Refactor: Unified pipeline execution, simplified UI, and fixed Docker config

- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.

AGENTS.md

@@ -27,14 +27,13 @@ git clone <repo>
 cd bttoxin-pipeline
 pixi install
 
-# 2. Start services (Docker recommended for full stack)
-# Using DaoCloud mirrors for faster builds in CN
-docker compose -f docker/compose/docker-compose.traefik.yml up -d --build
+# 2. Start services (Production with Traefik)
+# Using the unified production configuration
+docker compose -f docker/compose/docker-compose.traefik.yml -p compose up -d --build
 
 # Access:
 # Frontend: https://bttiaw.hzau.edu.cn (via Traefik)
-# Backend API: http://localhost:8000 (Internal)
-# Traefik Dashboard: http://localhost:8080
+# Backend API: http://bttoxin-pipeline:8000 (Internal)
 
 # 3. Development Mode (Local)
 pixi run web-start
@@ -475,3 +474,28 @@ docker exec bttoxin-pipeline nginx -T
 # Verify backend is running
 docker exec bttoxin-pipeline curl http://127.0.0.1:8000/api/health
 ```
+
+### Post-Mortem: Startup Failures & 404/403 Errors (2026-01 Update)
+
+**Symptoms:**
+- Website returns 404 Not Found or 403 Forbidden.
+- Container stuck in `Restarting` loop.
+- Logs show `exec: "uvicorn": executable file not found`.
+
+**Root Causes & Solutions:**
+
+1.  **Missing Environment Config**:
+    - **Cause**: `pixi.toml` and `pixi.lock` were missing in the final Docker image phase.
+    - **Fix**: Ensure `COPY --from=builder /app/pixi.toml ...` is present in Dockerfile.
+
+2.  **Port Conflict**:
+    - **Cause**: `docker-compose.yml` mapped `80:80` while Traefik already occupied port 80.
+    - **Fix**: Remove `ports` mapping in compose file; rely on Docker internal network (`frontend`) and Traefik labels.
+
+3.  **Frontend Permissions**:
+    - **Cause**: Built frontend files owned by root were not readable by Nginx user.
+    - **Fix**: Add `RUN chmod -R 755 /var/www/html` in Dockerfile.
+
+4.  **Health Check Path**:
+    - **Cause**: Nginx routed `/health` to `/api/health` but backend expected `/health`.
+    - **Fix**: Update Nginx config to proxy pass to correct endpoint.