fix: resolve 4 major architectural deadlock and OS dependency bugs

bootstrap.bat

@@ -1,19 +1,38 @@
 @echo off
 setlocal
 
-echo [1/3] Updating Git Submodules...
+:: Prevent git from hanging on auth prompts for submodules
+set GIT_TERMINAL_PROMPT=0
+
+echo [1/4] Checking and Initializing Agent Config (.env.agent)...
+if not exist ".agent\config\.env.agent" (
+    if exist ".agent\config\.env.agent.template" (
+        copy ".agent\config\.env.agent.template" ".agent\config\.env.agent" >nul
+        echo    -^> Created .agent\config\.env.agent from template.
+    ) else (
+        echo    -^> Warning: Template missing.
+    )
+) else (
+    echo    -^> .env.agent already exists.
+)
+
+echo [2/4] Updating Git Submodules...
 git submodule update --init --recursive
 
-echo [2/3] Bypassing PowerShell and Installing AI Local Dependencies...
+echo [3/4] Bypassing PowerShell and Installing AI Local Dependencies...
 cd .agent\env
 call npm install
 cd ..\..
 
-echo [3/3] Installing Universal AI Workflow Tool (get-shit-done-cc) Globally...
+echo [4/4] Installing Universal AI Workflow Tool (get-shit-done-cc) Globally...
 call npm install -g get-shit-done-cc@latest
 
 echo.
 echo ========================================================
 echo [OK] Zero-Click Bootstrap Complete. AI Agents are ready!
+echo --------------------------------------------------------
+echo [!] ACTION REQUIRED: 
+echo Please open '.agent\config\.env.agent' to set up 
+echo your Vikunja Project ID and Gitea Wiki URL tracking.
 echo ========================================================
 endlocal