Fix issue where terminal environment variables are not removed when they are commented out or deleted from .env files.

[StellaHuang95]

Fixes #936

The problem this PR fixed is when users comment out or remove a variable from their .env file:

API_KEY=secret
# DEBUG=true   ← commented out

The DEBUG variable remained in terminal environments because:

1. dotenv.parse() ignores commented lines (seems the right behavior per dotenv spec)
2. The returned object only contained active variables: { API_KEY: 'secret' }
3. The old code only iterated over keys in envVars and it never saw DEBUG
4. The delete() call was never reached for removed/commented variables

Solution is to call clear() before re-injecting variables, which makes the fix stays at the terminal injection layer rather than modifying the parsing layer, avoiding impacting on other consumers.

I also noticed some other issues with setting watcher, currently there's no file watcher watching the settings change, so a reload will be required when toggling the setting. We can consider adding a config listener.