feat: Add git repository root path normalization for code blocks

Introduce path normalization logic to handle absolute file paths relative to the git repository root. This enhances file handling for markdown code block extraction and application, particularly for scripts operating across different repository contexts.

Key improvements:
- Add `get_git_root()` function to detect git repository root
- Implement `normalize_path()` function to resolve absolute paths
- Provide verbose warnings when not in a git repository
- Improve path resolution for code block file targets

Author: vgrichina

apply-md

@@ -15,6 +15,11 @@ CONFIRM=false
 ONLY_FILES=""
 IGNORE_FILES=""
 
+# Function to get git repository root
+get_git_root() {
+    git rev-parse --show-toplevel 2>/dev/null
+}
+
 # Parse arguments
 while [[ "$#" -gt 0 ]]; do
     case $1 in
@@ -49,6 +54,12 @@ while [[ "$#" -gt 0 ]]; do
     esac
 done
 
+# Get git root if available
+GIT_ROOT=$(get_git_root)
+if [ -z "$GIT_ROOT" ] && [ "$VERBOSE" = true ]; then
+    echo "Warning: Not in a git repository, absolute paths will be treated as system paths"
+fi
+
 # Create backup directory if needed
 if [ "$BACKUP" = true ] && [ ! -d "$BACKUP_DIR" ]; then
     if [ "$DRY_RUN" = false ]; then
@@ -72,6 +83,18 @@ cleanup() {
 }
 trap cleanup EXIT
 
+# Function to normalize path relative to git root
+normalize_path() {
+    local path="$1"
+    if [ -n "$GIT_ROOT" ] && [[ "$path" == /* ]]; then
+        # Remove leading slash and resolve relative to git root
+        local rel_path="${path#/}"
+        echo "$GIT_ROOT/$rel_path"
+    else
+        echo "$path"
+    fi
+}
+
 # Extract code blocks and their file names
 extract_blocks() {
     local current_file=""
@@ -81,12 +104,13 @@ extract_blocks() {
     echo "$MARKDOWN" | while IFS= read -r line; do
         if [[ "$line" =~ ^[[:space:]]*\`\`\`([a-zA-Z0-9\+\-]+)[[:space:]]+(.+) ]]; then
             current_file="${BASH_REMATCH[2]}"
+            normalized_file=$(normalize_path "$current_file")
             in_block=true
             temp_file="$TEMP_DIR/$current_file"
             mkdir -p "$(dirname "$temp_file")"
             : > "$temp_file"  # Create empty file
             if [ "$VERBOSE" = true ]; then
-                echo "Starting code block for file: $current_file"
+                echo "Starting code block for file: $current_file (normalized: $normalized_file)"
             fi
             continue
         fi
@@ -137,7 +161,8 @@ apply_block() {
     fi
 
     # Normalize file path
-    file=$(realpath -m "$file" 2>/dev/null || echo "$file")
+    local normalized_file=$(normalize_path "$file")
+    file="$normalized_file"
 
     if [ ! -f "$file" ]; then
         if [ "$CREATE_MISSING" = true ]; then
@@ -223,6 +248,9 @@ if [ "$VERBOSE" = true ]; then
     if [ "$DRY_RUN" = true ]; then
         echo "Running in DRY RUN mode (no changes will be applied)"
     fi
+    if [ -n "$GIT_ROOT" ]; then
+        echo "Git repository root detected at: $GIT_ROOT"
+    fi
 fi
 
 extract_blocks