fix: restore dependency-ordered imports in core/__init__.py

isort alphabetized imports which broke the carefully ordered dependency
chain. Utils (config, logging) must be imported BEFORE data, io,
execution, engine, ui - since those modules reference metainformant.core
attributes at module level. Added isort: skip_file directive.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: docxology

src/metainformant/core/__init__.py

@@ -7,17 +7,29 @@
 
 from __future__ import annotations
 
-# 6. UI (Terminal Interface)
-# 5. Engine (Workflow Manager)
-# 4. Execution (Workflow)
-# Depends on IO and Utils
-# 3. IO (Input/Output)
-# Depends on Utils for logging/config
+# Import subpackages in dependency order (NOT alphabetical - order matters!)
+# isort: skip_file
+
+# 1. Utils (Foundation) - must be first, other modules depend on config/logging
+from . import utils  # noqa: E402
+from .utils import (  # noqa: E402
+    Timer,
+    config,
+    errors,
+    hash,
+    logging,
+    optional_deps,
+    progress,
+    rate_limiter,
+    symbols,
+    text,
+    timed,
+    timeout_after,
+)
+
 # 2. Data (Structures)
-# Import subpackages (reordered for dependency resolution)
-# 1. Utils (Foundation)
-from . import data, engine, execution, io, ui, utils
-from .data import (
+from . import data  # noqa: E402
+from .data import (  # noqa: E402
     validate_not_empty,
     validate_not_none,
     validate_path_exists,
@@ -26,22 +38,10 @@
     validate_type,
     validation,
 )
-from .engine import (
-    SampleStage,
-    SampleState,
-    WorkflowManager,
-)
-from .execution import (
-    cpu_count,
-    discover_configs,
-    discover_functions,
-    discovery,
-    parallel,
-    parallel_batch,
-    thread_map,
-    workflow,
-)
-from .io import (
+
+# 3. IO (Input/Output) - depends on Utils for logging/config
+from . import io  # noqa: E402
+from .io import (  # noqa: E402
     atomic_replace,
     atomic_write,
     cache,
@@ -53,8 +53,8 @@
     download_file,
     dump_json,
 )
-from .io import io as io_module
-from .io import (
+from .io import io as io_module  # noqa: E402
+from .io import (  # noqa: E402
     load_json,
     load_yaml,
     paths,
@@ -65,24 +65,34 @@
     verify_checksum_file,
     write_checksum_file,
 )
-from .ui import (
+
+# 4. Execution (Workflow) - depends on IO and Utils
+from . import execution  # noqa: E402
+from .execution import (  # noqa: E402
+    cpu_count,
+    discover_configs,
+    discover_functions,
+    discovery,
+    parallel,
+    parallel_batch,
+    thread_map,
+    workflow,
+)
+
+# 5. Engine (Workflow Manager)
+from . import engine  # noqa: E402
+from .engine import (  # noqa: E402
+    SampleStage,
+    SampleState,
+    WorkflowManager,
+)
+
+# 6. UI (Terminal Interface)
+from . import ui  # noqa: E402
+from .ui import (  # noqa: E402
     ProgressState,
     TerminalInterface,
 )
-from .utils import (
-    Timer,
-    config,
-    errors,
-    hash,
-    logging,
-    optional_deps,
-    progress,
-    rate_limiter,
-    symbols,
-    text,
-    timed,
-    timeout_after,
-)
 
 # Optional dependencies
 try: