docs: Added documentation on the updated mcp.json location for bundles

Sharing-Configurations.md

@@ -117,13 +117,13 @@ Restrict an install to a single asset category with `--filter`:
 
 | Filter       | Installs                                                                                       |
 |--------------|------------------------------------------------------------------------------------------------|
-| *(omitted)*  | `agents/`, `roles/`, `skills/`, `macros/`, `functions/tools/`, and merges `functions/mcp.json` |
+| *(omitted)*  | `agents/`, `roles/`, `skills/`, `macros/`, `functions/tools/`, and merges `mcp.json`           |
 | `agents`     | `agents/` only                                                                                 |
 | `roles`      | `roles/` only                                                                                  |
 | `skills`     | `skills/` only                                                                                 |
 | `macros`     | `macros/` only                                                                                 |
 | `functions`  | `functions/tools/` only (does **not** include `mcp.json`)                                      |
-| `mcp_config` | `functions/mcp.json` only (merged)                                                             |
+| `mcp_config` | `mcp.json` only (merged)                                                                       |
 
 ```sh
 coyote --install <source> --filter agents
@@ -165,10 +165,11 @@ Coyote recognizes these top-level directories. Anything outside them is ignored.
 │       └── SKILL.md              # YAML frontmatter + body
 ├── macros/
 │   └── <macro-name>.yaml         # Positional/rest variables + REPL command steps
-└── functions/
-    ├── tools/
-    │   └── *.sh / *.py / *.ts    # Global tools (auto chmod +x on install)
-    └── mcp.json                  # MCP server config (merged with local, not overwritten)
+├── functions/
+│   ├── tools/
+│   │   └── *.sh / *.py / *.ts    # Global tools (auto chmod +x on install)
+│   └── mcp.json                  # Historical MCP config location (still supported)
+└── mcp.json                      # MCP server config (merged with local, not overwritten)
 ```
 
 A few things to note:
@@ -177,6 +178,8 @@ A few things to note:
   do not need to use `--filter` for partial repos.
 - **`.git/` is excluded** from the scan automatically.
 - **Symlinks are rejected** by the install walker as a defense-in-depth measure.
+- **`mcp.json` may live at the bundle root or at the historical `functions/mcp.json`.** If both exist, the root-level
+  file wins, mirroring how Coyote resolves the user-scope config location.
 - **`functions/bin/` and `functions/utils/` are not recognized** (compiled at runtime / not in scope for sharing).
 - **The whole `config.yaml`** (global Coyote config) is **not** shared (see [What is not shared](#what-is-not-shared)).
 
@@ -364,8 +367,9 @@ Scripts written into `functions/tools/` are automatically marked executable base
 
 ## MCP configuration merge
 
-`functions/mcp.json` is the exception to the per-file conflict model. Instead of replacing your local file outright,
-Coyote **merges** the remote `mcp.json` into your existing one.
+The bundle's `mcp.json` (at the repo root, or the historical `functions/mcp.json` location) is the exception to
+the per-file conflict model. Instead of replacing your local file outright, Coyote **merges** the remote `mcp.json`
+into your existing one.
 
 ### Merge behavior