Fix installer upgrade issues from v4 to v6. and v6 custom files will no longer be lost (modified ones will though for now still)

bmad/_cfg/agent-party.xml

@@ -1,7 +1,7 @@
 <!-- Powered by BMAD-CORE™ -->
 <!-- Agent Manifest - Generated during BMAD installation -->
 <!-- This file contains a summary of all installed agents for quick reference -->
-<manifest id="bmad/_cfg/agent-party.xml" version="1.0" generated="2025-10-01T00:22:43.657Z">
+<manifest id="bmad/_cfg/agent-party.xml" version="1.0" generated="2025-10-01T00:47:33.050Z">
   <description>
     Complete roster of installed BMAD agents with summarized personas for efficient multi-agent orchestration.
     Used by party-mode and other multi-agent coordination features.
@@ -164,6 +164,6 @@
   <statistics>
     <total_agents>18</total_agents>
     <modules>bmm, cis, core, custom</modules>
-    <last_updated>2025-10-01T00:22:43.657Z</last_updated>
+    <last_updated>2025-10-01T00:47:33.050Z</last_updated>
   </statistics>
 </manifest>

bmad/_cfg/manifest.csv

@@ -1,11 +1,11 @@
 # BMAD Manifest
-# Generated: 2025-10-01T00:22:43.703Z
+# Generated: 2025-10-01T00:47:33.096Z
 
 ## Installation Info
 Property,Value
 Version,6.0.0-alpha.0
-InstallDate,2025-10-01T00:22:43.690Z
-LastUpdated,2025-10-01T00:22:43.703Z
+InstallDate,2025-10-01T00:47:33.083Z
+LastUpdated,2025-10-01T00:47:33.096Z
 
 ## Modules
 Name,Version,ShortTitle

bmad/_cfg/manifest.yaml

@@ -1,7 +1,7 @@
 installation:
   version: 6.0.0-alpha.0
-  installDate: "2025-10-01T00:22:43.664Z"
-  lastUpdated: "2025-10-01T00:22:43.664Z"
+  installDate: "2025-10-01T00:47:33.058Z"
+  lastUpdated: "2025-10-01T00:47:33.058Z"
 modules:
   - name: core
     version: ""