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.

tools/README.md

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+# BtToxin Analysis Modules
+
+This directory contains specialized analysis modules integrated into the BtToxin Pipeline. Each module focuses on identifying and characterizing specific genomic features that contribute to the insecticidal potential of *Bacillus thuringiensis* strains.
+
+## 1. BtToxin_Digger
+**Core Toxin Identification Module**
+
+This is the foundational module of the pipeline, responsible for identifying Cry, Cyt, and Vip toxin genes in bacterial genomes.
+
+*   **Function**:
+    *   Predicts Open Reading Frames (ORFs) from genomic sequences (.fna).
+    *   Translates coding sequences (CDS) to proteins.
+    *   Uses BLAST and HMM (Hidden Markov Models) to search against a curated database of known Bt toxins.
+    *   Identifies toxin candidates and classifies them into families/subfamilies based on sequence identity.
+*   **Key Metrics**: Sequence Identity (`Identity`), Coverage (`Coverage`), and HMM domain hits.
+*   **Role**: Provides the primary "evidence" ($w_i$) for the Shotter scoring system.
+
+## 2. BGC Analysis (bgc_analysis)
+**Biosynthetic Gene Cluster Detection**
+
+This module detects three specific classes of insecticidal protein gene clusters that serve as independent markers of insecticidal activity.
+
+*   **Targets**:
+    *   **ZWA**: Zwittermicin A biosynthetic gene cluster.
+    *   **Thu**: Thuringiensin (beta-exotoxin) biosynthetic gene cluster.
+    *   **TAA**: Toxin A (insecticidal protein) gene cluster.
+*   **Methodology**:
+    *   Uses BLAST/HMM to detect signature enzymes and backbone genes specific to these clusters.
+    *   Returns a binary status (Present/Absent) for each cluster type ($b_Z, b_T, b_A \in \{0, 1\}$).
+*   **Contribution to Scoring**:
+    *   The presence of these clusters acts as a **positive prior**, boosting the final toxicity score ($S_{\text{final}}$) because they represent functional insecticidal modules independent of Cry/Vip proteins.
+
+## 3. Mobilome Analysis (mobilome_analysis)
+**Mobile Genetic Element Quantification**
+
+This module quantifies the "mobilome"—the collection of mobile genetic elements—which correlates with a strain's ability to acquire, rearrange, and maintain toxin genes.
+
+*   **Targets**:
+    *   **Transposases**: Enzymes that facilitate gene movement.
+    *   **Plasmids**: Extrachromosomal DNA often carrying toxin genes in Bt.
+    *   **Phages**: Viral elements that can mediate horizontal gene transfer.
+*   **Methodology**:
+    *   Annotates and counts these elements in the genome.
+    *   Returns a total count or specific counts ($m$).
+*   **Contribution to Scoring**:
+    *   A higher mobilome count indicates a more "open" genome capable of HGT (Horizontal Gene Transfer).
+    *   Contributes a **positive prior** (via a saturation function $g(m)$) to the toxicity score, reflecting a higher potential for evolving or acquiring diverse toxin cocktails.
+
+## 4. CRISPR-Cas Analysis (crispr_cas_analysis)
+**Genome Defense System Characterization**
+
+This module characterizes the CRISPR-Cas immune systems, which act as barriers to foreign DNA (including plasmids and phages).
+
+*   **Targets**:
+    *   **Cas Proteins**: Identification of Cas gene clusters.
+    *   **CRISPR Arrays**: Detection of direct repeats and spacers.
+*   **Methodology**:
+    *   Classifies the system status into three levels: **Complete** (functional), **Incomplete** (degraded), or **Absent**.
+    *   Returns a status code $c \in \{0, 1, 2\}$ (0=Absent, 1=Incomplete, 2=Complete).
+*   **Contribution to Scoring**:
+    *   **Negative Prior**: A complete, functional CRISPR system ($c=2$) limits the intake of foreign plasmids (which often carry toxins).
+    *   Therefore, an **Absent** system allows for the highest potential of plasmid-borne toxin acquisition (Highest score boost), while a **Complete** system penalizes the prior probability (Lowest/No boost). This follows the logic: *Absent > Incomplete > Complete* for toxicity potential.
+
+---
+
+## Integration in Shotter Scoring
+
+These modules work together to refine the final insecticidal activity prediction:
+
+1.  **Evidence**: **BtToxin_Digger** provides direct evidence of toxin genes ($S_{\text{tox}}$).
+2.  **Priors**: **BGC**, **Mobilome**, and **CRISPR** modules provide a "genomic context" prior ($\Delta(\text{strain})$).
+
+The final score combines these using a logit-based adjustment:
+
+$$
+S_{\text{final}} = \sigma\left( \operatorname{logit}(S_{\text{tox}}) + \Delta(\text{strain}) \right)
+$$
+
+Where $\Delta(\text{strain})$ aggregates the positive boosts from BGCs/Mobilome and the adjustment from CRISPR status.
+
+For full mathematical details, see [docs/shotter_math_full_zh_typora.md](../docs/shotter_math_full_zh_typora.md).