export command produces manifest in different format and breaks the app commands

**Describe the bug**
With `aio rt export` the manifest we get looks like below.
```
project:
name: expproj
packages:
__APP_PACKAGE__:
```
Trying any of the app commands eg: `aio app logs` with this exported manifest fails with
```
TypeError: Cannot read property '__APP_PACKAGE__' of undefined
```
This is because app plugin expects the manifest format like below
```
project:
name: expproj
packages:
__APP_PACKAGE__:
```
Notice that `packages` is at the same level as `project`

**To Reproduce**
See above

**Expected behavior**
Should work

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Desktop (please complete the following information):**
- OS: [e.g. iOS]
- Browser [e.g. chrome, safari]
- Version [e.g. 22]

**Smartphone (please complete the following information):**
- Device: [e.g. iPhone6]
- OS: [e.g. iOS8.1]
- Browser [e.g. stock browser, safari]
- Version [e.g. 22]

**Additional context**
Add any other context about the problem here.

Start at the `aio rt export` command entry point and trace how it assembles the manifest. Compare its output with the structure expected by the `aio app` commands, then reproduce the export and run an app command to confirm that the generated `packages` nesting is corrected.

Written by the indexing model from the issue text.