CLI tool is not replacing '$' placeholders with environment variables

**Describe the bug**
CLI tool is not replacing '$' placeholders (indented more than one level) with environment variables.

**To Reproduce**
Example manifest file:
```yml
packages:
__APP_PACKAGE__:
version: 1.0.0
license: Adobe-2006
actions:
someAction:
function: dist/someAction
runtime: nodejs:10
web-export: true
annotations:
final: true
inputs:
eventingConnection:
bootstrapServers: $BOOTSTRAP_SERVERS
saslUsername: $SASL_USERNAME
```

**Expected behavior**
I expect aio cli tool to replace $ placeholders with environment variables regardless of the indentation level.

**Additional context**
An example error:
```
Error: Error connecting to the host: $BOOTSTRAP_SERVERS failed - getaddrinfo ENOTFOUND
```

Reproduce the issue with the provided manifest and nested inputs containing $BOOTSTRAP_SERVERS and $SASL_USERNAME. Start by tracing the CLI's manifest environment-variable substitution path; done means placeholders are replaced regardless of indentation and the provided connection error no longer contains the literal placeholder.

Written by the indexing model from the issue text.