diff --git a/5-metrics.py b/5-metrics.py
index 5f9a811..d4a833e 100644
--- a/5-metrics.py
+++ b/5-metrics.py
@@ -82,6 +82,14 @@ PHENOCAM_IMAGE_URL = (
 # ---------------------------------------------------------------------------
 
 
+def _window_mean(data: np.ndarray) -> float | None:
+    """Mean of a pixel window; ``None`` when every value is NaN."""
+    valid = data[~np.isnan(data)]
+    if valid.size == 0:
+        return None
+    return float(np.mean(valid))
+
+
 def _read_center_pixel(path: Path, lat: float, lon: float) -> float | None:
     """Return the 3×3 mean GCC value at (lat, lon) from a single-band raster.
 
@@ -103,9 +111,7 @@ def _read_center_pixel(path: Path, lat: float, lon: float) -> float | None:
         if nodata is not None:
             data = np.where(data == nodata, np.nan, data)
         data[data == 0] = np.nan
-        with np.errstate(all="ignore"):
-            val = np.nanmean(data)
-        return None if np.isnan(val) else float(val)
+        return _window_mean(data)
     except Exception:
         return None
 
@@ -334,9 +340,8 @@ def _read_multiband_center(
                 if nodata is not None:
                     data = np.where(data == nodata, np.nan, data)
                 data[data == 0] = np.nan
-                with np.errstate(all="ignore"):
-                    val = np.nanmean(data)
-                result[name] = None if np.isnan(val) else round(float(val), 6)
+                val = _window_mean(data)
+                result[name] = None if val is None else round(val, 6)
         return result
     except Exception:
         return {name: None for name in band_names}
diff --git a/run-pipeline.py b/run-pipeline.py
index db2c493..3c18dc9 100644
--- a/run-pipeline.py
+++ b/run-pipeline.py
@@ -1,9 +1,11 @@
 """Pipeline wrapper: run steps 1 → 2 → 3 → 4 → 5.
 
 Steps 1 and 2 run once for the whole year (skipped when their output already
-exists).  Steps 3–5 run site-by-site for every PASS site from
-``data/phenocam_screening/{year}.json``; a site is skipped entirely when
-``data/metrics/{year}/{site}/metrics.json`` already exists.
+exists).  Steps 3 and 4 run site-by-site for every PASS site from
+``data/phenocam_screening/{year}.json``; a site is skipped when
+``data/metrics/{year}/{site}/metrics.json`` already exists.  Step 5 always
+runs once at the end without ``--site`` so that ``manifest.json`` is written
+with all processed sites (not just the last one).
 
 Any failure stops the run immediately.  Fix the issue and re-run — completed
 steps and sites are skipped automatically.
@@ -11,7 +13,7 @@ steps and sites are skipped automatically.
 CLI:
 
 - ``--evaluation-year`` (default 2025)
-- ``--site``            single site to run steps 3–5 for (default: all PASS sites)
+- ``--site``            single site to run steps 3–4 for (default: all PASS sites)
 """
 
 from __future__ import annotations
@@ -36,7 +38,6 @@ GLOBAL_STEPS: list[tuple[str, Path]] = [
 PER_SITE_STEPS = [
     "3-sentinel-data.py",
     "4-fusion.py",
-    "5-metrics.py",
 ]