feat(pipeline): stage 04b port trim_above_water from dispatcher

pipeline/run_pipeline.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+# Run full pipeline for a mission: stages 02→03→04→05
+# Usage: ./run_pipeline.sh <mission> [worker]
+# Example: ./run_pipeline.sh 20260505-Lepradet auto
+
+set -euo pipefail
+
+MISSION=${1:-20260505-Lepradet}
+WORKER=${2:-auto}
+MANIFEST="/home/cosma/cosma-pipeline/${MISSION}/manifest.json"
+PIPELINE_DIR="$(cd "$(dirname "$0")" && pwd)/stages"
+PIPELINE_BASE="/home/cosma/cosma-pipeline"
+NAV_DIR="${PIPELINE_BASE}/data/${MISSION}/nav"
+NAV_FILT_DIR="${PIPELINE_BASE}/data/${MISSION}/nav_filtered"
+FRAMES_DIR="${PIPELINE_BASE}/data/${MISSION}/frames"
+
+RUN_ID="$(date +%Y%m%d_%H%M%S)"
+RUN_LOG_DIR="${PIPELINE_BASE}/runs/${RUN_ID}"
+mkdir -p "${RUN_LOG_DIR}"
+
+echo "=== Pipeline run ${RUN_ID} mission=${MISSION} worker=${WORKER} ===" | tee "${RUN_LOG_DIR}/run.log"
+echo "Start: $(date -u +%Y-%m-%dT%H:%M:%SZ)" | tee -a "${RUN_LOG_DIR}/run.log"
+
+# Stage 02: nav parse
+echo "" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "--- Stage 02: nav parse ---" | tee -a "${RUN_LOG_DIR}/run.log"
+python3 "${PIPELINE_DIR}/02_nav_parse.py" "${MANIFEST}" \
+    2>&1 | tee -a "${RUN_LOG_DIR}/stage02.log" "${RUN_LOG_DIR}/run.log"
+
+# Stage 03: nav filter
+echo "" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "--- Stage 03: nav filter ---" | tee -a "${RUN_LOG_DIR}/run.log"
+python3 "${PIPELINE_DIR}/03_nav_filter.py" "${NAV_DIR}" \
+    2>&1 | tee -a "${RUN_LOG_DIR}/stage03.log" "${RUN_LOG_DIR}/run.log"
+
+# Stage 04: frame extract
+echo "" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "--- Stage 04: frame extract ---" | tee -a "${RUN_LOG_DIR}/run.log"
+python3 "${PIPELINE_DIR}/04_frame_extract.py" --mission "${MISSION}" \
+    2>&1 | tee -a "${RUN_LOG_DIR}/stage04.log" "${RUN_LOG_DIR}/run.log"
+
+# Stage 05: inference (sequential, one segment at a time)
+echo "" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "--- Stage 05: inference ---" | tee -a "${RUN_LOG_DIR}/run.log"
+python3 "${PIPELINE_DIR}/05_inference.py" \
+    --frames-dir "${FRAMES_DIR}" \
+    --worker "${WORKER}" \
+    --mission "${MISSION}" \
+    2>&1 | tee -a "${RUN_LOG_DIR}/stage05.log" "${RUN_LOG_DIR}/run.log"
+
+echo "" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "=== Pipeline DONE $(date -u +%Y-%m-%dT%H:%M:%SZ) ===" | tee -a "${RUN_LOG_DIR}/run.log"
+echo "Logs: ${RUN_LOG_DIR}/"