
           echo ""
           echo "To fix this issue:"
           echo "1. Update your .github/copilot-instructions.md to match the source"
-          echo "2. Or run the update-copilot-instructions workflow"
+          echo "2. Or run the update-copilot-instructions.sh script in .github"
           echo "3. Or manually sync the files"
           echo ""
           echo "Source file location: flipU/${{ steps.download-source.outputs.source_path }}"
           exit 1
         fi
-    
+
     - name: Verify file integrity
       run: |
         echo "Verifying file integrity..."
-        
+
         # Check that the local file is not empty
         if [ ! -s .github/copilot-instructions.md ]; then
           echo "❌ Local copilot-instructions.md is empty"
           exit 1
         fi
-        
+
         # Check that it contains expected content patterns
         if ! grep -q -i "copilot\|instruction\|coding\|standard" .github/copilot-instructions.md; then
           echo "⚠️  Warning: File doesn't seem to contain typical copilot instruction content"
@@ -110,6 +110,6 @@ jobs:
         else
           echo "✅ File appears to contain valid copilot instructions"
         fi
-        
+
         echo "File size: $(wc -c < .github/copilot-instructions.md) bytes"
-        echo "Line count: $(wc -l < .github/copilot-instructions.md) lines"
\ No newline at end of file
+        echo "Line count: $(wc -l < .github/copilot-instructions.md) lines"

From 432498794d427812a80ac05389357e9e0aaa38cc Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 13:04:35 +1000
Subject: [PATCH 13/16] Update path in instructions for update script

---
 .github/update-copilot-instructions.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/update-copilot-instructions.sh b/.github/update-copilot-instructions.sh
index 82273bf..0b350c7 100755
--- a/.github/update-copilot-instructions.sh
+++ b/.github/update-copilot-instructions.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # Script to update copilot-instructions.md from flipU repository
-# Usage: ./scripts/update-copilot-instructions.sh
+# Usage: ./.github/update-copilot-instructions.sh
 # Note: This script should be run from the root of this repository
 #      and requires internet access with curl installed.
 

From faa2c43c2879f8936f92ab3e0509c96b3dd689c5 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 13:22:46 +1000
Subject: [PATCH 14/16] Update the feedback in workflow to get the script
 locally

---
 .github/workflows/check-copilot-instructions.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index ccdb9c0..5516433 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -86,9 +86,10 @@ jobs:
           echo ""
           echo "To fix this issue:"
           echo "1. Update your .github/copilot-instructions.md to match the source"
-          echo "2. Or run the update-copilot-instructions.sh script in .github"
-          echo "3. Or manually sync the files"
-          echo ""
+          echo "2. Or run the shell script in flipU to do this for you."
+          echo "   # Run these commands locally from the root of your repository"
+          echo "   > curl -O -L https://raw.githubusercontent.com/Displayr/flipU/master/.github/update-copilot-instructions.sh"
+          echo "   > bash update-copilot-instructions.sh"
           echo "Source file location: flipU/${{ steps.download-source.outputs.source_path }}"
           exit 1
         fi

From 4428a94d71ae536b7bb769c475b0d45369bafd5d Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 13:25:55 +1000
Subject: [PATCH 15/16] Add git command suggestions too

---
 .github/workflows/check-copilot-instructions.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/check-copilot-instructions.yml b/.github/workflows/check-copilot-instructions.yml
index 5516433..613da82 100644
--- a/.github/workflows/check-copilot-instructions.yml
+++ b/.github/workflows/check-copilot-instructions.yml
@@ -90,6 +90,9 @@ jobs:
           echo "   # Run these commands locally from the root of your repository"
           echo "   > curl -O -L https://raw.githubusercontent.com/Displayr/flipU/master/.github/update-copilot-instructions.sh"
           echo "   > bash update-copilot-instructions.sh"
+          echo "   > git add .github/copilot-instructions.md"
+          echo "   > git commit -m 'Update copilot-instructions.md to match flipU'"
+          echo "   > git push"
           echo "Source file location: flipU/${{ steps.download-source.outputs.source_path }}"
           exit 1
         fi

From e406eeeda33e391307d4977cf09c07eecf183128 Mon Sep 17 00:00:00 2001
From: jrwishart <justin.wishart@displayr.com>
Date: Fri, 3 Oct 2025 13:31:36 +1000
Subject: [PATCH 16/16] Remove update script as it'll live in flipU

---
 .github/update-copilot-instructions.sh | 134 -------------------------
 1 file changed, 134 deletions(-)
 delete mode 100755 .github/update-copilot-instructions.sh

diff --git a/.github/update-copilot-instructions.sh b/.github/update-copilot-instructions.sh
deleted file mode 100755
index 0b350c7..0000000
--- a/.github/update-copilot-instructions.sh
+++ /dev/null
@@ -1,134 +0,0 @@
-#!/bin/bash
-
-# Script to update copilot-instructions.md from flipU repository
-# Usage: ./.github/update-copilot-instructions.sh
-# Note: This script should be run from the root of this repository
-#      and requires internet access with curl installed.
-
-set -e  # Exit on any error
-
-# Colors for output
-RED='\033[0;31m'
-GREEN='\033[0;32m'
-YELLOW='\033[1;33m'
-BLUE='\033[0;34m'
-NC='\033[0m' # No Color
-
-# Function to print colored output
-print_status() {
-    echo -e "${BLUE}[INFO]${NC} $1"
-}
-
-print_success() {
-    echo -e "${GREEN}[SUCCESS]${NC} $1"
-}
-
-print_warning() {
-    echo -e "${YELLOW}[WARNING]${NC} $1"
-}
-
-print_error() {
-    echo -e "${RED}[ERROR]${NC} $1"
-}
-
-# Check if we're in a git repository
-if [ ! -d ".git" ]; then
-    print_error "This script must be run from the root of a git repository"
-    exit 1
-fi
-
-# Create .github directory if it doesn't exist
-if [ ! -d ".github" ]; then
-    print_status "Creating .github directory..."
-    mkdir -p .github
-fi
-
-# Try multiple possible paths for the copilot instructions
-POSSIBLE_PATHS=(
-    ".github/copilot-instructions.md"
-    "copilot-instructions.md"
-    ".github/copilot_instructions.md"
-    "docs/copilot-instructions.md"
-)
-
-TEMP_FILE="/tmp/copilot-instructions-temp.md"
-DESIRED_FILE=".github/copilot-instructions.md"
-
-print_status "Searching for copilot-instructions.md in flipU repository..."
-
-DOWNLOADED=false
-for path in "${POSSIBLE_PATHS[@]}"; do
-    print_status "Trying path: $path"
-
-    HTTP_CODE=$(curl -s -w "%{http_code}" \
-                     -H "Accept: application/vnd.github.v3.raw" \
-                     -o "/tmp/copilot-instructions-temp.md" \
-                     "https://api.github.com/repos/Displayr/flipU/contents/$path" 2>/dev/null || echo "000")
-
-    if [ "$HTTP_CODE" = "200" ]; then
-        # Check if we got actual content (not an error response)
-        if [ -f "/tmp/copilot-instructions-temp.md" ] && [ -s "/tmp/copilot-instructions-temp.md" ]; then
-            # Verify it's not a JSON error response
-            if ! grep -q '"message".*"Not Found"' "/tmp/copilot-instructions-temp.md" 2>/dev/null; then
-                print_success "Successfully downloaded from: $path"
-                mv $TEMP_FILE $DESIRED_FILE
-                DOWNLOADED=true
-                SOURCE_PATH=$path
-                break
-            fi
-        fi
-    elif [ "$HTTP_CODE" = "404" ]; then
-        print_status "File not found at: $path"
-    else
-        print_warning "HTTP $HTTP_CODE when accessing: $path"
-    fi
-done
-
-# Clean up temp file
-rm -f $TEMP_FILE
-
-if [ "$DOWNLOADED" = false ]; then
-    print_error "Could not find copilot-instructions.md in flipU repository"
-    print_error "Checked paths: ${POSSIBLE_PATHS[*]}"
-
-    # Try to list available files for debugging
-    print_status "Attempting to list available files in flipU..."
-    curl -s "https://api.github.com/repos/Displayr/flipU/contents" | \
-         grep '"name"' | head -10 || print_warning "Could not list repository contents"
-
-    exit 1
-fi
-
-# Verify the downloaded file
-if [ ! -s $DESIRED_FILE ]; then
-    print_error "Downloaded file is empty"
-    exit 1
-fi
-
-# Check if it looks like a valid copilot instructions file
-if ! grep -q -i "copilot\|instruction\|coding\|standard" $DESIRED_FILE; then
-    print_warning "Downloaded file may not contain typical copilot instruction content"
-    print_warning "Please verify the content manually"
-fi
-
-# Show file information
-FILE_SIZE=$(wc -c < $DESIRED_FILE)
-LINE_COUNT=$(wc -l < $DESIRED_FILE)
-
-print_success "File updated successfully!"
-print_status "Source: flipU/$SOURCE_PATH"
-print_status "Local: $DESIRED_FILE"
-print_status "Size: $FILE_SIZE bytes"
-print_status "Lines: $LINE_COUNT"
-
-# Check git status for informational purposes only
-if command -v git >/dev/null 2>&1; then
-    if git diff --quiet $DESIRED_FILE 2>/dev/null; then
-        print_status "No changes detected in ${DESIRED_FILE}"
-    else
-        print_status "Changes detected in ${DESIRED_FILE}"
-        print_status "File updated"
-    fi
-fi
-
-print_success "Update completed successfully!"