I’m experimenting with this now, and liking the following setup:

• mix new project --umbrella
• cd project/apps
• mix new db --sup --module Project.DB
• mix new app --sup --module Project.App or what have you for other otp apps
• mix phoenix.new site --module Project.Site
• Remove postgrex from site deps and applications, leave phoenix_ecto
• Add {:db, in_umbrella: true} to site and other app deps, also add :db to the application :applications config in their mix.exss
• Add ecto and postgrex to db deps and applications
• mv site/lib/site/repo.ex db/lib/db/repo.ex
• Rename all occurrences of Project.Site.Repo to Project.DB.Repo
• mv site/priv/repo db/priv
• mv site/web/models db/lib/db
• Mirror phoenix’s config/<env>.exs files setup in db
• Copy the /priv/static/ and /config/prod.secret.exs rules from site/.gitignore to db/.gitignore
• Move ecto_repos configuration to db/config.exs
• Move the repo adapter config in each site config/<env>.exs file to db
• Make sure the "phoenix" and "phoenix_html" filepaths in your site/package.json’s "dependencies" reference "file:../../deps/<dep>"
• Stop using phoenix model generators, use mix ecto.gen.migration -r Project.DB.Repo from the db app
• Freely access models, queries, etc from your other apps as Project.DB.<Model>

I think that’s about everything necessary that I did.

Further optional conveniences:

• Rename databases from "site_<env>" in these adapter configs to "project_<env>"
• Delete def model... from site/web/web.ex
• Make a db/lib/db/model.ex with a __using__ macro with the quote from your Project.Site.Web.model you just deleted
• Replace all occurrences of use Project.Site.Web, :model to use Project.DB.Model in db/lib/db/models
• Move site/mix.exs’s ecto aliases to db/mix.exs (optionally under a new db namespace instead of ecto)
• Move site/mix.exs’s test alias to the umbrella app’s mix.exs
• I removed all of the references to Project.DB.Repo in site/web/web.ex and other Ecto stuff and instead made it so that you can use Project.DB.<Model> to get aliases for both that model and the repo, then used that instead atop my controllers and channels. Ditto with my Project.DB.<Query>s.
• I changed all my otp app names to be prefaced with “project”, which requires changes in mix.exss, config/ files, db/lib/db/repo.ex, site/lib/site/endpoint.ex, and site/web/gettext.ex. You also have to rename your folders in the apps folder to follow the otp name, prefix and all, to avoid weird umbrella app and phoenix hot code reloading issues.
• I experimented with moving everything from site/web into site/lib/site. You have to remove "web" from the site’s "elixirc_paths" and rename references to the web dir with lib/site in brunch stuff, and change the root of your templates within your site/lib/web.ex directory. However, this destroys hot code reloading so I can’t say I recommend it.

That is my preferred way of structuring apps as well. At least two apps in an umbrella - a domain one and an api one. First handles all the persistence and knows nothing of https, the second one calls plain function from the first one and knows nothing of ecto or any other persistence mechanism.

Update: so yeah we did end up separating Ecto from Phoenix, and it was easy to do and easy to work with. There’s only some mild annoyances when running generators and stuff like that.

Now building my second Elixir project the same way. This time it’s a GraphQL API (using Absinthe) so there’s not even an HTML layer or controllers, making Phoenix a very thin layer for organising plugs and GraphQL schemas in a standard way really.

Here’s my short cheat sheet for starting projects this way: Redirecting...