BioF3 Deployment Layout Inventory

Date: 2026-06-13. Updated 2026-06-14 for remote archive actions. Scope: read-only inventory of local, ECS, and Dell deployment paths. Rule: do not delete, rename, or merge directories based on names alone. A cleanup candidate still needs a second check against PM2, Docker binds, nginx, cron, systemd, and current backup references.

Executive Summary

The runtime architecture is now standardized:

/api/platform/* -> ECS biof3-platform
/api/r/*        -> Dell R compute API compatibility
/api/py/*       -> Dell Python compute API compatibility
Database        -> ECS Docker PostgreSQL container biof3-pg
Large artifacts -> Dell local storage + OSS

The directory layout is still historically noisy:

• Local repo root mixes source, docs, deploy scripts, generated site exports, ignored local mirrors, and archives.
• ECS still has old-looking /opt directories. Some are active production mounts, so they must not be removed by name.
• Dell is correctly the compute node. It keeps R/Python compute, workers, large artifacts, cache/tmp, and tutorial/skills deploy support.

This document is the current authority for path ownership. When in doubt, mark the path as pending and verify references before changing it.

Current Production Authority

ECS: control plane, site edge, and PostgreSQL

Path / unit	Status	Evidence	Notes
PM2 biof3-platform	active	pm_cwd=/opt/biof3-platform/platform-server; script /opt/biof3-platform/platform-server/server.js; status online	Owns /api/platform/*.
/opt/biof3-platform	active	size 148M; mtime 2026-06-10; PM2 cwd; PG bind	Platform deploy root. Contains platform-server, r-server, and pgdata.
/opt/biof3-platform/pgdata	active, critical	Docker bind biof3-pg: /opt/biof3-platform/pgdata -> /var/lib/postgresql/data	Current production database volume. Do not delete.
/opt/frp-server	active, critical	systemd frps.service runs /opt/frp-server/frps -c /opt/frp-server/frps.ini; active ports are 7000, 6022, 3001, 3002, 8787	Dell tunnel server. Do not delete. Historical 8090, 5173, 18789, and public frp 5433 were removed 2026-06-13.
Docker biof3-pg	active, critical	bind above	ECS Docker PostgreSQL, not Aliyun managed RDS.
Docker biof3-nginx	active	binds /opt/biof3/app/nginx/biof3.conf, /opt/biof3/app/nginx/certs, /opt/biof3-tutorial/current-site	Public edge.
/opt/biof3-tutorial/current-site	active	nginx static bind; /opt/biof3-tutorial size 3.0G; mtime 2026-06-13	Static Docusaurus site.
/opt/biof3	active support, do not delete	Active binds for nginx config/certs and Waline data; Waline cron calls /opt/biof3/waline-backup.sh	Name looks generic but currently holds live nginx/Waline support files.
Docker biof3-waline	active	bind /opt/biof3/waline-data -> /app/data	Comments service data.
Docker halo / biof3-generator / halo-db	stopped, restart disabled	2026-06-13 set restart=no and stopped; /blog-old/ now returns 410; data archived with /opt/_deprecated-20260613/old_biof3	Do not restart unless explicitly rolling back legacy site data.
Cron /opt/biof3/waline-backup.sh	active	daily 03:30, writes to /opt/biof3-backups/waline; manual run succeeded 2026-06-13	Waline SQLite backup.
Cron /usr/local/bin/biof3-backup-ecs-pg.sh	active	daily 03:10	PG logical backup.
Cron /usr/local/bin/biof3-healthcheck.sh	active	every 2 minutes	ECS health monitoring.

ECS: pending or likely legacy paths

Path	Status	Evidence	Required before cleanup
/opt/biof3-r-server	archived legacy candidate	Moved 2026-06-13 to /opt/_deprecated-20260613/biof3-r-server; no ECS PM2/Docker/cron/systemd owner found before move	Reversible archive only; do not delete until after a normal monitoring cycle.
/opt/biof3-py-server	archived sensitive legacy candidate	Moved 2026-06-14 to /opt/_deprecated-20260613/biof3-py-server; no ECS process/Docker/PM2/cron/systemd owner found; contained .env and old pyserver.db	Reversible archive only; production /api/py still routes through frp to Dell.
/opt/old_biof3	archived sensitive historical bundle	Moved 2026-06-13 to /opt/_deprecated-20260613/old_biof3; size 1.7G; contains old app/db/env markers	Reversible archive only; do not use as compose source of truth and do not delete until after monitoring.
/opt/halo	archived legacy candidate	Moved 2026-06-13 to /opt/_deprecated-20260613/halo after frps was migrated to /opt/frp-server; no process/Docker/cron/systemd owner found before move	Reversible archive only; do not delete until after a normal monitoring cycle.
/opt/proxy	active system tool, not BioF3	mihomo runs from /opt/proxy/mihomo, listening on 9981 and 198.18.0.1:2143; /usr/local/bin/proxy references it	Do not archive as part of BioF3 cleanup unless the system proxy is intentionally retired.
/opt/biof3-oss	archived legacy candidate	Moved 2026-06-13 to /opt/_deprecated-20260613/biof3-oss; no ECS PM2/Docker/cron/systemd owner found before move	Reversible archive only; do not delete until after a normal monitoring cycle.

Dell: compute node and artifact storage

Path / unit	Status	Evidence	Notes
PM2 biof3-r-server	active	pm_cwd=/opt/biof3-r-server; script /opt/biof3-r-server/server.js; status online	R compute API mode.
PM2 biof3-r-worker	active	pm_cwd=/opt/biof3-r-server; script /opt/biof3-r-server/worker.js; status online	R worker claims PG tasks.
PM2 biof3-py-server	active	cwd /root; script /opt/biof3-py-server/start-py-server.sh; status online	Python compute API mode.
PM2 biof3-py-worker	active	pm_cwd=/opt/biof3-py-server; script /opt/biof3-py-server/worker.js; status online	Python worker claims PG tasks.
/opt/biof3-r-server	active	size 80M; mtime 2026-06-13; PM2 cwd/script; cron backup path	Do not stop or remove.
/opt/biof3-py-server	active	size 50M; mtime 2026-06-13; PM2 script/cwd	Do not stop or remove.
/etc/biof3.env	active, sensitive	root-owned 600; used by Dell R server/worker and PG tunnel-aware runtime	Do not print contents.
/opt/biof3-py-server/.env	active, sensitive	root-owned 600; used by Python server/worker	Do not print contents.
/root/.pm2/dump.pm2	active, sensitive	root-owned 600; current PM2 resurrect snapshot with environment keys	Keep for PM2 recovery; do not commit or print.
Docker omichub_react_backend_1	active	binds /mnt/storage_16tb/omichub -> /app/data, R library, app logs	R container/runtime.
Docker biof3_python_1	active	binds /mnt/storage_16tb/omichub/biof3-py-tmp and /mnt/storage_16tb/omichub/biof3-tool-jobs	Python runtime and tool-job artifacts.
/mnt/storage_16tb/omichub	active, critical	Docker data bind	Large result files, tool jobs, cache, tmp.
/opt/biof3-tutorial	active	size 445M; mtime 2026-06-08	Site release/snapshot support.
/opt/biof3-tutorial-src	active	size 495M; mtime 2026-06-08; cron biof3-skills-auto-deploy.sh	Skills auto-deploy source.
systemd biof3-pg-tunnel.service	active	localhost:5433 -> ECS biof3-pg:5432	Dell database access tunnel.
systemd frpc.service	active	frp client to Aliyun; active remote ports 6022, 3001, 3002, 8787	Public compute routing. 5433 is handled by biof3-pg-tunnel.service, not frp.
Cron /opt/biof3-r-server/backup.sh	active	daily 04:00	Legacy SQLite backup remains as compatibility/rollback evidence.
Cron /usr/local/bin/biof3-skills-auto-deploy.sh	active	weekly Monday 03:00	Uses tutorial source/deploy paths.

Dell: pending or likely legacy paths

Path	Status	Evidence	Required before cleanup
/opt/biof3	archived sensitive historical bundle	Moved 2026-06-14 to /opt/_deprecated-20260613/biof3; no Docker mount, PM2 owner, process cwd, cron, or systemd owner found before move; contained old env/db/app markers	Reversible archive only; archive root is 700 and children are root-only. Do not delete until after monitoring.
/opt/biof3-frontend	archived legacy candidate	Moved 2026-06-13 to /opt/_deprecated-20260613/biof3-frontend; no Dell PM2/Docker/cron/systemd owner found before move	Reversible archive only; do not delete until after a normal monitoring cycle.
/opt/clash-for-linux	pending system tool	size 45M; old mtime	Not clearly BioF3. Leave unless system owner confirms.
/opt/htslib	pending dependency/source	size 190M; old mtime	May be bioinformatics dependency. Do not remove without tool checks.
/opt/quarto	pending dependency/source	size 419M; old mtime	May be report-rendering dependency. Do not remove without tool checks.

Local Repository Layout

The local checkout is a monorepo plus generated/runtime artifacts. It is not a 1:1 mirror of either server, and that is expected.

Local path	Status	Role
src/, docs/, blog/, static/	source	Docusaurus site and content.
r-server/	source/runtime package	Shared Node backend code. Used by Dell R compute and by ECS platform through platform-server.
platform-server/	source wrapper	Thin ECS platform entry. Sets BIOF3_RUN_MODE=platform and requires ../r-server/server.js.
py-server/	source/runtime package	Python compute API and worker.
scripts/, deploy/, infra/, deploy.sh	source/ops	Deployment, smoke, backup, nginx, and operational tooling.
test/	source/test	Local tests.
.kiro/	local project memory	Steering docs and progress records.
build/, .docusaurus/	generated, ignored	Docusaurus build output/cache.
exports/, static/exports/	generated, ignored	Export artifacts.
node_modules/, r-server/node_modules/, py-server/node_modules/	dependencies, ignored	Local install artifacts.
..r-server-remote/, .r-server-remote/, ..py-server-remote/	ignored mirrors	Local snapshots from remote servers, not source of truth.
.waline-data/	local runtime, ignored	Local Waline data.
_archive/	ignored archive	Old patches/docs, not active source.
.biof3-secrets, .env*	secrets, ignored	Never commit.

Current large local generated/ignored sizes:

Path	Size
build/	755M
exports/	466M
static/	686M
node_modules/	3.3G in earlier audit

Standard Paths Going Forward

Use these paths for new deploy and operational work:

Purpose	Standard path
ECS platform API	/opt/biof3-platform
ECS platform entry	/opt/biof3-platform/platform-server/server.js
ECS platform shared backend code	/opt/biof3-platform/r-server
ECS PostgreSQL data	/opt/biof3-platform/pgdata
ECS static site	/opt/biof3-tutorial/current-site
ECS nginx/Waline support + stopped Halo data	/opt/biof3
Dell R compute	/opt/biof3-r-server
Dell Python compute	/opt/biof3-py-server
Dell large artifacts	/mnt/storage_16tb/omichub
Dell tutorial/skills source	/opt/biof3-tutorial-src
Dell tutorial deploy support	/opt/biof3-tutorial

Do not introduce new production roots such as /root/biof3, /opt/biof3-app, or another *-server directory unless there is a written migration plan.

Cleanup Safety Gate

Before changing any pending path, run the relevant checks and save the result in the cleanup note:

# Local
git status --short --ignored
rg -n "/opt/path-or-name|service-name" docs .kiro deploy.sh infra scripts

# ECS or Dell
pm2 jlist
docker inspect <container> --format '{{range .HostConfig.Binds}}{{println .}}{{end}}'
crontab -l
systemctl list-units --type=service --all --no-pager | grep -Ei 'biof3|frp|autossh|path-or-name'
find /etc/systemd /usr/local/bin /opt -maxdepth 3 -type f -print0 \
  | xargs -0 grep -Il 'path-or-name' 2>/dev/null

If a path is referenced by any active process, Docker bind, cron, systemd unit, backup job, nginx config, or rollback runbook, it is not safe to remove.

Verification Commands Used

No secret values were read or printed. The audit used only process metadata, Docker binds, cron lines, systemd service names, directory sizes, and mtimes.

git status --short
git status --short --ignored
find docs/ops -maxdepth 2 -type f -print | sort
find . -maxdepth 2 -type d \( -name .git -o -name node_modules \) -prune -o -maxdepth 2 -type d -print | sort
du -sh .kiro docs r-server py-server platform-server scripts infra deploy test src static blog build exports _archive
ssh aliyun 'pm2 jlist; docker inspect ...; crontab -l; systemctl list-units ...; du -sh /opt/...; stat -c "%y %n" /opt/...'
ssh dell 'pm2 jlist; docker inspect ...; crontab -l; systemctl list-units ...; du -sh /opt/...; stat -c "%y %n" /opt/...'