refactor: migrate tools Python modules under pure_auto_codeql

Move CodeQL compose/LSP/extract helpers into pure_auto_codeql.tools
with top-level re-export shims. Keep tools/mcp_ripgrep at the repo
root for Node build tooling and doctor path checks.

Author: bx33661

docs/package_architecture.md

@@ -16,10 +16,10 @@ migration window.
 | `Information` | `pure_auto_codeql.information` | Migrated (top-level re-export shim kept) |
 | `prompts` | `pure_auto_codeql.prompts` | Migrated (top-level re-export shim kept; `.md` assets co-located) |
 | `utils` | `pure_auto_codeql.utils` | Migrated (top-level re-export shim kept) |
+| `tools` | `pure_auto_codeql.tools` | Migrated Python modules (top-level re-export shim kept; `tools/mcp_ripgrep` stays at repo root) |
 | `api` | `pure_auto_codeql.api` | Planned staged migration |
 | `core` | `pure_auto_codeql.core` | Planned staged migration |
 | `services` | `pure_auto_codeql.services` | Planned staged migration |
-| `tools` | `pure_auto_codeql.tools` | Planned staged migration |
 
 ## Compatibility Surface
 

pure_auto_codeql/tools/__init__.py

@@ -0,0 +1,6 @@
+"""LangChain tools for CodeQL operations."""
+
+from .codeql_compose import CodeQLComposeTool
+
+__all__ = ['CodeQLComposeTool']
+