refactor: remove dead production code and stale files

LSP-confirmed 0-usage deletions across packages:
- core: graph_cache, cache_manager, parallel_executor, query_optimizer,
  alerting, metrics_collector, rate_limiter, dead decay methods
- cli: query_executor, progress_ui, wizard, dead planning methods
- context-code: hybrid_retriever_v1_backup, dead git/bm25/embedding methods
- soar: dead assess/retrieve methods
- spawner: dead circuit_breaker/heartbeat/observability/recovery methods
- examples: heartbeat_monitoring.py

Also removes corresponding tests for deleted code.

Author: hamr0

examples/heartbeat_monitoring.py

@@ -185,99 +185,3 @@ def parse_file(self, path: Path) -> AgentInfo | None:
             logger.warning("Validation failed for %s - %s", path, error_msg)
             return None
 
-    def parse_content(self, content: str, source_file: str | None = None) -> AgentInfo | None:
-        """Parse agent metadata from a string containing frontmatter.
-
-        Useful for testing or when agent content is provided directly
-        rather than from a file.
-
-        Args:
-            content: String containing markdown with YAML frontmatter
-            source_file: Optional source file path to include in metadata
-
-        Returns:
-            AgentInfo if successfully parsed and validated, None otherwise
-
-        Example:
-            >>> parser = AgentParser()
-            >>> content = '''---
-            ... id: test-agent
-            ... role: Test Agent
-            ... goal: Testing purposes
-            ... ---
-            ... # Test Agent
-            ... '''
-            >>> agent = parser.parse_content(content)
-            >>> print(agent.id)
-            test-agent
-
-        """
-        try:
-            post = frontmatter.loads(content)
-        except Exception as e:
-            logger.warning(
-                "Failed to parse frontmatter from content: %s (%s)",
-                type(e).__name__,
-                str(e),
-            )
-            return None
-
-        if not post.metadata:
-            logger.warning("No frontmatter found in content - expected YAML between --- delimiters")
-            return None
-
-        # Add source_file if provided
-        metadata = dict(post.metadata)
-        if source_file:
-            metadata["source_file"] = source_file
-
-        try:
-            agent = AgentInfo.model_validate(metadata)
-            logger.debug("Successfully parsed agent %s from content", agent.id)
-            return agent
-
-        except ValidationError as e:
-            errors = e.errors()
-            missing_fields = [err["loc"][0] for err in errors if err["type"] == "missing"]
-
-            if missing_fields:
-                logger.warning(
-                    "Validation failed for content - missing required fields: %s",
-                    ", ".join(str(f) for f in missing_fields),
-                )
-            else:
-                logger.warning(
-                    "Validation failed for content: %s",
-                    str(e),
-                )
-            return None
-
-    def extract_frontmatter(self, path: Path) -> dict[str, Any] | None:
-        """Extract raw frontmatter without validation.
-
-        Useful for debugging or when you need the raw metadata without
-        Pydantic validation.
-
-        Args:
-            path: Path to the agent markdown file
-
-        Returns:
-            Dictionary of frontmatter metadata, or None if extraction fails
-
-        Example:
-            >>> parser = AgentParser()
-            >>> raw = parser.extract_frontmatter(Path("agent.md"))
-            >>> print(raw)
-            {'id': 'my-agent', 'role': 'My Role', ...}
-
-        """
-        resolved_path = Path(path).expanduser().resolve()
-
-        if not resolved_path.exists() or not resolved_path.is_file():
-            return None
-
-        try:
-            post = frontmatter.load(resolved_path)
-            return dict(post.metadata) if post.metadata else None
-        except Exception:
-            return None

packages/cli/src/aurora_cli/agent_discovery/parser.py

@@ -943,20 +943,6 @@ async def configure_mcp_servers(
     return created, updated, skipped, validation_warnings
 
 
-def get_mcp_capable_from_selection(tool_ids: list[str]) -> list[str]:
-    """Filter tool IDs to only those that support MCP.
-
-    Args:
-        tool_ids: List of all selected tool IDs
-
-    Returns:
-        List of tool IDs that have MCP support
-
-    """
-    from aurora_cli.configurators.mcp import MCPConfigRegistry
-
-    return [tid for tid in tool_ids if MCPConfigRegistry.supports_mcp(tid)]
-
 
 def detect_claude_hooks(project_path: Path) -> dict[str, bool]:
     """Detect if Claude Code hooks are configured.

packages/cli/src/aurora_cli/commands/init_helpers.py

@@ -119,11 +119,3 @@ async def _update_file_with_markers(
         # The template already includes markers, so write as-is
         file_path.write_text(new_content, encoding="utf-8")
 
-    def get_command_list(self) -> list[str]:
-        """Get list of available command names.
-
-        Returns:
-            List of command names that will be created
-
-        """
-        return list(get_all_command_templates().keys())