Remove duplicate Docker build files in alyx repo (drift risk)

[oliche]

Problem

alyx/deploy/docker/ (in the alyx repo) duplicates iblsre/alyx/containers/docker/ — Dockerfile, Dockerfile_base, apache-conf, and settings files independently maintained in both places, building/pushing the same Docker Hub tags (internationalbrainlab/alyx_apache[_base]:latest).

iblsre is the pipeline actually used in production (confirmed against openalyx's live container). But alyx/docs/03_deployment.md ("Building the docker containers") still documents building from the alyx repo's own copy, to the same tags — a footgun: following that doc silently overwrites the production image with a possibly out-of-sync build. This is how our WSGI daemon config drifted between the two copies (see #151).

One exception: alyx/deploy/docker/settings-deploy.py is genuinely used by .github/workflows/main.yml to run CI under production-like settings, so it must stay.

Proposed fix

• Delete the redundant build machinery from alyx/deploy/docker/: Dockerfile, Dockerfile_base, apache-conf-alyx, 000-default-conf-alyx (keep settings-deploy.py / settings_lab-deploy.py for CI).
• Update docs/03_deployment.md's "Building the docker containers" section to point at iblsre instead of documenting a second build path.

Related: #151

[k1o0]

I agree that we have to remove all these confusing duplicate files. I don't like iblsre because it contains a lot of IBL-specific stuff and separating the settings templates from the main repo makes releasing env changes difficult (if we add a setting we may have to update iblsre, alyx, and the docker containers together, which is annoying).

Personally I see no good reason for keeping any alyx-related stuff in iblsre, except for the Ansible worklfow. I think we should pare down the compose files to a single file for production. This file could still work without issue on a localhost. We keep it in the deploy dir of this repo and update the external install instructions to download the compose file and env template via curl. This will reduce confusion from having a cloned Alyx repo both inside and outside the container.

We can still have documentation for recipes, and can keep the all our various internal docker-compose files in ibldevtools.

Do you see any issues with this?

[oliche]

int-brain-lab/iblsre#32
cortex-lab/alyx#1018

[oliche]

Resolved, in the direction proposed in the comment thread above rather than the original
issue body: cortex-lab/alyx is now the single build/compose source of truth (deploy/app/),
not iblsre — release 3.6.0 made this real via alyx#1018 + iblsre#32/#33/#35, with
CI/CD (build-image.yml) building and pushing on every tagged release. docs/03_deployment.md
documents that flow (and the manual fallback, which also now lives in alyx/deploy/app/docker/).

Just removed the now-fully-redundant duplicate on the iblsre side (iblsre@e21ec3f):
alyx/containers/docker/ (old Dockerfiles, apache conf, build/push scripts, smoke test) and
the old standalone alyx/containers/deploy-web/docker-compose.yaml + template.env (kept
docker-compose.ibl.yaml, still used as the IBL-specific overlay by
ansible_deploy_alyx.yaml). Both alyx-test and openalyx are fully cut over to this flow and
verified. iblsre now holds only deploy orchestration (ansible + per-server compose
overlays) and encrypted env, per the second comment above.

One follow-up not yet done: cazettes hasn't been migrated to this flow yet, and its own
cazettes_setup.yaml/update procedure still pointed at the now-deleted
deploy-web/docker-compose.yaml — that'll need fixing as part of its eventual cutover.