🛠️ Update various documentation, scripts, and configuration templates to enhance clarity, functionality, and maintainability across the project

docs/architecture.md

@@ -13,6 +13,9 @@ Git-based after a resource is published.
 - `resources/instructions/`: shared instruction packs
 - `resources/agents/`: shared custom agents for local chat and overlays
 - `resources/hooks/`: shared hook definitions
+- `config/mcp/`: tracked MCP templates and example machine-local overrides
+- `install/merge-managed-mcp-config.mjs`: managed MCP merge and prune logic for user config files
+- `install/mcp/`: wrapper scripts for MCP servers that need runtime adaptation
 - `templates/repo-overlay/`: files that can be copied into another repository for
   repository-scoped behavior
 
@@ -29,6 +32,14 @@ Bootstrap prefers linking default discovery paths back to this repository:
 This keeps the repository authoritative while still using default discovery
 locations whenever possible.
 
+For MCP, bootstrap uses generated user-level config instead of links:
+
+- VS Code user `mcp.json`
+- Copilot CLI user `~/.copilot/mcp-config.json`
+
+Those generated files come from tracked templates plus machine-local data in
+`.local/mcp.local.jsonc`.
+
 ## Propagation Model
 
 There are only two supported creation paths:
@@ -38,3 +49,11 @@ There are only two supported creation paths:
 
 Once a resource lands in the repository, commit and push it. Other systems pick
 it up through `install/update.*` or future scheduled sync.
+
+Managed MCP propagation follows the same rule, but with a split between shared
+and local inputs:
+
+- Shared defaults and server definitions are tracked in the repo
+- Machine-local secrets and enablement stay in `.local/`
+- `install/update.*` pulls the repo and reruns bootstrap so the generated MCP
+  files refresh from the latest templates on every machine