fix: Prevent duplicate manifest entries and update GitHub Copilot tool names

- Deduplicate module lists in manifest generator using Set to prevent duplicate entries in installed manifests
- Update GitHub Copilot tool names to match official VS Code documentation (November 2025)
- Clean up legacy bmad/, bmd/, and web-bundles directories

src/core/_module-installer/install-config.yaml

@@ -4,13 +4,16 @@ prompt:
   - "Welcome and thank you for choosing BMAD™! This is the Core Configuration."
   - "This will impact all selected modules, either additions or upgrades."
 
-# This is injected into the custom agent activation rules
+bmad_folder:
+  prompt: "What is the root that all modules should be installed to?"
+  default: ".bmad"
+  result: "{value}"
+
 user_name:
   prompt: "What is your name?"
   default: "BMad"
   result: "{value}"
 
-# This is injected into the custom agent activation rules and most workflows
 communication_language:
   prompt: "Preferred Chat Language?"
   default: "English"
@@ -21,7 +24,6 @@ document_output_language:
   default: "English"
   result: "{value}"
 
-# This is injected into the custom agent activation rules
 output_folder:
   prompt: "Where should the generated output default save location be?"
   default: "docs"