With --project-dir set, dbt_modules is not honored

[beckjake]

Describe the bug

If you use the --project-dir flag, dbt does not look for dependencies in the correct place. The packages.yml/dbt_project.yml/etc is all loaded correctly, but the search for dependencies doesn't appear to honor the project directory.

I assume it's looking in ./dbt_modules instead of ${project_dir}/dbt_modules, though I haven't looked into it too deeply.

Steps To Reproduce

• Create a dbt project that uses a dependency. dbt_utils is nice.
• Run dbt deps
• Try to dbt compile your project from a different directory, using --project-dir.

Expected behavior

Things should work!

Screenshots and log output

Encountered an error:
Runtime Error
  Compilation Error in model blah (models/blah.sql)
    'dbt_utils' is undefined

System information

Which database are you using dbt with?
Any DB

The output of dbt --version:

0.17.0

The operating system you're using:
Any OS

The output of python --version:
Any Python

Additional context

We have a test for this in the CLI invocation tests, it just doesn't actually use any dependencies so it doesn't hit this error!

[drewbanin]

This appears to be a regression - let's fix this for 0.17.1 (and make sure to add tests)

[beckjake]

Fixed in #2534