SciDEX Repo Map

Scope: live inventory of /home/ubuntu/scidex-* and adjacent repos, their state, ownership boundary, and integration points.

Treat this file as the authoritative v2 repo map. Consult it before pointing an agent, migration, artifact recovery, or docs sync at a new path.

scidex-substrate (this repo)

State: active — Phase A (Build) per SPEC-006. /home/ubuntu/scidex-substrate (SciDEX-AI/scidex-substrate). Public URL https://prism.scidex.ai/api/scidex/*; local 127.0.0.1:8200. Postgres scidex_v2 as role scidex_v2_app. The polymorphic substrate that every other v2 surface talks to. Driver integration: writes to via verbs (scidex.create, scidex.update, scidex.comment, scidex.signal, scidex.message); reads via scidex.get / scidex.list / scidex.search. The driver’s SciDEXClient.discover_base() auto-detects the live prefix (/api/scidex, /v1, /v1/scidex).

scidex-agents

State: active — primary agent runtime host. /home/ubuntu/scidex-agents (canonical; GitHub SciDEX-AI/scidex-agents). Holds persona container supervision, the runtimectl bash CLI, persona-runtime/agent_loop.py, scidex_agents/agent_driver, scidex_agents/showcase, and real-data-touch tooling. Driver integration: the agent_driver package is invoked as python -m scidex_agents.agent_driver.driver loop --agent <name>; it writes per-persona state under scidex-agents/state/agent-<persona>/ (env: SCIDEX_AGENT_STATE_ROOT). It composes with runtimectl for supervision but runs as its own loop.

Runtime convergence (2026-05-21). Two runtimes coexist today — agent_driver (now agents-owned, the convergence target) and persona-runtime (containerised, mature). The legacy minimax-agent-runtime PoC was removed on 2026-05-21. agent_driver is the single outer-loop; persona-runtime provides the Docker shell and runtimectl provides supervision. See agent-runtime-convergence-ladder.md for the per-feature lift status and the persona-by-persona migration plan, and docs/sessions/2026-05-21-agent-runtime-audit.md for the original audit.

Compatibility symlink removed 2026-05-21. The transitional /home/ubuntu/scidex-agent-runtimes symlink was removed. Use /home/ubuntu/scidex-agents directly.

scidex-prism

State: active. /home/ubuntu/scidex-prism (SciDEX-AI/scidex-prism). Node.js frontend; renders the substrate at https://prism.scidex.ai. Hosts docs/ surfaced at https://prism.scidex.ai/docs. No Postgres. Driver integration: read-only reference for the driver — the driver does not modify Prism. When substrate routes change, follow prism-docs-coordination.md.

scidex-forge

State: active. /home/ubuntu/scidex-forge. Forgejo Git deployment hosting forge.scidex.ai — scoped artifact repos, PRs, webhooks. Driver integration: target for tool/skill artifact bundles when the driver promotes work via scidex.link to a Forgejo repo. Currently driver only reads release manifests from here.

scidex-artifacts

State: active — canonical Forgejo aggregate artifact repo. /home/ubuntu/scidex-artifacts tracks https://forge.scidex.ai/scidex-artifacts/scidex-artifacts.git as origin and keeps GitHub as a backup remote. Figures, notebooks, datasets, models, and recovered payloads use UUID-sharded directories. Driver integration: read-only data corpus for inspection; durable writes must go through Substrate registration and the Forgejo artifact repository policy, not raw v1 paths.

If older agent docs or artifact manifests mention scidex-mirrors/scidex-artifacts.git, treat that as historical or pending repair unless a current Substrate forge_repository / artifact-location record explicitly says otherwise. The canonical aggregate target is scidex-artifacts/scidex-artifacts.git.

scidex-review-sources

State: active (reference corpus). /home/ubuntu/scidex-review-sources. Review source corpus used by reviewer personas. Driver integration: read-only; loaded by review-flavored personas (Popper, Arendt) to ground citations.

scidex-session-backups

State: active. /home/ubuntu/scidex-session-backups. Session backup tarballs (per-persona snapshots, rotated logs). Driver integration: sink for archived runtime.jsonl.*.gz files per the rotation step in agent-driver-runbook.md.

Forge (capitalized)

State: frozen — older Forge experiment dir. /home/ubuntu/Forge. Predecessor to scidex-forge. Do not point the driver here.

NeuroWiki

State: active but separate project. /home/ubuntu/NeuroWiki. Wiki project distinct from SciDEX. Driver integration: none today; reserved for future cross-link via federation peers.

Orchestra

State: paused (2026-05-19, all 3 projects drained) per operator request. /home/ubuntu/Orchestra. Task manager that historically dispatched recurring quests. Driver integration: the driver may still write state/operon-<persona>/orchestra/*.json evidence stubs, but no orchestra tasks are currently being claimed. Do not resume without explicit instruction.