add fix link/ref script

fix-link.sh

@@ -1,51 +1,28 @@
 #!/bin/bash
 
-# Check if input file is provided
-if [ $# -ne 1 ]; then
-    echo "Usage: $0 <input_file>"
+INPUT_FILE="$1"
+
+if [[ ! -f "$INPUT_FILE" ]]; then
+    echo "Error: Input file does not exist."
     exit 1
 fi
 
-input_file="$1"
+while IFS=':' read -r file_path line_err status desc data; do
+    # Trim whitespace from variables
+    file_path="$(echo "$file_path" | xargs)"
+    line_err="$(echo "$line_err" | xargs)"
+    status="$(echo "$status" | xargs)"
+    desc="$(echo "$desc" | xargs)"
+    data="$(echo "$data" | xargs | tr -d "'")"  # Remove quotes from data
 
-# Check if file exists
-if [ ! -f "$input_file" ]; then
-    echo "Error: File '$input_file' not found"
-    exit 1
-fi
-
-# Process each line of the input file
-while IFS= read -r line || [ -n "$line" ]; do
-    # Skip empty lines
-    [ -z "$line" ] && continue
-    
-    # Extract filepath (everything before first colon)
-    filepath=$(echo "$line" | cut -d: -f1)
-    
-    # Extract status (WARNING)
-    status="WARNING"
-    
-    # Split based on different patterns
-    if [[ "$line" =~ "WARNING: toctree contains reference to nonexisting document" ]]; then
-        description="toctree contains reference to nonexisting document"
-        data=$(echo "$line" | sed "s|^.*$description ||")
-    elif [[ "$line" =~ "WARNING: undefined label:" ]]; then
-        description="undefined label:"
-        data=$(echo "$line" | sed "s|^.*$description ||")
-    else
-        # For the first line with deprecated substitutions
-        description=$(echo "$line" | sed "s|^.*WARNING: ||" | sed "s| \[.*$||")
-        data=$(echo "$line" | grep -o "\[.*$" | tr -d '[]')
+    if [[ -f "$file_path" ]]; then
+        if [[ "$desc" == "undefined label" ]]; then
+            fixed_data="$(echo "$data" | tr '\\/_' '-')"
+            sed -i "s@$data@$fixed_data@g" "$file_path"
+        elif [[ "$desc" == *"toctree contains reference to nonexisting document"* ]]; then
+            fixed_data="$(echo "$data" | tr '\\/_' '-')"
+            sed -i "s@$data@$fixed_data@g" "$file_path"
+        fi
     fi
-    
-    # Replace /, \, and _ with - in data
-    modified_data=$(echo "$data" | tr '/\\_' '-')
-    
-    # Print the results
-    echo "filepath = $filepath"
-    echo "status = $status"
-    echo "description = $description"
-    echo "data = $modified_data"
-    echo "-------------------"
-    
-done < "$input_file"
+
+done < "$INPUT_FILE"