Updated deployment notes

apps/deploy.mdx

@@ -32,6 +32,7 @@ kernel deploy my_app.py --env MY_ENV_VAR=my_value # Can add multiple env vars de
 ## Deployment notes
 
 - The `entrypoint_file_name` is the file name where you [defined](/apps/develop) your app.
+- **The entrypoint file and dependency manifest (`package.json` for JS/TS, `pyproject.toml` for Python) must both be in the root directory of your project.**
 - Include a `.gitignore` file to exclude dependency folders like `node_modules` and `.venv`.
 - Kernel assumes the root directory contains at least this file structure:
 

reference/cli/apps.mdx

@@ -12,6 +12,10 @@ Deploy an app to Kernel from the current directory.
 | `--env <ENV_VAR=VAL>`, `-e` | Adds environment variables to the app. May be specified multiple times. Optional. |
 | `--env-file <file>` | Read environment variables from a .env file. May be specified multiple times. Optional. |
 
+<Info>
+The entrypoint file and dependency manifest (`package.json` for JS/TS, `pyproject.toml` for Python) must both be in the root directory of your project.
+</Info>
+
 ## `kernel invoke <app_name> <action_name>`
 Invoke a specific app action by its name. Generates an Invocation.