feat: Enhance code block file path resolution and parsing

Improve handling of file paths in code blocks by normalizing repository root paths and refining markdown parsing logic. This ensures more accurate and robust file reference detection and processing.

Author: vgrichina

docs/apply-md.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-The `apply-md` tool extracts code blocks from markdown (typically LLM responses) and applies them to your filesystem.
+The `apply-md` tool extracts code blocks from markdown (typically LLM responses) and applies them to your filesystem. It supports both relative and absolute paths, with absolute paths resolved relative to the git repository root when run within a git repository.
 
 ## Usage
 
@@ -20,17 +20,19 @@ cat llm_response.md | ./apply-md --dry-run --verbose
 | `--backup-dir=<dir>` | Directory for backups | "./.backups" |
 | `--file-marker=<regex>` | Regex to identify target files from markdown | "```[a-z]+ (.+)" |
 | `--skip-unchanged` | Skip files with no changes | False |
-| `--verbose` | Show detailed output about changes | False |
+| `--verbose` | Show detailed output about changes, including git root detection | False |
 | `--confirm` | Prompt for confirmation before applying each change | False |
 | `--only-files=<pattern>` | Only apply changes to files matching pattern | None |
 | `--ignore-files=<pattern>` | Ignore changes for files matching pattern | None |
 
 ## How It Works
 
 1. The tool reads markdown content from stdin
-2. It looks for code blocks that specify a filename (e.g., ```javascript src/utils.js)
-3. It extracts the code from these blocks
-4. It applies the code to the corresponding files in your filesystem
+2. If run within a git repository, it detects the repository root
+3. It looks for code blocks that specify a filename (e.g., ```javascript src/utils.js or ```bash /apply-md)
+4. Absolute paths (starting with /) are resolved relative to the git root when applicable
+5. It extracts the code from these blocks
+6. It applies the code to the corresponding files in your filesystem
 
 ## Examples
 
@@ -74,23 +76,53 @@ Only apply changes to specific files:
 cat llm_response.md | ./apply-md --only-files="*.js"
 ```
 
+### Using Absolute Paths
+
+Apply changes using absolute paths relative to git root:
+
+```bash
+echo -e "```bash /scripts/test.sh\necho 'test'\n```" | ./apply-md --create-missing
+```
+
 ## Expected Markdown Format
 
-The script expects code blocks in this format:
+The script expects code blocks in these formats:
 
-````
-```javascript src/utils.js
-function add(a, b) {
-  return a + b;
-}
+### Relative Path
+```markdown
+    ```javascript src/utils.js
+    function add(a, b) {
+      return a + b;
+    }
+    ```
 ```
-````
 
-The language specification is optional, but the filename is required.
+### Absolute Path (from git root)
+```markdown
+    ```bash /scripts/deploy.sh
+    #!/bin/bash
+    echo "Deploying..."
+    ```
+```
+
+The language specification is optional, but the filename is required. Absolute paths (starting with /) will be resolved relative to the git repository root when run within a git repository.
 
 ## Tips
 
 - Always use `--dry-run` first to preview changes
+- Use `--verbose` to see the detected git root and normalized paths
 - Consider using `--backup` for important changes
-- Use `--verbose` to see details about what's changing
-- For complex changes, use `--confirm` to review each change individually
+- Use `--confirm` to review each change individually
+- When using absolute paths, ensure you're running from within a git repository
+- If not in a git repository, absolute paths will be treated as system paths
+
+## Git Integration
+
+When run within a git repository:
+- Detects the repository root automatically
+- Converts absolute paths (e.g., `/src/main.js`) to relative paths from the git root
+- Shows the detected git root in verbose mode
+
+If not in a git repository:
+- Absolute paths are treated as system absolute paths
+- A warning is shown in verbose mode