refactor: Remove CAM metadata markers from live prompt files

- Remove embedded <!-- cam-prompt-id: xyz --> markers from live prompt files
- Implement content-based sync tracking instead of marker-based tracking
- Add get_matching_prompt_id() and _normalize_content_for_comparison() methods
- Update status command to use content comparison for installation detection
- Clean up live prompt files (CLAUDE.md, copilot-instructions.md) by removing markers
- Update tests to expect clean live files without markers

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: James Zhu

.github/copilot-instructions.md

@@ -6,6 +6,4 @@ This is a test instruction file for GitHub Copilot CLI custom instructions suppo
 
 - Write clear, maintainable code
 - Test everything before committing
-- Follow the repository's coding style
-
-<!-- cam-prompt-id: 02ee63f9 -->
+- Follow the repository's coding style

CLAUDE.md

@@ -13,6 +13,4 @@ rm -rf dist/*
 ./install.sh uninstall
 ./install.sh
 cp ~/.config/code-assistant-manager/providers.json.bak ~/.config/code-assistant-manager/providers.json
-```
-
-<!-- cam-prompt-id: 71b21925 -->
+```

code_assistant_manager/cli/prompts_commands.py

@@ -30,6 +30,47 @@ def _find_prompt_by_name(manager: PromptManager, name: str) -> Optional[Prompt]:
     return None
 
 
+def _strip_metadata_from_content(content: str) -> str:
+    """
+    Strip metadata headers from content that shouldn't be part of the prompt.
+
+    This includes:
+    - YAML front matter (--- ... ---)
+    - Existing metadata headers from show command output
+    - CAM prompt ID markers
+    """
+    import re
+
+    # First strip CAM prompt ID markers
+    from code_assistant_manager.prompts.base import PROMPT_ID_PATTERN
+    content = PROMPT_ID_PATTERN.sub("", content).strip()
+
+    # Strip YAML front matter
+    yaml_pattern = r'^---\s*\n.*?\n---\s*\n'
+    content = re.sub(yaml_pattern, '', content, flags=re.DOTALL).strip()
+
+    # Strip metadata headers that look like the show command output
+    # Look for patterns like "Prompt: ..." or "ID: ..." at the beginning
+    lines = content.splitlines()
+
+    # Find where actual content starts (after metadata headers)
+    content_start_idx = 0
+    for i, line in enumerate(lines):
+        # Stop at the first line that doesn't look like metadata
+        if not re.match(r'^(Prompt|ID|Description|Status|Default|Content|Imported from):\s*', line, re.IGNORECASE):
+            # Also skip empty lines at the beginning
+            if line.strip():
+                content_start_idx = i
+                break
+        content_start_idx = i + 1
+
+    # If we found metadata headers, return content starting after them
+    if content_start_idx > 0 and content_start_idx < len(lines):
+        return '\n'.join(lines[content_start_idx:]).strip()
+
+    return content.strip()
+
+
 def _generate_fancy_name() -> str:
     """Generate a fancy, creative name for a prompt."""
     adjectives = [
@@ -133,6 +174,8 @@ def add_prompt(
             typer.echo(f"Error: File not found: {file}")
             raise typer.Exit(1)
         content = file.read_text()
+        # Strip metadata headers that shouldn't be part of the prompt content
+        content = _strip_metadata_from_content(content)
     elif not sys.stdin.isatty():
         # Read from stdin (piped input)
         content = sys.stdin.read()
@@ -222,6 +265,9 @@ def update_prompt(
             typer.echo("Error: File is empty")
             raise typer.Exit(1)
 
+        # Strip metadata headers that shouldn't be part of the prompt content
+        content = _strip_metadata_from_content(content)
+
     # Check if new name conflicts with existing prompt
     if new_name and new_name != name:
         existing_prompt = _find_prompt_by_name(manager, new_name)
@@ -332,6 +378,9 @@ def import_prompt(
     from code_assistant_manager.prompts.base import PROMPT_ID_PATTERN
     content = PROMPT_ID_PATTERN.sub("", content).strip()
 
+    # Strip metadata headers that shouldn't be part of the prompt content
+    content = _strip_metadata_from_content(content)
+
     # Generate or validate name
     if not name:
         # Generate a fancy name with app context and ensure it's unique
@@ -467,27 +516,32 @@ def status(
     # Build installation map: prompt_id -> [(app, level, file_path), ...]
     install_map = {}  # prompt_id -> list of (app, level, file_path) tuples
     untracked = []    # list of (app, level, preview) for untracked installs
-    
+
     for app in VALID_APP_TYPES:
         handler = manager.get_handler(app)
-        
+
         for level in ["user", "project"]:
             proj = project_dir if level == "project" else None
             file_path = handler.get_prompt_file_path(level, proj)
-            
+
             if not file_path or not file_path.exists():
                 continue
-                
+
             content = file_path.read_text().strip()
             if not content:
                 continue
-            
-            installed_id = handler.get_installed_prompt_id(level, proj)
-            
-            if installed_id:
-                if installed_id not in install_map:
-                    install_map[installed_id] = []
-                install_map[installed_id].append((app, level, file_path))
+
+            # Check if any configured prompt matches this content
+            matched_prompt_id = None
+            for prompt_id, prompt in prompts.items():
+                if handler.get_matching_prompt_id(prompt.content, level, proj):
+                    matched_prompt_id = prompt_id
+                    break
+
+            if matched_prompt_id:
+                if matched_prompt_id not in install_map:
+                    install_map[matched_prompt_id] = []
+                install_map[matched_prompt_id].append((app, level, file_path))
             else:
                 preview = content[:30].replace('\n', ' ')
                 if len(content) > 30:

code_assistant_manager/prompts/base.py

@@ -224,9 +224,8 @@ def sync_prompt(
         # Normalize header to match this tool's name
         content = self._normalize_header(content, filename=file_path.name)
 
-        # Embed prompt ID marker at the end if provided
-        if prompt_id:
-            content = content.rstrip() + "\n\n" + PROMPT_ID_MARKER.format(prompt_id) + "\n"
+        # NOTE: We no longer embed prompt ID markers in live files
+        # Sync status is tracked by content comparison instead
 
         # Ensure parent directory exists
         file_path.parent.mkdir(parents=True, exist_ok=True)
@@ -251,6 +250,9 @@ def get_installed_prompt_id(
         """
         Extract the prompt ID from an installed prompt file.
 
+        NOTE: This method is deprecated. We no longer embed prompt ID markers
+        in live files. Use get_matching_prompt_id() for content-based matching.
+
         Args:
             level: Prompt level ("user" or "project")
             project_dir: Optional project directory for project level prompts
@@ -265,6 +267,65 @@ def get_installed_prompt_id(
         match = PROMPT_ID_PATTERN.search(content)
         return match.group(1) if match else None
 
+    def get_matching_prompt_id(
+        self,
+        expected_content: str,
+        level: str = "user",
+        project_dir: Optional[Path] = None,
+    ) -> Optional[str]:
+        """
+        Check if the live content matches any configured prompt.
+
+        This method compares content to determine sync status without
+        requiring embedded markers in the live files.
+
+        Args:
+            expected_content: The expected prompt content to match against
+            level: Prompt level ("user" or "project")
+            project_dir: Optional project directory for project level prompts
+
+        Returns:
+            The prompt ID if content matches a configured prompt, None otherwise
+        """
+        from code_assistant_manager.prompts.manager import PromptManager
+
+        live_content = self.get_live_content(level, project_dir)
+        if not live_content:
+            return None
+
+        # Strip markers and normalize both contents for comparison
+        normalized_live = self._normalize_content_for_comparison(live_content)
+        normalized_expected = self._normalize_content_for_comparison(expected_content)
+
+        # If contents match, return a synthetic ID for tracking
+        # We use content hash as a stable identifier
+        if normalized_live == normalized_expected:
+            import hashlib
+            content_hash = hashlib.md5(normalized_expected.encode('utf-8')).hexdigest()[:8]
+            return f"content-{content_hash}"
+
+        return None
+
+    def _normalize_content_for_comparison(self, content: str) -> str:
+        """
+        Normalize content for comparison by stripping markers and standardizing format.
+
+        Args:
+            content: Raw content
+
+        Returns:
+            Normalized content for comparison
+        """
+        # Strip CAM markers
+        content = PROMPT_ID_PATTERN.sub("", content).strip()
+
+        # Strip metadata headers that shouldn't be part of comparison
+        content = self._strip_metadata_header(content)
+
+        # Normalize whitespace
+        lines = [line.rstrip() for line in content.splitlines()]
+        return "\n".join(lines).strip()
+
     def get_live_content(
         self,
         level: str = "user",

tests/unit/test_prompts.py

@@ -282,11 +282,12 @@ def test_sync_to_app(self, temp_config_dir, temp_prompt_dir):
 
         manager.sync_to_app("test", "claude")
 
-        # Check prompt was synced to file (with ID marker)
+        # Check prompt was synced to file (without ID marker - we use content comparison now)
         assert prompt_file.exists()
         content = prompt_file.read_text()
         assert "My test content" in content
-        assert "<!-- cam-prompt-id: test -->" in content
+        # No longer expect CAM prompt ID markers in live files
+        assert "<!-- cam-prompt-id: test -->" not in content
 
     def test_sync_to_app_project_level(self, temp_config_dir, temp_prompt_dir):
         """Project-level sync writes to project CLAUDE.md."""
@@ -303,7 +304,8 @@ def test_sync_to_app_project_level(self, temp_config_dir, temp_prompt_dir):
         assert prompt_file.exists()
         content = prompt_file.read_text()
         assert "Project scoped content" in content
-        assert "<!-- cam-prompt-id: test -->" in content
+        # No longer expect CAM prompt ID markers in live files
+        assert "<!-- cam-prompt-id: test -->" not in content
 
     def test_get_live_content(self, temp_config_dir, temp_prompt_dir):
         """Test getting live prompt content."""