[Bug]: --env-file not available at top-level

### Problem description

Environment variables inside .env (passed as --env-file) are not accessible in main module.

### Steps to reproduce

https://gist.github.com/iacore/7f33b19d8e5f0db8420531be8c8d8bd8

```
git clone https://gist.github.com/7f33b19d8e5f0db8420531be8c8d8bd8.git test_repo
cd test_repo
bash deploy
```

output:

```
× Deployment failed.
error: The deployment failed: UNCAUGHT_EXCEPTION

AssertionError
at assert (https://jsr.io/@std/assert/1.0.13/assert.ts:21:11)
at file:///src/main.ts:3:1
```

### Expected behavior

Deployment should succeed

### Environment

_No response_

### Possible solution

_No response_

### Additional context

_No response_

Clone the reproduction gist, enter test_repo, and run bash deploy to reproduce the failure in src/main.ts. Trace how --env-file values reach the top-level module; done means the assertion passes and deployment succeeds.

Written by the indexing model from the issue text.