`meltano upgrade` steps after upgrading package fail because old code is used
Running `meltano upgrade` to upgrade v1.35.0 to v1.36.0 didn't go as smoothly as it could have:
```sh
$ meltano upgrade
Upgrading `meltano` package...
[snip]
Installing collected packages: meltano
Attempting uninstall: meltano
Found existing installation: meltano 1.35.0
Uninstalling meltano-1.35.0:
Successfully uninstalled meltano-1.35.0
Running setup.py install for meltano ... done
Successfully installed meltano-1.36.0
The `meltano` package has been upgraded.
Reloading UI if running...
Updating files managed by plugins...
[2020-06-17 10:21:58,050|E|MainThread|root] Meltano could not update /Users/douwemaan/Development/meltano-projects/demo-project/orchestrate/dags/meltano.py: [Errno 2] No such file or directory: '/Users/douwemaan/.pyenv/versions/3.7.6/envs/meltano-demo-project/lib/python3.7/site-packages/meltano/core/bundle/dags/meltano.py'
[2020-06-17 10:21:58,050|E|MainThread|root] Meltano could not update /Users/douwemaan/Development/meltano-projects/demo-project/transform/profile/profiles.yml: [Errno 2] No such file or directory: '/Users/douwemaan/.pyenv/versions/3.7.6/envs/meltano-demo-project/lib/python3.7/site-packages/meltano/core/bundle/transform/profile/profiles.yml'
Applying migrations to system database...
[2020-06-17 10:21:58,052|I|MainThread|alembic.runtime.migration] Context impl SQLiteImpl.
[2020-06-17 10:21:58,053|I|MainThread|alembic.runtime.migration] Will assume non-transactional DDL.
System database up-to-date.
Recompiling models...
[2020-06-17 10:22:01,325|E|MainThread|root] Meltano could not parse the `discovery.yml` returned by the server.
Meltano and your Meltano project have been upgraded!
```
We could have `meltano upgrade` upgrade the package and then shell out to `meltano upgrade --skip-package`, so we get the new implementation.
issue