fix: make upload timeouts configurable, default to 1 hour (#942)

[alanbchristie]

Summary

Closes #942 (in this repo). Large file uploads (e.g. 6 GiB) were producing 504 Gateway Timeout because every hop in the request path had its own timeout, and the in-container nginx capped at 1000s (~16.7 min).

• nginx.conf / django_nginx.conf are now envsubst templates. All timeout directives derive from STACK_NGINX_TIMEOUT_S (default 3600s) rendered by launch-stack.sh before nginx -tq runs. envsubst is scoped to that single variable so nginx's own $vars (e.g. $http_host, $; regex anchors) pass through untouched.
• Gunicorn worker timeout is now driven by STACK_GUNICORN_TIMEOUT_S (default 3600s), replacing the hard-coded 3000s.
• Dockerfile pulls in gettext-base (provides envsubst) and stages the nginx configs as templates under /etc/nginx/templates/.
• Django DATA_UPLOAD_MAX_MEMORY_SIZE (default 10 GiB) and FILE_UPLOAD_MAX_MEMORY_SIZE (default 2.5 MiB, Django's own default made explicit) are now env-driven Django settings so request-body and in-memory upload thresholds are visible and tunable.

⚠️ Companion change required in fragalysis-stack-kubernetes

The Kubernetes NGINX ingress controller (v1.12.0) is configured in fragalysis-stack-kubernetes, not here. Its defaults (60s) will still produce 504s regardless of this PR. The ingress (or per-route annotations on the upload endpoint) must be raised in lockstep:

nginx.ingress.kubernetes.io/proxy-read-timeout:    "3600"
nginx.ingress.kubernetes.io/proxy-send-timeout:    "3600"
nginx.ingress.kubernetes.io/proxy-connect-timeout: "75"
nginx.ingress.kubernetes.io/proxy-body-size:       "0"

The two new Django env vars (DATA_UPLOAD_MAX_MEMORY_SIZE, FILE_UPLOAD_MAX_MEMORY_SIZE) and the two new stack env vars (STACK_NGINX_TIMEOUT_S, STACK_GUNICORN_TIMEOUT_S) should be surfaced as stack_* Ansible variables in the playbook repo if they need to be tunable per-deployment.

Test plan

• Python syntax check: python -m py_compile fragalysis/settings.py gunicorn.conf.py
• Bash syntax check: bash -n launch-stack.sh
• envsubst rendering simulated locally — both files render correctly, nginx $vars and regex anchors preserved
• pre-commit passes on the changed files
• docker compose up -d --build succeeds and nginx -tq (run inside launch-stack.sh) passes — please verify in a real container build; skipped here as it re-runs the full apt/texlive layer (~10+ min)
• docker compose exec backend cat /etc/nginx/nginx.conf | grep timeout shows 3600s on all seven directives; same for /etc/nginx/sites-available/default.conf
• Override test: set STACK_NGINX_TIMEOUT_S=120 in compose, restart, confirm rendered values change
• docker compose exec backend python manage.py shell -c "from django.conf import settings; print(settings.DATA_UPLOAD_MAX_MEMORY_SIZE, settings.FILE_UPLOAD_MAX_MEMORY_SIZE)" returns the expected ints
• End-to-end upload of a large file (>1 GiB) against a dev cluster with the ingress annotations above applied — confirms no 504

🤖 Generated with Claude Code

[alanbchristie]

NOTE This has been merged to the unification branch there is (probably) no reason to merge this to staging.