refactor: move writable-dir constants to core.paths, fix workflow->tools layer violation

OUTPUT_DIR/INPUT_DIR/GEO_CACHE_DIR + _resolve_dir lived in src/tools/rna/_base.py,
so src/workflows/integration.py imported upward from the tools layer to reach
OUTPUT_DIR -- a dependency-direction violation (tools sits above workflows).

These are shared infrastructure (env-resolved writable dirs) both layers need, so
they belong in core. Move them to src/core/paths.py; _base.py re-exports them
(unchanged for tool submodules) and integration.py imports from core.paths. Path
resolution is byte-for-byte identical (same base dir <root>/src, same env-var/tmp
fallback). No functional change. repo-quality-monitor architecture check: 0 findings.

src/core/paths.py

@@ -0,0 +1,43 @@
+"""
+Writable directory resolution for the agent.
+
+These are shared infrastructure constants — an env-resolved input/output/cache
+location — needed by both the ``tools`` layer (which writes analysis artifacts)
+and the ``workflows`` layer (which writes combined datasets). They live in
+``core`` so both layers can import them downward without violating the layering
+contract (``tools`` and ``workflows`` both build on ``core``).
+"""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+# core/paths.py lives at <root>/src/core/, so two levels up is <root>/src —
+# the same base directory the tool package historically resolved against.
+PROJECT_ROOT = Path(__file__).parent.parent.resolve()
+_DEFAULT_INPUT = PROJECT_ROOT / "tmp" / "inputs"
+_DEFAULT_OUTPUT = PROJECT_ROOT / "tmp" / "outputs"
+_DEFAULT_GEO_CACHE = PROJECT_ROOT / "tmp" / "geo_cache"
+
+
+def _resolve_dir(env_var: str, project_default: Path, hf_fallback: Path) -> Path:
+    """Return a writable directory: env var > project default > /tmp fallback."""
+    env_val = os.environ.get(env_var)
+    if env_val:
+        p = Path(env_val)
+        p.mkdir(parents=True, exist_ok=True)
+        return p
+    try:
+        project_default.mkdir(parents=True, exist_ok=True)
+        return project_default
+    except PermissionError:
+        hf_fallback.mkdir(parents=True, exist_ok=True)
+        return hf_fallback
+
+
+INPUT_DIR = _resolve_dir("RNA_INPUT_DIR", _DEFAULT_INPUT, Path("/tmp/decoupleRpy/inputs"))
+OUTPUT_DIR = _resolve_dir("RNA_OUTPUT_DIR", _DEFAULT_OUTPUT, Path("/tmp/decoupleRpy/outputs"))
+GEO_CACHE_DIR = _resolve_dir(
+    "RNA_GEO_CACHE_DIR", _DEFAULT_GEO_CACHE, Path("/tmp/decoupleRpy/geo_cache")
+)

src/tools/rna/_base.py

@@ -28,32 +28,14 @@ from pydeseq2.ds import DeseqStats
 matplotlib.use("Agg")
 import matplotlib.pyplot as plt
 
-# Project structure
-PROJECT_ROOT = Path(__file__).parent.parent.parent.resolve()
-_DEFAULT_INPUT = PROJECT_ROOT / "tmp" / "inputs"
-_DEFAULT_OUTPUT = PROJECT_ROOT / "tmp" / "outputs"
-_DEFAULT_GEO_CACHE = PROJECT_ROOT / "tmp" / "geo_cache"
-
-
-def _resolve_dir(env_var: str, project_default: Path, hf_fallback: Path) -> Path:
-    """Return a writable directory: env var > project default > /tmp fallback."""
-    env_val = os.environ.get(env_var)
-    if env_val:
-        p = Path(env_val)
-        p.mkdir(parents=True, exist_ok=True)
-        return p
-    try:
-        project_default.mkdir(parents=True, exist_ok=True)
-        return project_default
-    except PermissionError:
-        hf_fallback.mkdir(parents=True, exist_ok=True)
-        return hf_fallback
-
-
-INPUT_DIR = _resolve_dir("RNA_INPUT_DIR", _DEFAULT_INPUT, Path("/tmp/decoupleRpy/inputs"))
-OUTPUT_DIR = _resolve_dir("RNA_OUTPUT_DIR", _DEFAULT_OUTPUT, Path("/tmp/decoupleRpy/outputs"))
-GEO_CACHE_DIR = _resolve_dir(
-    "RNA_GEO_CACHE_DIR", _DEFAULT_GEO_CACHE, Path("/tmp/decoupleRpy/geo_cache")
+# Project structure. Writable directories now live in core.paths (shared
+# infrastructure both tools and workflows build on); re-exported here so tool
+# submodules keep importing them from _base unchanged.
+from src.core.paths import (  # noqa: E402
+    GEO_CACHE_DIR,
+    INPUT_DIR,
+    OUTPUT_DIR,
+    PROJECT_ROOT,
 )
 
 # Timestamp for unique outputs

src/workflows/integration.py

@@ -38,7 +38,7 @@ from typing import TYPE_CHECKING
 import anndata as ad
 import numpy as np
 
-from src.tools.rna._base import OUTPUT_DIR
+from src.core.paths import OUTPUT_DIR
 
 if TYPE_CHECKING:
     from anndata import AnnData