chore: update Docker deployment for standalone backend

[aditya-damerla128]

Summary

• rebuild the reference-server Dockerfile around the standalone backend build order: spec, clients/typescript, then reference-server
• keep SQLite and uploaded file state under configurable persistent storage via DATA_DIR/DB_PATH and /data in Docker
• add Docker build-context hygiene with a root .dockerignore
• document docker run, env-file, and GitHub Actions secret/variable deployment paths
• allow manager admins to be configured by forwarded user id or email on first trusted login

Stack

• Stacked on Add manager auth backend bridge #176 (manager auth backend bridge)
• Closes Update Docker Deployment and Dockerfile per Gap Analysis Discussion #178

Verification

• npm run build (spec)
• npm run build (clients/typescript)
• npm run build (reference-server)
• npm test (reference-server): 42/42 passing
• docker build -f reference-server/Dockerfile -t ozwellai-reference-server:issue-178-auth-admin .
• Docker run with mounted /data, TRUST_FORWARD_AUTH_HEADERS=true, ADMIN_EMAILS=admin@example.test
• verified /health, Docker health, first-login admin assignment, manager agent creation, and chat completion with the created agent key

[Copilot]

Pull request overview

Updates the reference-server’s production Docker deployment and runtime persistence configuration, while extending manager-admin bootstrap logic to support admin assignment by email on first trusted login.

Changes:

• Reworks the reference-server/Dockerfile into a multi-package build (spec → TS client → reference-server) and sets Docker-default runtime env/volume for persistent state.
• Adds DATA_DIR support so uploaded files and default SQLite DB location can live under a configurable persistent directory.
• Extends manager admin bootstrap configuration to allow admin assignment via ADMIN_EMAILS (case-insensitive), with corresponding test coverage and documentation updates.

Reviewed changes

Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
reference-server/Dockerfile	Rebuilds Docker image around standalone backend build order and sets runtime defaults/healthcheck.
.dockerignore	Adds root build-context exclusions to keep local/dev artifacts out of images.
reference-server/src/storage/agents.ts	Adds DATA_DIR-based default DB path and admin-by-email bootstrap support.
reference-server/src/routes/files.ts	Stores uploaded file state under DATA_DIR instead of a fixed ./data path.
reference-server/test/manager-auth.test.js	Tests admin bootstrap via configured emails in addition to external user IDs.
reference-server/README.md	Documents Docker build/run, env-file usage, and storage expectations.
reference-server/.env.example	Adds example config for DATA_DIR/DB_PATH and manager forwarded-header admin options.

[aditya-damerla128]

Startup Steps:
git clone https://github.com/mieweb/ozwellai-api.git
cd ozwellai-api
git switch chore/docker-deployment-issue-178

docker build -f reference-server/Dockerfile -t ozwellai-reference-server:pr-188 .

docker volume create ozwell-reference-data

docker run -d
--name ozwell-reference-server
--restart unless-stopped
-p 3000:3000
--mount type=volume,source=ozwell-reference-data,target=/data
-e TRUST_FORWARD_AUTH_HEADERS=true
-e ADMIN_EMAILS=adamerla128@gmail.com
-e LLM_BASE_URL="https://YOUR_LLM_BASE_URL"
-e LLM_API_KEY="YOUR_LLM_API_KEY"
-e LLM_ALLOWED_MODELS="gpt-4o-mini,gpt-4o"
ozwellai-reference-server:pr-188