From 298f00728d60f9c46cc2658e49b674647e1c1061 Mon Sep 17 00:00:00 2001
From: kyro <60421602+mucjustin@users.noreply.github.com>
Date: Tue, 29 Sep 2026 16:10:09 +0800
Subject: [PATCH] fix: preserve workspace config and make analysis portable

---
 README.en.md                                  |  3 ++-
 README.md                                     |  3 ++-
 ml-analysis/mpa_ml_analysis.py                |  3 ++-
 .../scripts/Initialize-MpaWorkspace.ps1       | 12 ++++++++++-
 tests/Test-WorkspaceScripts.ps1               | 20 +++++++++++++++++++
 5 files changed, 37 insertions(+), 4 deletions(-)

diff --git a/README.en.md b/README.en.md
index 7a7aa52..d9c6a78 100644
--- a/README.en.md
+++ b/README.en.md
@@ -56,7 +56,7 @@ Two behavioral gates run throughout:
 | | Feature | One-liner |
 |---|---|---|
 | 🧭 | MPA Research Spine | Eight-step verifiable research thread |
-| 🛣️ | Ten research routes | Course/case/policy/lit/design/fieldwork/data/thesis/defence |
+| 🛣️ | Twelve task routes | Course, case, policy, literature, design, fieldwork, data, thesis, defence, and related tasks |
 | 🔗 | Course-to-capstone reuse | Notes, cases, code become assets; re-verify before reuse |
 | 🧠 | MPA knowledge ontology | Theory map + China governance contexts + thinking checklist |
 | 🛡️ | Data before writing | Audit first, write second, never mask gaps |
@@ -83,6 +83,7 @@ $skillRoot = Join-Path $HOME '.agents\skills\mpa-skill'
 ```
 
 Default config goes to `%APPDATA%\mpa-skill\config.json`. Does not modify Zotero database or Obsidian settings. Add `-WhatIf` to preview; run `Test-MpaEnvironment.ps1` to check your setup.
+If the config file already exists, initialization stops and preserves it. Pass a new `-ConfigPath` to create another configuration.
 
 ### Update and uninstall
 
diff --git a/README.md b/README.md
index 69c831e..f7e257d 100644
--- a/README.md
+++ b/README.md
@@ -56,7 +56,7 @@
 | | 特性 | 一句话 |
 |---|---|---|
 | 🧭 | MPA Research Spine | 八步可核验研究主线，先识别缺口再动笔 |
-| 🛣️ | 十条研究路由 | 课程/案例/政策/文献/设计/田野/数据/论文/答辩，按需组合 |
+| 🛣️ | 十二条任务路由 | 课程、案例、政策、文献、设计、田野、数据、论文、答辩等，按需组合 |
 | 🔗 | 课程→毕业复用 | 笔记、案例、代码可沉淀为研究资产，复用前回原始来源核验 |
 | 🧠 | MPA 知识本体 | 理论地图 + 中国治理情境 + 思维清单 + 课程映射 |
 | 🛡️ | 数据先于写作 | 先审计再写作，不靠改写掩盖缺口 |
@@ -83,6 +83,7 @@ $skillRoot = Join-Path $HOME '.agents\skills\mpa-skill'
 ```
 
 默认配置写入 `%APPDATA%\mpa-skill\config.json`，不修改 Zotero 数据库或 Obsidian 设置。预览操作加 `-WhatIf`；检查环境用 `Test-MpaEnvironment.ps1`。
+若配置文件已存在，初始化会停止并保留原文件；要创建另一套配置，请指定新的 `-ConfigPath`。
 
 ### 更新与卸载 (Update & Uninstall)
 
diff --git a/ml-analysis/mpa_ml_analysis.py b/ml-analysis/mpa_ml_analysis.py
index 1555920..e9dc30f 100644
--- a/ml-analysis/mpa_ml_analysis.py
+++ b/ml-analysis/mpa_ml_analysis.py
@@ -5,6 +5,7 @@
 """
 
 import json, re, os, warnings
+from pathlib import Path
 warnings.filterwarnings("ignore")
 
 import numpy as np
@@ -25,7 +26,7 @@
 from scipy.stats import chi2
 
 # ── paths ──
-REPO = r"E:\CodexProjects\mpa-skill-public"
+REPO = Path(__file__).resolve().parents[1]
 OUT = os.path.join(REPO, "ml-analysis", "output")
 os.makedirs(OUT, exist_ok=True)
 
diff --git a/skills/mpa-skill/scripts/Initialize-MpaWorkspace.ps1 b/skills/mpa-skill/scripts/Initialize-MpaWorkspace.ps1
index a74463c..7c3e031 100644
--- a/skills/mpa-skill/scripts/Initialize-MpaWorkspace.ps1
+++ b/skills/mpa-skill/scripts/Initialize-MpaWorkspace.ps1
@@ -30,6 +30,9 @@ if ([string]::IsNullOrWhiteSpace($ConfigPath)) {
     $ConfigPath = Join-Path $env:APPDATA 'mpa-skill\config.json'
 }
 $resolvedConfig = Resolve-FullPath $ConfigPath
+if (Test-Path -LiteralPath $resolvedConfig) {
+    throw "ConfigPath already exists: $resolvedConfig. Choose another ConfigPath to preserve the existing configuration."
+}
 
 if ([string]::IsNullOrWhiteSpace($ZoteroExecutable)) {
     $candidates = [System.Collections.Generic.List[string]]::new()
@@ -75,7 +78,14 @@ if (-not $WhatIf) {
     [IO.Directory]::CreateDirectory($configDirectory) | Out-Null
     $json = [pscustomobject]$paths | ConvertTo-Json
     $utf8 = New-Object Text.UTF8Encoding($false)
-    [IO.File]::WriteAllText($resolvedConfig, $json + [Environment]::NewLine, $utf8)
+    $stream = [IO.File]::Open($resolvedConfig, [IO.FileMode]::CreateNew, [IO.FileAccess]::Write)
+    try {
+        $writer = New-Object IO.StreamWriter($stream, $utf8)
+        $writer.Write($json + [Environment]::NewLine)
+        $writer.Dispose()
+    } finally {
+        $stream.Dispose()
+    }
 }
 
 [pscustomobject]@{
diff --git a/tests/Test-WorkspaceScripts.ps1 b/tests/Test-WorkspaceScripts.ps1
index c6ebfdf..90d2a2f 100644
--- a/tests/Test-WorkspaceScripts.ps1
+++ b/tests/Test-WorkspaceScripts.ps1
@@ -50,6 +50,26 @@ try {
     Assert-True ($config.zotero_executable -ceq $zoteroPath) 'explicit Zotero executable was not preserved'
     Assert-True ($result.ConfigPath -ceq [IO.Path]::GetFullPath($configPath)) 'initializer summary config path differs'
 
+    $originalConfig = [IO.File]::ReadAllBytes($configPath)
+    $secondWorkspace = Join-Path $testRoot 'SecondWorkspace'
+    $existingConfigRejected = $false
+    try {
+        $null = & $initializeScript -WorkspaceRoot $secondWorkspace -ConfigPath $configPath
+    } catch {
+        $existingConfigRejected = $true
+    }
+    Assert-True $existingConfigRejected 'existing config was silently replaced'
+    Assert-True (-not (Test-Path -LiteralPath $secondWorkspace)) 'existing config rejection created a workspace'
+    Assert-True ([Convert]::ToBase64String([IO.File]::ReadAllBytes($configPath)) -ceq [Convert]::ToBase64String($originalConfig)) 'existing config changed'
+
+    $whatIfRejected = $false
+    try {
+        $null = & $initializeScript -WorkspaceRoot $secondWorkspace -ConfigPath $configPath -WhatIf
+    } catch {
+        $whatIfRejected = $true
+    }
+    Assert-True $whatIfRejected 'WhatIf did not report existing config conflict'
+
     $whatIfRoot = Join-Path $testRoot 'WhatIfWorkspace'
     $whatIfConfig = Join-Path $isolatedAppData 'what-if.json'
     $null = & $initializeScript -WorkspaceRoot $whatIfRoot -ConfigPath $whatIfConfig -WhatIf