Improved single sites metrics calculation.

run-pipeline.py

@@ -1,11 +1,9 @@
 """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 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).
+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.
 
 Any failure stops the run immediately.  Fix the issue and re-run — completed
 steps and sites are skipped automatically.
@@ -13,7 +11,7 @@ steps and sites are skipped automatically.
 CLI:
 
 - ``--evaluation-year`` (default 2025)
-- ``--site``            single site to run steps 3–4 for (default: all PASS sites)
+- ``--site``            single site to run steps 3–5 for (default: all PASS sites)
 """
 
 from __future__ import annotations
@@ -38,6 +36,7 @@ GLOBAL_STEPS: list[tuple[str, Path]] = [
 PER_SITE_STEPS = [
     "3-sentinel-data.py",
     "4-fusion.py",
+    "5-metrics.py",
 ]
 
 
@@ -101,7 +100,7 @@ def main(argv: list[str] | None = None) -> int:
                     f"[pipeline] {script} failed (exit {rc}); cannot continue"
                 )
 
-    # --- Per-site steps (steps 3–5) ---
+    # --- Per-site steps (steps 3, 4, 5) ---
     sites = _load_pass_sites(year)
     if args.site:
         if args.site not in sites: