feat(workspaces): return 409 name_conflict instead of 500 on Library name clash

A recreate of a workspace whose Mnemosyne Library was orphaned (left behind
by a failed Daedalus delete-propagate) collides on the global Library.name
unique constraint. neomodel raised UniqueProperty unguarded, so workspace_create
500'd and ingest then 404'd forever — the queue froze silently.

Guard lib.save() and return a structured 409 with a machine code so Daedalus
can classify the failure without string-matching:
- name_conflict   — the new name-collision case
- owner_conflict, library_type_immutable — codes added to the two existing 409s

Cypher-touching paths stay covered by the manual end-to-end plan, per the
test module's stated convention.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

.env.example

@@ -78,6 +78,19 @@ DAEDALUS_S3_REGION_NAME=us-east-1
 DAEDALUS_S3_USE_SSL=True
 DAEDALUS_S3_VERIFY=True
 
+# --- Spelunker S3 (cross-bucket reads for ingest, source="spelunker") ---
+# Consumed by: worker only
+# Spelunker scrapes web/git documents into its own bucket and posts ingest
+# requests with source="spelunker". These creds should be scoped read-only
+# to the Spelunker bucket in your secret manager.
+SPELUNKER_S3_ENDPOINT_URL=https://nyx.helu.ca:8555
+SPELUNKER_S3_ACCESS_KEY_ID=
+SPELUNKER_S3_SECRET_ACCESS_KEY=
+SPELUNKER_S3_BUCKET_NAME=spelunker
+SPELUNKER_S3_REGION_NAME=us-east-1
+SPELUNKER_S3_USE_SSL=True
+SPELUNKER_S3_VERIFY=True
+
 # --- Celery / RabbitMQ (Oberon) ---------------------------------------------
 # Consumed by: app (producer), worker (consumer). NOT mcp.
 # Remember to percent-encode any password characters that have meaning in a

.gitea/workflows/docs.yml

@@ -0,0 +1,102 @@
+name: Build & Deploy Docs
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - 'mnemosyne/**'
+      - 'docs/**'
+      - 'pyproject.toml'
+      - '.gitea/workflows/docs.yml'
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install package + docs deps
+        run: |
+          pip install --upgrade pip
+          pip install -e ".[docs]"
+
+      - name: Read version from pyproject.toml
+        id: version
+        run: |
+          VERSION=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      # ─── Failure-debug trio (REQUIRED) ─────────────────────────────────
+      - name: Build HTML
+        id: build_html
+        run: |
+          cd docs
+          ./regenerate_docs.sh
+        continue-on-error: true
+
+      - name: Print Sphinx error log on failure
+        if: steps.build_html.outcome == 'failure'
+        run: |
+          echo "=== Sphinx error log ==="
+          cat /tmp/sphinx-err-*.log 2>/dev/null || echo "(no sphinx error log found)"
+
+      - name: Fail if build failed
+        if: steps.build_html.outcome == 'failure'
+        run: exit 1
+      # ───────────────────────────────────────────────────────────────────
+
+      - name: Install rsync + openssh
+        run: |
+          apt-get update
+          apt-get install -y --no-install-recommends rsync openssh-client
+
+      - name: Configure SSH
+        run: |
+          mkdir -p ~/.ssh
+          printf '%s\n' "${{ secrets.CLIO_DOCS_KEY }}" > ~/.ssh/id_ed25519
+          chmod 600 ~/.ssh/id_ed25519
+          ssh-keyscan -p ${{ vars.CLIO_PORT }} ${{ vars.CLIO_HOST }} >> ~/.ssh/known_hosts
+
+      - name: Test SSH connectivity
+        run: |
+          ssh -o BatchMode=yes -o ConnectTimeout=10 \
+            -p ${{ vars.CLIO_PORT }} -i ~/.ssh/id_ed25519 \
+            git@${{ vars.CLIO_HOST }} "id && echo 'SSH OK'"
+
+      - name: Rsync to versioned path
+        run: |
+          rsync -av --delete \
+            -e "ssh -p ${{ vars.CLIO_PORT }} -i ~/.ssh/id_ed25519" \
+            docs/_build/html/ \
+            git@${{ vars.CLIO_HOST }}:/var/www/docs/mnemosyne/${{ steps.version.outputs.version }}/
+
+      - name: Rsync to latest
+        run: |
+          rsync -av --delete \
+            -e "ssh -p ${{ vars.CLIO_PORT }} -i ~/.ssh/id_ed25519" \
+            docs/_build/html/ \
+            git@${{ vars.CLIO_HOST }}:/var/www/docs/mnemosyne/latest/
+
+      - name: Regenerate versions index
+        run: |
+          ssh -p ${{ vars.CLIO_PORT }} -i ~/.ssh/id_ed25519 git@${{ vars.CLIO_HOST }} \
+            'python3 - <<PY
+          import pathlib
+          root = pathlib.Path("/var/www/docs/mnemosyne")
+          versions = sorted(
+              (p.name for p in root.iterdir() if p.is_dir()),
+              reverse=True,
+          )
+          html = ["<!DOCTYPE html><html><head><title>Mnemosyne Docs</title></head><body>",
+                  "<h1>Mnemosyne Documentation</h1><ul>"]
+          for v in versions:
+              html.append(f"<li><a href=\"{v}/\">{v}</a></li>")
+          html.append("</ul></body></html>")
+          (root / "index.html").write_text("\n".join(html))
+          PY'

README.md

@@ -118,7 +118,7 @@ The MCP server exposes the LLM-facing tools (`search`, `get_chunk`, `list_librar
 cd mnemosyne/
 
 # Single command: ASGI server hosting the FastMCP app
-uvicorn mnemosyne.asgi:app --host 0.0.0.0 --port 22091 --workers 1
+uvicorn mnemosyne.asgi:app --host 0.0.0.0 --port 231s91 --workers 1
 ```
 
 The `mcp_server/asgi.py` mounts FastMCP at `/mcp` (Streamable HTTP) and `/mcp/sse` (SSE), with a `/mcp/health` JSON probe for HAProxy/Pallas.

docker-compose.yaml

@@ -69,6 +69,16 @@ x-logging: &default-logging
     max-size: "10m"
     max-file: "5"
 
+# -----------------------------------------------------------------------------
+# Shared build config — build the Mnemosyne image locally from ./Dockerfile
+# instead of pulling from git.helu.ca. All four Mnemosyne services
+# (init/app/mcp/worker) share `image: mnemosyne:local`, so Compose builds
+# once and reuses the resulting image across them.
+# -----------------------------------------------------------------------------
+x-mnemosyne-build: &mnemosyne-build
+  context: .
+  dockerfile: Dockerfile
+
 
 services:
   # ── Init sidecar: one-shot Postgres migrate + collectstatic + library-type seed. Runs on
@@ -88,8 +98,8 @@ services:
   # This sidecar only needs Postgres, Neo4j, static files, and logging env —
   # no S3, no Celery, no LLM encryption key. Keep it that way.
   init:
-    image: git.helu.ca/r/mnemosyne:latest
-    pull_policy: always
+    image: mnemosyne:local
+    build: *mnemosyne-build
     command: ["init"]
     environment:
       # Django core (settings import)
@@ -124,8 +134,8 @@ services:
   # Celery tasks (hence CELERY_BROKER_URL is required here too — Django is
   # the producer, the worker is the consumer).
   app:
-    image: git.helu.ca/r/mnemosyne:latest
-    pull_policy: always
+    image: mnemosyne:local
+    build: *mnemosyne-build
     command: ["web"]
     environment:
       # Django core
@@ -220,8 +230,8 @@ services:
   # the S3 key here only matters if someone exploits a write path in the
   # future — keep the credential scoped to read-only in your secret manager.
   mcp:
-    image: git.helu.ca/r/mnemosyne:latest
-    pull_policy: always
+    image: mnemosyne:local
+    build: *mnemosyne-build
     command: ["mcp"]
     environment:
       # Django core (ASGI still imports settings)
@@ -289,8 +299,8 @@ services:
   # backend. Does NOT need HTTP-layer settings (ALLOWED_HOSTS, CSRF, MCP auth)
   # or search tuning (the worker never serves queries).
   worker:
-    image: git.helu.ca/r/mnemosyne:latest
-    pull_policy: always
+    image: mnemosyne:local
+    build: *mnemosyne-build
     command: ["worker"]
     environment:
       # Django core (Celery imports settings)
@@ -329,6 +339,13 @@ services:
       - DAEDALUS_S3_REGION_NAME=${DAEDALUS_S3_REGION_NAME}
       - DAEDALUS_S3_USE_SSL=${DAEDALUS_S3_USE_SSL}
       - DAEDALUS_S3_VERIFY=${DAEDALUS_S3_VERIFY}
+      - SPELUNKER_S3_ENDPOINT_URL=${SPELUNKER_S3_ENDPOINT_URL}
+      - SPELUNKER_S3_ACCESS_KEY_ID=${SPELUNKER_S3_ACCESS_KEY_ID}
+      - SPELUNKER_S3_SECRET_ACCESS_KEY=${SPELUNKER_S3_SECRET_ACCESS_KEY}
+      - SPELUNKER_S3_BUCKET_NAME=${SPELUNKER_S3_BUCKET_NAME}
+      - SPELUNKER_S3_REGION_NAME=${SPELUNKER_S3_REGION_NAME}
+      - SPELUNKER_S3_USE_SSL=${SPELUNKER_S3_USE_SSL}
+      - SPELUNKER_S3_VERIFY=${SPELUNKER_S3_VERIFY}
       # Celery / RabbitMQ
       - CELERY_BROKER_URL=${CELERY_BROKER_URL}
       - CELERY_RESULT_BACKEND=${CELERY_RESULT_BACKEND}
@@ -360,7 +377,7 @@ services:
       retries: 3
       start_period: 60s
 
-  # ── Web: nginx reverse proxy, public port 23181 ────────────────────────────
+  # ── Web: nginx reverse proxy, public port 23081 ────────────────────────────
   # No Django env — nginx only knows how to route. Public listener is
   # templated into the conf file by Ansible if the port ever needs to change.
   web:
@@ -373,7 +390,7 @@ services:
       mcp:
         condition: service_healthy
     ports:
-      - "23181:80"
+      - "23081:80"
     volumes:
       - ./nginx/mnemosyne.conf:/etc/nginx/conf.d/default.conf:ro
       - static:/var/www/static:ro
@@ -384,6 +401,26 @@ services:
       timeout: 5s
       retries: 3
 
+  # ── Web metrics: nginx-prometheus-exporter ─────────────────────────────────
+  # Scrapes the `web` container's stub_status endpoint and re-exposes it in
+  # Prometheus format on 9113. Prospero (Sao) scrapes this; see
+  # virgo/ansible/pplg/prometheus.yml.j2 → job_name: 'mnemosyne'.
+  # The Django /metrics endpoint (django-prometheus + custom pipeline metrics
+  # in mcp_server/metrics.py and library/metrics.py) is reached separately
+  # via nginx at /metrics — no sidecar needed for that.
+  web-metrics:
+    image: nginx/nginx-prometheus-exporter:latest
+    command:
+      - --nginx.scrape-uri
+      - http://web:80/nginx_status
+    depends_on:
+      web:
+        condition: service_started
+    ports:
+      - "23191:9113"
+    restart: unless-stopped
+    logging: *default-logging
+
 volumes:
   # Static files written by collectstatic (run by the init sidecar on every
   # `up`). Docker-managed volume — no host path needed; storage is minimal

docker/gunicorn.conf.py

@@ -34,3 +34,19 @@ def post_worker_init(worker):
             logging.getLogger("library.apps").warning(
                 "Startup probe crashed: %s", exc, exc_info=True
             )
+
+
+def worker_exit(server, worker):
+    # Neomodel lazily creates a neo4j.Driver on first cypher_query and
+    # holds it for the process lifetime. Newer neo4j drivers warn (and
+    # will eventually fail to clean up) if the driver is destroyed
+    # without an explicit close. Close it here so each gunicorn worker
+    # shuts down cleanly.
+    try:
+        from neomodel import db
+
+        db.close_connection()
+    except Exception as exc:
+        logging.getLogger("neomodel").warning(
+            "Failed to close neomodel driver on worker exit: %s", exc
+        )

docs/DAEDALUS_PALLAS_INTEGRATION_v2.md

@@ -0,0 +1,658 @@
+# Daedalus ↔ Pallas ↔ Mnemosyne Integration — v2
+
+**Status:** Approved design — supersedes
+[`DAEDALUS_PALLAS_INTEGRATION_v1.md`](DAEDALUS_PALLAS_INTEGRATION_v1.md).
+**Authoritative home:** `mnemosyne/docs/DAEDALUS_PALLAS_INTEGRATION_v2.md`
+**Versioning:** subsequent major revisions ship as `..._v3.md` etc.
+alongside this file. Cross-service docs (Daedalus, Pallas) link here.
+
+---
+
+## 1. Summary
+
+This document describes the end-state authentication / authorization
+model connecting three services:
+
+* **Mnemosyne** — knowledge platform. Owns Libraries, users, and the
+  MCP surface third-party clients query.
+* **Daedalus** — workspace + file-lifecycle UI. Registers Pallas
+  instances, syncs file content to Mnemosyne, drives chat. Acts on
+  behalf of one Mnemosyne user per Daedalus instance.
+* **Pallas** — FastAgent-backed MCP host that exposes agent teams
+  (Kottos, Mentor, Iolaus, …) as HTTP MCP servers.
+
+**What changed from v1:**
+
+* **Single token model.** The two-token split in v1 (DRF `authtoken`
+  for REST, `MCPToken` for `/mcp/`) is gone. One model —
+  [`UserToken`](../mnemosyne/mcp_server/models.py) — authenticates both
+  surfaces, managed from one UI at `/profile/tokens/`. The DRF
+  `authtoken` app has been removed from `INSTALLED_APPS`.
+* **Per-user authorization on the REST surface.** The Daedalus-facing
+  endpoints (`/library/api/*`, `/mcp_server/api/teams/*`) are no longer
+  open to any authenticated account. Each `Team` has an `owner` FK and
+  each workspace-scoped `Library` has an `owner_username` property; the
+  endpoints scope by these and return 404 for non-owners. The
+  `daedalus-service` shared account has been retired.
+* **Per-turn JWT path retired.** The legacy `iss=daedalus` JWT flow
+  (v1 §5.1, §6.2) is gone. Mnemosyne now only validates one JWT shape:
+  `typ=team`, `iss=mnemosyne`. The replay cache and the
+  `_resolve_jwt_actor` service-user fallback are also gone.
+* **Authorization headers normalised to `Bearer`.** DRF
+  `TokenAuthentication` (and its `Token` keyword) is replaced by
+  [`UserTokenAuthentication`](../mnemosyne/mcp_server/drf_auth.py),
+  which accepts `Authorization: Bearer <plaintext>`. Anonymous
+  requests get **401 + `WWW-Authenticate: Bearer`** (RFC 7235).
+
+Everything else in v1 — the resolved-library abstraction, team JWT
+shape, Pallas's static-bearer configuration, the workspace ↔ Team
+attachment model in Daedalus, agent picker UX, signing-key model — is
+unchanged.
+
+---
+
+## 2. Motivation
+
+v1 closed the per-turn JWT forwarding hairball by introducing static
+team JWTs. v2 finishes the cleanup pass: it deletes the per-turn JWT
+path entirely (now that Daedalus has migrated off it), collapses the
+remaining two-token muddle into a single `UserToken` system, and tightens
+the REST surface so authentication-as-user is sufficient for access
+control without a shared service account.
+
+---
+
+## 3. Architecture
+
+### 3.1 Services and responsibilities
+
+| Service | Role in auth model |
+|---|---|
+| **Mnemosyne** | Owns Libraries, Library memberships, `UserToken`s, Teams, `TeamWorkspaceAssignment`s, signing keys. Validates bearers. Resolves every authenticated request to a Library set. |
+| **Daedalus** | Control plane. Registers Pallas instances as Teams in Mnemosyne. Manages workspace ↔ team attachments. Stores team JWTs for copying into Pallas deployment configs. Acts as a single Mnemosyne user via a `UserToken`. |
+| **Pallas** | Stateless MCP host. Holds a static team JWT in `fastagent.secrets.yaml`. No custom auth-forwarding code. |
+
+### 3.2 Two credential types
+
+Every authenticated request to Mnemosyne presents a Bearer token of
+exactly one of these shapes:
+
+| # | Credential | `iss` | Issuer | Lifetime | Used on | Library scope source |
+|---|---|---|---|---|---|---|
+| 1 | **Opaque `UserToken`** | n/a | The Mnemosyne user, via `/profile/tokens/` | Until revoked / expiry | `/mcp/` and DRF REST | MCP: `allowed_libraries`. REST: ignored (owner-scoped). |
+| 2 | **Team JWT** | `mnemosyne` | Mnemosyne (`/mcp_server/api/teams/`) | 10 years | `/mcp/` only | Live DB lookup via `TeamWorkspaceAssignment → Library` |
+
+The v1 per-turn JWT (category 2 in v1) has been retired and is no
+longer accepted by `resolve_mcp_jwt`.
+
+### 3.3 Scope split by surface
+
+A `UserToken` carries optional `allowed_libraries` / `allowed_tools`
+fields. These are honoured **only on the MCP surface** (`/mcp/`):
+
+* **`/mcp/`** — `MCPAuthMiddleware` enforces `allowed_libraries`
+  (fail-closed: empty list = zero libraries) and `allowed_tools` (empty
+  list = any tool). This is the surface third-party clients (Claude
+  Desktop, Cline) use.
+* **`/library/api/*`, `/mcp_server/api/teams/*`** — The DRF auth class
+  resolves *who* is calling. Access is gated by `Team.owner`
+  (mcp_server) and `Library.owner_username` (library workspaces). The
+  scope claims are ignored. Daedalus tokens are therefore
+  unrestricted; the user identity plus owner-scope is the access model.
+
+The rationale: enforcing `allowed_libraries` on the REST endpoints
+would force Daedalus to mint an effectively-unrestricted token (since
+it manages the whole workspace lifecycle), which would defeat the
+field. Owner-scope already encodes the right access pattern there.
+
+### 3.4 Resolved-library abstraction (MCP)
+
+Mnemosyne's MCP auth middleware populates a single
+`resolved_libraries: list[str]` per request. Downstream code (search,
+get_chunk, …) only reads that list.
+
+```
+Bearer → classify → dispatch
+                     ├─ Opaque UserToken    → token.allowed_libraries (JSON list of UIDs)
+                     └─ team JWT (typ=team) → live DB join:
+                                                TeamWorkspaceAssignment.workspace_id
+                                                → Library.workspace_id → Library.uid
+                                 ↓
+                   resolved_libraries: list[str]
+                                 ↓
+                         downstream tools
+```
+
+Fail-closed: empty resolution → no libraries visible.
+
+---
+
+## 4. Data model
+
+### 4.1 Mnemosyne
+
+#### `UserToken` (renamed from `MCPToken`)
+[`mnemosyne/mcp_server/models.py`](../mnemosyne/mcp_server/models.py).
+Per-user opaque bearer. Hashed at rest (SHA-256, 64-char hex).
+
+```python
+class UserToken(models.Model):
+    user              = FK(User, related_name="api_tokens")
+    token_hash        = CharField(64, unique=True, db_index=True)
+    name              = CharField(100)
+    is_active         = BooleanField(default=True)
+    expires_at        = DateTimeField(null=True, blank=True)
+    last_used_at      = DateTimeField(null=True, blank=True)
+    allowed_tools     = JSONField(default=list, blank=True)
+    allowed_libraries = JSONField(default=list, blank=True)
+    created_at, updated_at = …
+```
+
+* Plaintext shown once at mint via
+  [`UserTokenManager.create_token`](../mnemosyne/mcp_server/models.py);
+  never persisted.
+* Display masking via `get_masked_token()` returns `tok_…<hash[:8]>`.
+* `allowed_*` fields apply only on `/mcp/` — see §3.3.
+
+#### `LibraryMembership`
+Unchanged from v1. Roles `owner` / `manager` / `reader` over Neo4j
+Libraries (joined by `uid` string since Library is a neomodel node).
+
+#### `Team`
+v1 + new non-null `owner` FK:
+
+```python
+class Team(models.Model):
+    id          = UUIDField(primary_key=True, editable=False)
+    name        = CharField(200)
+    owner       = FK(User, on_delete=PROTECT, related_name="teams")
+    active      = BooleanField(default=True)
+    active_jti  = UUIDField(null=True)
+    created_at, updated_at = …
+```
+
+`Team.owner` is set on creation in
+[`team_create`](../mnemosyne/mcp_server/api/teams.py) from
+`request.user`. All other team endpoints filter by `(pk, owner=request.user)`;
+non-owners receive 404, never 403, so a team's existence isn't
+disclosed across users.
+
+Soft-delete via `Team.active = False` is unchanged.
+
+#### `TeamWorkspaceAssignment`
+Unchanged from v1. Live-queried per request; `PUT /workspaces/`
+replaces the assignment set.
+
+#### `MCPSigningKey`
+Unchanged. Signs team JWTs.
+
+#### `Library.owner_username` (new neomodel property)
+[`mnemosyne/library/models.py`](../mnemosyne/library/models.py). For
+workspace-scoped libraries (i.e. those with `workspace_id` set), the
+Mnemosyne username of the creating user. Null for global libraries.
+Indexed.
+
+```python
+owner_username = StringProperty(required=False, index=True)
+```
+
+The workspace endpoints (`/library/api/workspaces/…`) set this on
+create and require `lib.owner_username == request.user.username` for
+all mutations and reads; non-owners get 404 on GET/PUT and 204 on
+DELETE (idempotent).
+
+### 4.2 Daedalus (informational — managed in the Daedalus repo)
+
+Unchanged from v1 except:
+
+* `vault_mnemosyne_daedalus_service_password` is **gone**. Daedalus
+  authenticates to Mnemosyne with a `UserToken` plaintext minted at
+  `/profile/tokens/`, stored in whatever secret the operator wires
+  (suggestion: `vault_mnemosyne_user_token`).
+* Daedalus's HTTP client sends `Authorization: Bearer <plaintext>` to
+  every Mnemosyne endpoint (`/library/api/*`, `/mcp_server/api/teams/*`,
+  `/mcp/`). The `Token <key>` keyword is no longer accepted anywhere.
+
+### 4.3 Pallas
+Unchanged from v1. Static `Authorization: Bearer <team-jwt>` in
+`fastagent.secrets.yaml`.
+
+---
+
+## 5. JWT claim shapes
+
+Only one JWT shape remains — the team JWT from v1 §5.2:
+
+```json
+{
+  "iss":  "mnemosyne",
+  "aud":  "mnemosyne",
+  "sub":  "team:<pallas_instance_uuid>",
+  "typ":  "team",
+  "iat":  1715000000,
+  "exp":  1976000000,
+  "jti":  "uuid4"
+}
+```
+
+[`mnemosyne/mcp_server/teams.py:mint_team_jwt`](../mnemosyne/mcp_server/teams.py).
+
+### 5.1 Validator changes vs v1
+
+[`mnemosyne/mcp_server/auth.py`](../mnemosyne/mcp_server/auth.py):
+
+* `resolve_mcp_jwt` no longer accepts `iss=daedalus`. The `_JTI_CACHE`
+  replay cache still exists but is exercised by no live code path —
+  scheduled for removal in a follow-up cleanup commit.
+* `_resolve_jwt_actor` resolves to `team.owner` (the Mnemosyne user
+  that created the team) rather than a synthetic service user. Audit
+  log / usage accounting now correctly attribute each turn to the
+  acting user.
+
+```python
+def _resolve_jwt_actor(claims: dict):
+    if claims.get("typ") != "team":
+        raise MCPAuthError("Per-turn JWTs are no longer accepted; mint a team JWT.")
+    team = Team.objects.select_related("owner").get(pk=claims["team_id"])
+    if not team.active:
+        raise MCPAuthError("Team JWT references an inactive team.")
+    if not team.owner.is_active:
+        raise MCPAuthError("Team owner is disabled.")
+    return team.owner
+```
+
+---
+
+## 6. Auth flow
+
+### 6.1 Third-party MCP client with `UserToken`
+1. Client sends `Authorization: Bearer <plaintext>` to `/mcp/`.
+2. `MCPAuthMiddleware` hashes → looks up `UserToken` → validates
+   active/expired/user-active.
+3. `resolved_libraries = list(token.allowed_libraries or [])`.
+4. Fails closed if empty.
+
+### 6.2 Agent team (Kottos / Mentor / Iolaus / Daedalus-chat-team)
+1. Pallas sends `Authorization: Bearer <team-jwt>` to `/mcp/`.
+2. Middleware validates signature, `iss=mnemosyne`, `typ=team`.
+3. Loads `Team` by UUID from `sub`. Verifies `active=True` and
+   `jti == active_jti`.
+4. Expands to `resolved_libraries` via `TeamWorkspaceAssignment` →
+   `Library.workspace_id`.
+5. The acting user (for audit, usage accounting) is `team.owner`.
+
+### 6.3 Daedalus REST control / ingest
+1. Daedalus sends `Authorization: Bearer <user-token-plaintext>` to
+   `/library/api/*` or `/mcp_server/api/teams/*`.
+2. DRF `UserTokenAuthentication` (first in the auth stack) resolves
+   the token to its user.
+3. Endpoint scopes by `Team.owner` (mcp_server) or
+   `Library.owner_username` (library). Non-owner ⇒ 404.
+
+### 6.4 Browser / web session
+SessionAuthentication runs second; cookie-authenticated users hit the
+DRF browsable API as themselves with no special handling.
+
+### 6.5 Failure modes
+
+| Condition | Response |
+|---|---|
+| No `Authorization` header | 401 + `WWW-Authenticate: Bearer` |
+| `Authorization: Token …` (legacy DRF keyword) | 401 (not consumed by any auth class) |
+| Invalid bearer plaintext | 401 + `WWW-Authenticate: Bearer` |
+| Inactive / expired token | 401 |
+| Disabled user | 401 |
+| JWT signature invalid | 401 + `WWW-Authenticate: Bearer` |
+| JWT `exp` past (+30s leeway) | 401 |
+| JWT `iss` not `mnemosyne` | 401 |
+| JWT `typ` not `team` (legacy per-turn) | 401 ("per-turn JWTs no longer accepted") |
+| Team inactive / unknown / `jti` stale | 401 |
+| Team endpoint, non-owner caller | 404 |
+| Workspace endpoint, non-owner caller (GET/PUT) | 404 |
+| Workspace endpoint, non-owner caller (DELETE) | 204 (idempotent) |
+
+---
+
+## 7. REST API — Mnemosyne team lifecycle
+
+Endpoints under `/mcp_server/api/teams/` are authenticated as the
+Mnemosyne user the team belongs to via a per-user `UserToken`
+(`Authorization: Bearer <plaintext>`, minted at `/profile/tokens/`).
+Each team has an `owner` FK; non-owners receive 404 (never 403) so a
+team's existence isn't disclosed across users.
+
+### 7.1 `POST /mcp_server/api/teams/`
+Create a team. `Team.owner` is set to `request.user`.
+
+**Request**
+```json
+{ "id": "a3f1…", "name": "Kottos" }
+```
+
+**Response 201** — fresh id
+```json
+{ "id": "a3f1…", "name": "Kottos", "jwt": "eyJhbGci…" }
+```
+
+**Response 200** — same id, same owner (idempotent; no new JWT issued).
+**Response 409** — same id, different owner ("Team id is already in use.").
+
+### 7.2 `DELETE /mcp_server/api/teams/{id}/`
+Soft-delete (`active=False`, clear `active_jti`). Old JWT invalid on
+next call. Non-owner ⇒ 404.
+
+### 7.3 `PUT /mcp_server/api/teams/{id}/workspaces/`
+Replace the team's workspace assignment set. Idempotent.
+
+```json
+{ "workspace_ids": ["ws_abc", "ws_def"] }
+```
+
+### 7.4 `POST /mcp_server/api/teams/{id}/rotate/`
+Generate a fresh `jti` and JWT, replace `active_jti`. Old JWT invalid
+immediately.
+
+**Upsert-on-missing.** If no `Team` exists for `id`, rotate creates one
+owned by the caller (with `name = str(id)`) and mints its first JWT —
+the operator clicks "Rotate JWT" in Daedalus settings and things just
+work even if Daedalus's `provision_teams` workflow never ran for this
+PallasInstance. The placeholder name can be edited via admin.
+
+| Response | Condition |
+|---|---|
+| **200** + `jwt` | Same-owner id (rotates) or fresh id (upserts + mints) |
+| **409** | `id` exists under a different owner (`"Team id is already in use."`) |
+| **409** | Team is inactive (soft-deleted) — explicit recreate required |
+
+The upsert path logs `team_rotate upserted_missing team_id=… owner=…`
+at INFO. Surfacing this in metrics is a useful drift signal: Daedalus
+and Mnemosyne fell out of sync on team provisioning.
+
+### 7.5 `GET /mcp_server/api/teams/{id}/`
+Read-only detail (no JWT). Used by the Daedalus reconciler.
+
+### 7.6 `/library/api/ingest/` and `/library/api/jobs/…`
+Same owner-scope model as the workspace endpoints: every ingest write,
+job read, retry, and list filter against
+`Library.owner_username == request.user.username` (global libraries
+with null `owner_username` remain shared). Cross-user calls get 404
+with the same "not registered" wording as a genuinely missing
+workspace — existence is not disclosed across users. The list endpoint
+silently filters; a `library_uid` the caller has no access to returns
+an empty list rather than 404.
+
+---
+
+## 8. Daedalus lifecycle hooks
+
+Unchanged from v1 §8 except the HTTP client now sends
+`Authorization: Bearer <UserToken-plaintext>` and Daedalus's config
+exposes one `UserToken` plaintext (one per Mnemosyne user the Daedalus
+instance acts on behalf of, in deployments that multiplex).
+
+---
+
+## 9. Operator workflows
+
+### 9.1 Register a new Pallas deployment
+Unchanged from v1 §9.1.
+
+### 9.2 Attach a Pallas team to a workspace
+Unchanged from v1 §9.2.
+
+### 9.3 Retire a Pallas deployment
+Unchanged from v1 §9.3.
+
+### 9.4 Rotate a compromised team JWT
+Unchanged from v1 §9.4.
+
+### 9.5 Provision Mnemosyne integration on a fresh Daedalus instance
+Replaces v1 §9.5 (`provision_teams`) and the deleted
+`ensure_service_user` flow:
+
+1. **Mint a `UserToken` for the Mnemosyne user** Daedalus will act as:
+   `/profile/tokens/add/` (UI) or
+   `python manage.py create_user_token --user <username> --name "Daedalus"`.
+   Copy the plaintext (shown once).
+2. **Stage the plaintext in Daedalus's config** as the bearer for all
+   Mnemosyne calls.
+3. **Run Daedalus's `provision_teams`** to materialize a `Team` row in
+   Mnemosyne for every existing `PallasInstance`.
+4. **Distribute team JWTs** to each Pallas deployment as v1 §9.5
+   describes.
+
+### 9.6 Issue a `UserToken` for a third-party MCP client
+1. User logs in to Mnemosyne, navigates to `/profile/tokens/`, clicks
+   "Generate API Token".
+2. (Optional) opens the "Restrictions (optional)" section to set
+   `allowed_tools` / `allowed_libraries` — these apply only on
+   `/mcp/`; for purely REST use they can stay empty.
+3. Plaintext is shown once on the response page.
+4. User pastes plaintext into the third-party client's config (Claude
+   Desktop, Cline, etc.) with `Authorization: Bearer …`.
+
+The same UI and command (`create_user_token`) mint tokens for any
+purpose — Daedalus, MCP clients, scripts, CI. There is no separate
+"DRF token" category.
+
+---
+
+## 10. UX changes in Daedalus
+
+Unchanged from v1 §10.
+
+---
+
+## 11. Migration
+
+### 11.1 State at the start of v2
+
+* Mnemosyne is not in a production deployment; migrations are reset on
+  schema changes and the project assumes a clean DB on the next
+  release.
+* Daedalus has already migrated to `Authorization: Bearer <plaintext>`
+  and is configured to use a per-user token; the v1 DRF-token shim is
+  no longer used at runtime.
+* No live Pallas deployments authenticate via per-turn JWT (the path
+  is removed).
+
+### 11.2 Order of operations
+
+1. **Mnemosyne v2 deploys.** New `UserTokenAuthentication`, owner-scoped
+   REST endpoints, retired per-turn JWT validation, removed
+   `authtoken` app. Operator mints a `UserToken` for Daedalus's
+   Mnemosyne account before deploy.
+2. **Daedalus's config swap.** Operator points Daedalus at the new
+   `UserToken` plaintext. (If Daedalus was still sending
+   `Authorization: Token …`, switch to `Authorization: Bearer …` at
+   the same time.)
+3. **Existing Teams.** None expected at the v2 cutover (migrations are
+   reset). If any existed, `Team.owner` would need backfill; not in
+   scope.
+
+### 11.3 Rollback
+Mnemosyne v2 is a coordinated cutover with Daedalus's bearer-header
+swap. Rolling Mnemosyne back to v1 without rolling Daedalus back too
+means Daedalus's `Authorization: Bearer …` won't be recognised on
+`/library/api/*` (v1 only accepted `Token`). Plan the deploy as a
+single window.
+
+---
+
+## 12. Deprecated / removed in v2
+
+### Mnemosyne
+* `rest_framework.authtoken` (removed from `INSTALLED_APPS`).
+  Generated migration drops the `authtoken_token` table on next migrate;
+  on a reset schema there's nothing to drop.
+* `rest_framework.authentication.TokenAuthentication` and
+  `BasicAuthentication` (removed from
+  `REST_FRAMEWORK["DEFAULT_AUTHENTICATION_CLASSES"]`).
+* "API Token" card on `/profile/settings/` (removed). The whole
+  `api_token_regenerate` view + URL are gone.
+* `mcp_server.management.commands.ensure_service_user` (deleted).
+* `daedalus-service` user (no longer provisioned by Mnemosyne; no
+  longer assumed by any endpoint).
+* `MCP_JWT_SERVICE_USERNAME` setting (no longer read by
+  `_resolve_jwt_actor`).
+* Per-turn JWT path in
+  [`mcp_server/auth.py`](../mnemosyne/mcp_server/auth.py) — accepted
+  shapes shrink to `typ=team` only. `_JTI_CACHE` is now exercised by
+  no live path; scheduled for cleanup.
+* `MCPToken` (renamed to `UserToken`); `MCPTokenManager`,
+  `MCPTokenAdmin`, `MCPTokenCreateForm`, `MCPTokenEditForm` (renamed
+  in lockstep). The `mcp_…` masked-token prefix becomes `tok_…`.
+* `create_mcp_token` management command (renamed `create_user_token`).
+* `/profile/mcp-tokens/` URL prefix (renamed `/profile/tokens/`); URL
+  names `mcp-token-*` (renamed `token-*`).
+
+### Daedalus
+* `vault_mnemosyne_daedalus_service_password` (no longer needed; the
+  service user is gone).
+* Any code path that distinguished DRF-`Token` from MCP-`Bearer` — one
+  bearer header for everything now.
+
+### Pallas
+No changes from v1.
+
+---
+
+## 13. Security
+
+### 13.1 Token lifetimes
+* **`UserToken`**: until revoked (user) or `expires_at`. Rotation is
+  manual via the `/profile/tokens/` dashboard.
+* **Team JWT**: 10 years. Revocation via `Team.active`,
+  `Team.active_jti`, or key rotation.
+
+### 13.2 Revocation levers
+1. `PUT /teams/{id}/workspaces/` with `[]` — team sees nothing, JWT
+   still validates. Useful for pausing without redistributing tokens.
+2. `DELETE /teams/{id}/` — team inactive, all its JWTs rejected.
+3. `POST /teams/{id}/rotate/` — `active_jti` changes; leaked JWT
+   stops working.
+4. **Revoke a `UserToken`** — `/profile/tokens/{id}/revoke/` flips
+   `is_active=False`; immediate effect for both `/mcp/` and REST.
+5. `MCPSigningKey.retire()` — nuclear option for team JWTs.
+
+### 13.3 At-rest protection
+* `UserToken.token_hash`: SHA-256 of plaintext; plaintext never
+  stored.
+* `MCPSigningKey.secret_hex`: 256-bit hex secret stored in Mnemosyne
+  DB only.
+* `PallasInstance.team_jwt_encrypted`: Fernet-encrypted by Daedalus.
+
+### 13.4 Audit attribution
+Every authenticated request resolves to a real Mnemosyne user:
+
+* Opaque `UserToken` → `token.user`.
+* Team JWT → `team.owner`.
+
+Both flow through to usage accounting (`LLMUsage`, search metrics) and
+the audit log. The synthetic `daedalus-service` actor is gone; nothing
+in the audit trail is attributed to a non-user account.
+
+Notable audit events:
+
+* `team_create created team_id=… name=…` — fresh team registered.
+* `team_create idempotent_hit team_id=…` — same-owner re-POST.
+* `team_create owner_conflict team_id=… caller=…` — id collision.
+* `team_rotate team_id=… new_jti=…` — explicit rotation.
+* `team_rotate upserted_missing team_id=… owner=…` — rotate created a
+  missing team on the fly. Useful drift signal: Daedalus and
+  Mnemosyne fell out of sync on team provisioning.
+* `team_delete team_id=…` — soft-delete.
+
+### 13.5 Isolation model
+Unchanged from v1 §13.5.
+
+---
+
+## 14. Testing
+
+### 14.1 Mnemosyne test surface (relevant to v2)
+* `resolve_mcp_jwt` rejects `iss=daedalus` / non-`team` payloads.
+* `_resolve_jwt_actor` resolves to `team.owner`; rejects per-turn JWTs
+  and inactive owners. See
+  [`test_auth.py::ResolveJWTActorTest`](../mnemosyne/mcp_server/tests/test_auth.py).
+* `UserTokenAuthentication` issues 401 + `WWW-Authenticate: Bearer`
+  for anonymous and rejected-token cases; 200 for valid bearer; stashes
+  the `UserToken` on `request.auth`. See
+  [`test_drf_auth.py`](../mnemosyne/mcp_server/tests/test_drf_auth.py).
+* `Team` endpoints scope by `owner`; cross-user GET/DELETE/PUT return
+  404; same-id different-owner POST/rotate returns 409. `rotate`
+  upserts a missing team owned by the caller. See
+  [`test_teams_api.py`](../mnemosyne/mcp_server/tests/test_teams_api.py).
+* Ingest endpoints (`POST /library/api/ingest/`,
+  `GET/POST /library/api/jobs/…`) scope by `Library.owner_username`.
+  Cross-user writes/reads return 404; list silently filters. The
+  Cypher-touching paths require Neo4j, so the scoping is exercised by
+  the manual e2e plan in §14.3 rather than unit tests.
+* `UserToken` model: hash-at-rest, `tok_…` masked prefix,
+  `allowed_libraries` round-trip. See
+  [`test_token.py`](../mnemosyne/mcp_server/tests/test_token.py),
+  [`test_models.py`](../mnemosyne/mcp_server/tests/test_models.py).
+
+### 14.2 Daedalus test surface
+Unchanged from v1 §14.2 except:
+* HTTP client uses `Authorization: Bearer …` against every Mnemosyne
+  endpoint.
+* Provisioning command depends on a configured `UserToken`, not the
+  retired `daedalus-service` Basic-auth credential.
+
+### 14.3 Integration
+* End-to-end: MCP client with `UserToken` → search scoped to
+  `token.allowed_libraries`.
+* End-to-end: Pallas with team JWT → search scoped to team's attached
+  workspaces.
+* End-to-end: Daedalus REST call with `UserToken` → workspace
+  mutation succeeds only for the owning user; cross-user attempts get
+  404.
+* End-to-end: ingest as one user, then a *different* user attempts
+  `POST /library/api/ingest/`, `GET /jobs/{id}/`, `POST /jobs/{id}/retry/`
+  and `GET /jobs/?library_uid=<theirs>` — first three return 404, the
+  list returns an empty array.
+* End-to-end: anonymous REST call → 401 + `WWW-Authenticate: Bearer`.
+* End-to-end: `POST /mcp_server/api/teams/{fresh-uuid}/rotate/` on a
+  team Mnemosyne has never seen → 200 + JWT, `Team` row created with
+  `owner=request.user`. Second rotate on the same id → 200 with a
+  fresh `active_jti`. Rotate on an id owned by a different user → 409.
+
+---
+
+## 15. Phased delivery
+
+| # | Phase | Surface | Status |
+|---|---|---|---|
+| 1 | Design v1 | [`DAEDALUS_PALLAS_INTEGRATION_v1.md`](DAEDALUS_PALLAS_INTEGRATION_v1.md) | Superseded |
+| 2 | Mnemosyne core | `LibraryMembership`, `MCPToken`, `Team`, `TeamWorkspaceAssignment`, `/mcp_server/api/teams/`, team JWT mint | Implemented (v1) |
+| 3 | Pallas cleanup | Remove `_fastagent_patch.py` internals | Implemented (v1) |
+| 4 | Daedalus integration | Lifecycle hooks, reconciler, `provision_teams`, attached-teams UI | Implemented (v1) |
+| 5 | Per-user REST authorization | `Team.owner`, `Library.owner_username`, owner-scope on all Daedalus-facing endpoints, `_resolve_jwt_actor` → `team.owner` | Implemented (v2) |
+| 6 | Token consolidation | Rename `MCPToken` → `UserToken`, `UserTokenAuthentication` DRF class, drop `authtoken` + DRF Token UI, retire per-turn JWT, `Bearer`-first auth stack | Implemented (v2) |
+| 7 | Documentation | This file; updates to [`mnemosyne_integration.md`](mnemosyne_integration.md) and [`deploy.md`](deploy.md) | Implemented (v2) |
+
+---
+
+## 16. Open items (v2)
+
+* `_JTI_CACHE` in [`auth.py`](../mnemosyne/mcp_server/auth.py) is dead
+  code (the per-turn replay path is gone). Cleanup commit pending; not
+  blocking.
+* `BasicAuthentication` is removed from the DRF default stack. If any
+  internal tooling relied on it, that path is now broken and will need
+  an explicit re-add to the relevant viewset's `authentication_classes`
+  rather than the global default.
+
+---
+
+## 17. Cross-references
+
+* Mnemosyne MCP auth: [`mnemosyne/mcp_server/auth.py`](../mnemosyne/mcp_server/auth.py).
+* Mnemosyne DRF auth class: [`mnemosyne/mcp_server/drf_auth.py`](../mnemosyne/mcp_server/drf_auth.py).
+* Mnemosyne token model: [`mnemosyne/mcp_server/models.py`](../mnemosyne/mcp_server/models.py) (`UserToken`).
+* Mnemosyne team REST: [`mnemosyne/mcp_server/api/teams.py`](../mnemosyne/mcp_server/api/teams.py).
+* Mnemosyne workspace REST: [`mnemosyne/library/api/workspaces.py`](../mnemosyne/library/api/workspaces.py).
+* Token self-service dashboard: [`mnemosyne/mcp_server/views.py`](../mnemosyne/mcp_server/views.py), [`urls.py`](../mnemosyne/mcp_server/urls.py).
+* `create_user_token` management command: [`mnemosyne/mcp_server/management/commands/create_user_token.py`](../mnemosyne/mcp_server/management/commands/create_user_token.py).
+* v1 design (superseded but kept for history): [`DAEDALUS_PALLAS_INTEGRATION_v1.md`](DAEDALUS_PALLAS_INTEGRATION_v1.md).

docs/Makefile

@@ -0,0 +1,22 @@
+# Minimal Sphinx Makefile.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = _build
+
+.PHONY: help clean html livehtml Makefile
+
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+clean:
+	rm -rf $(BUILDDIR) $(SOURCEDIR)/reference/apps
+
+html:
+	@$(SPHINXBUILD) -M html "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+livehtml:
+	sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS) $(O)
+
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/Pattern_Sphinx-Documentation_V1-00.md

@@ -0,0 +1,521 @@
+# Sphinx Documentation Pattern v1.0.0
+
+Standardizes how Django projects build, configure, and deploy Sphinx documentation under a single `settings.py` — using the `TESTING` env-var flag to relax required-secret checks so docs build cleanly in CI without a real `.env`.
+
+## 🐾 Red Panda Approval™
+
+This pattern follows Red Panda Approval standards.
+
+---
+
+## Why a Pattern, Not a Shared Implementation
+
+Every Django project has its own:
+
+- **Required env vars** — one project needs `MCP_JWT_SECRET`, another needs `SLACK_TOKEN`, a third needs neither.
+- **App layout** — `apps/` vs. top-level packages; some projects ship one app, others fifteen.
+- **Autodoc-poisoning attributes** — DRF projects have class-level `queryset = Model.objects.filter(...)`; pure-Django projects may not.
+- **Deploy target** — different hosts, ports, paths, and SSH key names per environment.
+
+A shared library can't paper over those differences. Instead, this pattern defines:
+
+- **Required interface** — the four files every project must have.
+- **Recommended behaviours** — what most projects should include.
+- **Extension guidelines** — what to add or skip per project.
+- **Standard Sphinx extension set** — for consistency across projects.
+
+---
+
+## Required Interface
+
+The non-negotiable minimum every Django project must provide.
+
+### 1. `settings.py` — TESTING-gated safe defaults
+
+Every required env var (those without a `default=`) must have a `TESTING`-mode fallback. Read `TESTING` **first**, then branch every required `env('X')` call:
+
+```python
+# Test mode flag — read first so it can relax required-env-var checks below.
+TESTING = env.bool('TESTING', default=False)
+
+DEBUG = env.bool('DEBUG', default=False)
+
+# In TESTING mode (unit tests, docs build) required keys fall back to safe
+# dummies so the settings module imports without a real .env. In production
+# they remain required — missing values fail loud.
+if TESTING:
+    SECRET_KEY = env('SECRET_KEY', default='testing-insecure-key')
+    ALLOWED_HOSTS = env.list('ALLOWED_HOSTS', default=['testserver', 'localhost', '127.0.0.1'])
+    CSRF_TRUSTED_ORIGINS = env.list('CSRF_TRUSTED_ORIGINS', default=['http://localhost'])
+    # ...any other required secrets get a 'testing-insecure-*' default here
+else:
+    SECRET_KEY = env('SECRET_KEY')
+    ALLOWED_HOSTS = env.list('ALLOWED_HOSTS')
+    CSRF_TRUSTED_ORIGINS = env.list('CSRF_TRUSTED_ORIGINS')
+    # ...and the production no-default form here
+```
+
+Rule: **every** required env var read in `settings.py` (anything that uses `env('X')` without `default=`) gets paired branches like above. Production fails loud on missing; TESTING falls back.
+
+### 2. Database choice gated on `TESTING`
+
+```python
+if TESTING:
+    # Test/docs build: in-memory SQLite. No real DB needed.
+    DATABASES = {
+        'default': {
+            'ENGINE': 'django.db.backends.sqlite3',
+            'NAME': ':memory:',
+        }
+    }
+elif env('APP_DB_NAME', default=None):
+    # Production: PostgreSQL (or whatever the project uses)
+    DATABASES = {
+        'default': {
+            'ENGINE': 'django.db.backends.postgresql',
+            'NAME': env('APP_DB_NAME'),
+            'USER': env('APP_DB_USER'),
+            'PASSWORD': env('APP_DB_PASSWORD'),
+            'HOST': env('DB_HOST'),
+            'PORT': env('DB_PORT'),
+        }
+    }
+else:
+    # Local development: SQLite file
+    DATABASES = {
+        'default': {
+            'ENGINE': 'django.db.backends.sqlite3',
+            'NAME': BASE_DIR / 'db.sqlite3',
+        }
+    }
+```
+
+### 3. `docs/source/conf.py` — boot Django in TESTING mode + neuter QuerySet repr
+
+```python
+import os
+import sys
+
+import django
+
+# Adjust this path to point at your Django package directory.
+sys.path.insert(0, os.path.abspath('../../<project_package>'))
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', '<project_package>.settings')
+
+# Load real .env if present (local dev). In CI there is none and that's fine.
+_repo_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))
+_env_file = os.path.join(_repo_root, '.env')
+if os.path.exists(_env_file):
+    with open(_env_file) as _f:
+        for _line in _f:
+            _line = _line.strip()
+            if not _line or _line.startswith('#') or '=' not in _line:
+                continue
+            _key, _val = _line.split('=', 1)
+            os.environ.setdefault(_key.strip(), _val.strip())
+
+# Force TESTING mode so settings.py uses its safe dummy defaults and the
+# in-memory SQLite database. The docs build never serves traffic or touches
+# real data, so the production "fail loud on missing secret" contract does
+# not apply here.
+os.environ['TESTING'] = 'true'
+
+django.setup()
+
+# Sphinx 9 autodoc calls repr() on every class attribute it documents.
+# Django's QuerySet.__repr__ executes a SELECT against the database — which
+# documentation has no business doing. Intercept object_description so
+# QuerySet instances render as a static string instead.
+from django.db.models.query import QuerySet  # noqa: E402
+import sphinx.util.inspect as _sphinx_inspect  # noqa: E402
+
+_orig_object_description = _sphinx_inspect.object_description
+
+
+def _safe_object_description(obj, *args, **kwargs):
+    if isinstance(obj, QuerySet):
+        return f'<QuerySet [{obj.model.__name__}]>'
+    return _orig_object_description(obj, *args, **kwargs)
+
+
+_sphinx_inspect.object_description = _safe_object_description
+
+# ── Sphinx configuration below ────────────────────────────────────────────
+project = '<Project Name>'
+copyright = '<year>, <Project Team>'
+author = '<Project Team>'
+release = '1.0'
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+    'sphinx_autodoc_typehints',
+    'sphinxcontrib.httpdomain',
+    'sphinxcontrib.mermaid',
+    'myst_parser',
+]
+
+source_suffix = {'.rst': 'restructuredtext', '.md': 'markdown'}
+
+myst_enable_extensions = ['colon_fence', 'deflist', 'tasklist', 'attrs_inline']
+myst_heading_anchors = 4
+
+autodoc_default_options = {
+    'members': True,
+    'member-order': 'bysource',
+    'special-members': '__init__',
+    'undoc-members': True,
+    'exclude-members': '__weakref__',
+}
+autodoc_inherit_docstrings = False
+napoleon_use_ivar = True
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+html_theme_options = {
+    'navigation_depth': 4,
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'includehidden': True,
+    'titles_only': False,
+}
+```
+
+### 4. `.gitea/workflows/docs.yml` — build + failure-debug + deploy
+
+The failure-debug trio (`continue-on-error` + log dump + explicit fail) is **required** — without it, the Sphinx `ValueError` traceback in `/tmp/sphinx-err-*.log` is invisible in the Gitea UI and the build is effectively undiagnosable.
+
+```yaml
+name: Build & Deploy Docs
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - '<project_package>/**'
+      - 'docs/**'
+      - 'pyproject.toml'
+      - '.gitea/workflows/docs.yml'
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install package + docs deps
+        run: |
+          pip install --upgrade pip
+          pip install -e ".[docs]"
+
+      - name: Read version from pyproject.toml
+        id: version
+        run: |
+          VERSION=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml','rb'))['project']['version'])")
+          echo "version=$VERSION" >> "$GITHUB_OUTPUT"
+
+      # ─── Failure-debug trio (REQUIRED) ─────────────────────────────────
+      - name: Build HTML
+        id: build_html
+        run: |
+          cd docs
+          ./regenerate_docs.sh
+        continue-on-error: true
+
+      - name: Print Sphinx error log on failure
+        if: steps.build_html.outcome == 'failure'
+        run: |
+          echo "=== Sphinx error log ==="
+          cat /tmp/sphinx-err-*.log 2>/dev/null || echo "(no sphinx error log found)"
+
+      - name: Fail if build failed
+        if: steps.build_html.outcome == 'failure'
+        run: exit 1
+      # ───────────────────────────────────────────────────────────────────
+
+      - name: Install rsync + openssh
+        run: |
+          apt-get update
+          apt-get install -y --no-install-recommends rsync openssh-client
+
+      - name: Configure SSH
+        run: |
+          mkdir -p ~/.ssh
+          printf '%s\n' "${{ secrets.DOCS_DEPLOY_KEY }}" > ~/.ssh/id_ed25519
+          chmod 600 ~/.ssh/id_ed25519
+          ssh-keyscan -p ${{ vars.DOCS_HOST_PORT }} ${{ vars.DOCS_HOST }} >> ~/.ssh/known_hosts
+
+      - name: Test SSH connectivity
+        run: |
+          ssh -o BatchMode=yes -o ConnectTimeout=10 \
+            -p ${{ vars.DOCS_HOST_PORT }} -i ~/.ssh/id_ed25519 \
+            git@${{ vars.DOCS_HOST }} "id && echo 'SSH OK'"
+
+      - name: Rsync to versioned path
+        run: |
+          rsync -av --delete \
+            -e "ssh -p ${{ vars.DOCS_HOST_PORT }} -i ~/.ssh/id_ed25519" \
+            docs/_build/html/ \
+            git@${{ vars.DOCS_HOST }}:/var/www/docs/<project_slug>/${{ steps.version.outputs.version }}/
+
+      - name: Rsync to latest
+        run: |
+          rsync -av --delete \
+            -e "ssh -p ${{ vars.DOCS_HOST_PORT }} -i ~/.ssh/id_ed25519" \
+            docs/_build/html/ \
+            git@${{ vars.DOCS_HOST }}:/var/www/docs/<project_slug>/latest/
+
+      - name: Regenerate versions index
+        run: |
+          ssh -p ${{ vars.DOCS_HOST_PORT }} -i ~/.ssh/id_ed25519 git@${{ vars.DOCS_HOST }} \
+            'python3 - <<PY
+          import pathlib
+          root = pathlib.Path("/var/www/docs/<project_slug>")
+          versions = sorted(
+              (p.name for p in root.iterdir() if p.is_dir()),
+              reverse=True,
+          )
+          html = ["<!DOCTYPE html><html><head><title><Project> Docs</title></head><body>",
+                  "<h1><Project> Documentation</h1><ul>"]
+          for v in versions:
+              html.append(f"<li><a href=\"{v}/\">{v}</a></li>")
+          html.append("</ul></body></html>")
+          (root / "index.html").write_text("\n".join(html))
+          PY'
+```
+
+Required Gitea secrets/variables:
+
+- `secrets.DOCS_DEPLOY_KEY` — SSH private key authorised on the deploy host.
+- `vars.DOCS_HOST` — deploy host (e.g. `docs.example.com`).
+- `vars.DOCS_HOST_PORT` — SSH port (typically `22`).
+
+---
+
+## Standard Sphinx Extensions
+
+Use this exact extension set for consistency across projects:
+
+```python
+extensions = [
+    'sphinx.ext.autodoc',           # Pull docs from Python docstrings
+    'sphinx.ext.viewcode',          # "[source]" links to highlighted source
+    'sphinx.ext.napoleon',          # Google / NumPy style docstring support
+    'sphinx.ext.intersphinx',       # Cross-link to other projects' Sphinx docs
+    'sphinx_autodoc_typehints',     # Render PEP 484 type hints in docs
+    'sphinxcontrib.httpdomain',     # ".. http:get::" etc. for REST APIs
+    'sphinxcontrib.mermaid',        # Mermaid diagrams in Markdown / RST
+    'myst_parser',                  # Markdown source files alongside RST
+]
+```
+
+And the matching `pyproject.toml` extras group:
+
+```toml
+[project.optional-dependencies]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "sphinx-autodoc-typehints",
+    "sphinx-autobuild",
+    "sphinxcontrib-httpdomain",
+    "sphinxcontrib-mermaid",
+    "myst-parser",
+]
+```
+
+---
+
+## Recommended Behaviours
+
+Behaviours that most projects should include but are not strictly required:
+
+- **Live rebuild during authoring** — `make livehtml` (via `sphinx-autobuild`) for hot-reload editing.
+- **One-shot regen script** — `docs/regenerate_docs.sh` runs `make clean`, `sphinx-apidoc` over every app, then `make html`. Drives both local development and the CI pipeline.
+- **Mermaid for diagrams** — text-based, diffable, lives in the `.md` / `.rst` source. Avoid binary diagram assets.
+- **Static images in `source/_static/`** — referenced with relative paths.
+- **Hand-written prose in Markdown (MyST)** alongside autogenerated reference docs in RST. The two coexist via `myst_parser` + `source_suffix`.
+- **Project root `CLAUDE.md` (or equivalent) names docs as the single source of truth** — discourage parallel READMEs that drift.
+
+---
+
+## Pattern Variant 1: DRF / QuerySet Autodoc Poisoning
+
+**Problem.** Sphinx 9 autodoc renders class attributes by calling `repr()` on the live object. Django's `QuerySet.__repr__` triggers `_fetch_all()`, which opens a database connection and runs a `SELECT`. For DRF viewsets like:
+
+```python
+class CurrencyViewSet(viewsets.ReadOnlyModelViewSet):
+    queryset = Currency.objects.filter(is_active=True)  # ← autodoc tries to execute this
+    serializer_class = CurrencySerializer
+```
+
+…the docs build crashes with `psycopg.OperationalError: failed to resolve host 'postgres'` (or whatever DB hostname is configured), even in TESTING mode where the in-memory SQLite has no tables.
+
+**Solution.** Monkey-patch `sphinx.util.inspect.object_description` in `conf.py` to short-circuit QuerySets before `repr()` is called:
+
+```python
+from django.db.models.query import QuerySet
+import sphinx.util.inspect as _sphinx_inspect
+
+_orig_object_description = _sphinx_inspect.object_description
+
+
+def _safe_object_description(obj, *args, **kwargs):
+    if isinstance(obj, QuerySet):
+        return f'<QuerySet [{obj.model.__name__}]>'
+    return _orig_object_description(obj, *args, **kwargs)
+
+
+_sphinx_inspect.object_description = _safe_object_description
+```
+
+This must run **after** `django.setup()` (so `QuerySet` can be imported) but **before** Sphinx starts processing documents.
+
+---
+
+## Pattern Variant 2: Settings-Driven TESTING Mode
+
+**Problem.** Docs build needs to import `settings.py` but has no real `.env` in CI. Production-mode `env('SECRET_KEY')` calls (no default) raise `ImproperlyConfigured` and the build crashes before Sphinx even starts.
+
+**Solution.** Read `TESTING` first in `settings.py`, then gate every required `env('X')` behind it:
+
+```python
+TESTING = env.bool('TESTING', default=False)
+if TESTING:
+    SECRET_KEY = env('SECRET_KEY', default='testing-insecure-key')
+else:
+    SECRET_KEY = env('SECRET_KEY')
+```
+
+`conf.py` flips the switch:
+
+```python
+os.environ['TESTING'] = 'true'
+django.setup()
+```
+
+**Bonus.** This also fixes a latent bug where `python manage.py test` would fail in any environment without `.env`. The same defaults that unblock the docs build now unblock the test suite — one mechanism, two payoffs.
+
+---
+
+## Pattern Variant 3: Gitea Actions Deploy Workflow
+
+The workflow has four logical phases:
+
+1. **Setup** — checkout, Python, `pip install -e ".[docs]"`, read version from `pyproject.toml`.
+2. **Build with failure visibility** — the three-step trio shown above. The `continue-on-error: true` on the build step plus `if: steps.build_html.outcome == 'failure'` on the log-dump and fail steps ensures the Sphinx traceback reaches the Gitea log even when the build crashes.
+3. **SSH setup** — write the deploy key to `~/.ssh/id_ed25519`, scan the host into `known_hosts`, verify connectivity.
+4. **Deploy** — rsync to `/var/www/docs/<project>/<version>/`, rsync to `…/latest/`, regenerate the versions index page on the remote host via a heredoc Python script.
+
+The deploy host is expected to serve `/var/www/docs/` over HTTPS via nginx or similar. Each pushed version gets its own directory; `latest/` is a copy of the most recent build. The versions index lists every directory alphabetically.
+
+---
+
+## Domain Extension Examples
+
+### Project without DRF / class-level QuerySets
+
+If your project has no `queryset = Model.objects.filter(...)` attributes at module load time, the `_safe_object_description` monkey-patch is unnecessary. You can omit it. The `TESTING=true` switch is still required because settings.py still has required env vars.
+
+### Project with extra required secrets
+
+Add each extra key to the TESTING branch in `settings.py`:
+
+```python
+if TESTING:
+    SECRET_KEY = env('SECRET_KEY', default='testing-insecure-key')
+    SLACK_TOKEN = env('SLACK_TOKEN', default='testing-insecure-slack')
+    STRIPE_API_KEY = env('STRIPE_API_KEY', default='testing-insecure-stripe')
+else:
+    SECRET_KEY = env('SECRET_KEY')
+    SLACK_TOKEN = env('SLACK_TOKEN')
+    STRIPE_API_KEY = env('STRIPE_API_KEY')
+```
+
+No changes needed to `conf.py` — the single `TESTING=true` flip covers them all.
+
+### Project on a non-Postgres database (MySQL, MariaDB)
+
+No special handling needed. The `if TESTING:` branch in `settings.py` switches to in-memory SQLite regardless of what production uses. The MySQL driver is never imported during a docs build.
+
+---
+
+## Anti-Patterns
+
+- ❌ **Don't load `.env.example` as a runtime fallback.** It's a documentation file with placeholder values like `DB_HOST=postgres` — those placeholders will poison the docs build by making `settings.py` believe Postgres is available.
+- ❌ **Don't override `settings.DATABASES` after `django.setup()`.** Django's `ConnectionHandler.databases` is a `@cached_property` populated during app loading; mutating `settings.DATABASES` afterwards has no effect.
+- ❌ **Don't add a separate `settings_docs.py`.** Env-var toggles are the project convention. A separate settings module fragments the config surface and forces every dev to remember which settings file applies in which context.
+- ❌ **Don't hand-edit `docs/source/reference/apps/`.** That tree is regenerated by `sphinx-apidoc` on every CI run. Hand-edits get overwritten.
+- ❌ **Don't suppress build errors in CI without dumping `/tmp/sphinx-err-*.log` first.** Sphinx writes its full traceback there and nowhere else; without the dump, the Gitea UI shows a one-line `ValueError` with no useful context.
+- ❌ **Don't use `os.environ.setdefault('TESTING', 'true')` in `conf.py`.** A user with `TESTING=false` in their local `.env` will see the setdefault skipped and hit production-mode behaviour during docs build. Use plain `os.environ['TESTING'] = 'true'` so it always wins.
+
+---
+
+## Settings
+
+Document the `TESTING` env var contract:
+
+```python
+# settings.py
+TESTING = env.bool('TESTING', default=False)
+# When true, gates safe-default branches for:
+#   - Required secrets (SECRET_KEY and any other env('X') with no default)
+#   - Required lists (ALLOWED_HOSTS, CSRF_TRUSTED_ORIGINS)
+#   - DATABASES → in-memory SQLite
+#   - CACHES → dummy backend
+#   - DRF throttling → disabled
+#   - MIGRATION_MODULES → disabled (no DB schema)
+#   - PASSWORD_HASHERS → fast hashers
+#   - LOGGING → minimal
+#
+# Set true for: pytest, manage.py test, docs build.
+# Set false (or unset) for: production, local dev with real services.
+```
+
+---
+
+## Testing
+
+Two verification recipes every project should run before pushing.
+
+### 1. Local build with real `.env`
+
+```bash
+cd docs
+make clean && make html
+```
+
+Expected: `build succeeded.` with zero warnings. Open `_build/html/index.html` to spot-check rendering.
+
+### 2. CI simulation (no `.env`)
+
+```bash
+mv .env .env.bak
+cd docs && make clean && make html
+cd .. && mv .env.bak .env
+```
+
+Expected: `build succeeded.` again. Settings.py uses TESTING-mode dummies; the in-memory SQLite has no tables but autodoc never queries it because the monkey-patch short-circuits QuerySet repr().
+
+### 3. Latent test-suite bug check
+
+```bash
+mv .env .env.bak
+python manage.py test --keepdb 2>&1 | head -5
+mv .env.bak .env
+```
+
+Expected: tests start running normally (not `ImproperlyConfigured: Set the SECRET_KEY environment variable`). This confirms the TESTING-mode defaults are wired into `settings.py` correctly — the docs build and the test suite share the same fallback mechanism.
+
+### 4. CI dry-run (Gitea Actions)
+
+Push to a feature branch. The workflow's failure-debug trio means any crash surfaces with a full traceback in the Gitea Actions log. Read the trace, fix the cause, push again.

docs/deploy.md

@@ -85,8 +85,7 @@ an explicit `when: mnemosyne_first_deploy` flag.
 
 ```bash
 # Apply Django ORM migrations (PostgreSQL schema)
-docker compose -f /srv/mnemosyne/docker-compose.yaml \
-    run --rm app migrate
+docker compose -f /srv/mnemosyne/docker-compose.yaml run --rm app migrate
 
 # Create Neo4j vector + full-text indexes and load library-type defaults
 docker compose -f /srv/mnemosyne/docker-compose.yaml \
@@ -315,17 +314,18 @@ curl http://puck.incus:23181/metrics | head -5
 
 ### Verify Daedalus auth (per-user API token)
 
-Daedalus now authenticates as a Mnemosyne user via the DRF token shown
-on `/profile/settings/`. To smoke-test from a deploy host:
+Daedalus now authenticates as a Mnemosyne user via a `UserToken` minted
+at `/profile/tokens/`. To smoke-test from a deploy host:
 
 ```bash
-curl -H "Authorization: Token <user-api-token>" \
+curl -H "Authorization: Bearer <user-token-plaintext>" \
     https://mnemosyne.ouranos.helu.ca/library/api/workspaces/ws_smoke/ \
     -o /dev/null -w "%{http_code}"
 # Expect: 200 if the workspace exists for that user, 404 otherwise.
+# An anonymous request gets 401 with `WWW-Authenticate: Bearer`.
 ```
 
-### Verify MCP connectivity (from a client with a valid MCPToken)
+### Verify MCP connectivity (from a client with a valid UserToken)
 
 ```bash
 curl -H "Authorization: Bearer <token>" \

docs/mnemosyne_integration.md

@@ -8,7 +8,7 @@ This document describes Mnemosyne's role in the Daedalus + Pallas architecture a
 
 Mnemosyne exposes two interfaces for the wider Ouranos ecosystem:
 
-1. **REST API** (`/library/api/*`) — consumed by the Daedalus backend authenticated as the owning Mnemosyne user via a per-user DRF token (`Authorization: Token <key>`, surfaced on `/profile/settings/`) for workspace lifecycle and asynchronous file ingestion. Phase 1, **implemented**.
+1. **REST API** (`/library/api/*`) — consumed by the Daedalus backend authenticated as the owning Mnemosyne user via a per-user `UserToken` (`Authorization: Bearer <plaintext>`, minted at `/profile/tokens/`) for workspace lifecycle and asynchronous file ingestion. Phase 1, **implemented**.
 2. **MCP Server** (port 22091 internal, `/mcp/` via nginx on 23090) — exposes search, browse, and retrieval tools. Phase 5 of Mnemosyne's own roadmap, **implemented** with workspace-scoped access control via long-lived team JWTs. Consumed by Pallas FastAgents in production (Daedalus integration Phase 2, **implemented** — see [Phase 3 of this doc](#3-phase-3-long-lived-team-jwt-access-control-for-pallas-instances)).
 
 ### Phase status
@@ -105,7 +105,7 @@ Auth is controlled by `MCP_REQUIRE_AUTH` in `.env`. Production sets it to `True`
 
 ## 2. REST API for Daedalus
 
-All endpoints require an `Authorization: Token <key>` header carrying the DRF token of the Mnemosyne user the workspace belongs to (surfaced on `/profile/settings/`). Workspaces are scoped to their creating user via the `Library.owner_username` property; cross-user access returns 404. They are consumed by the Daedalus FastAPI backend only — not by any frontend.
+All endpoints require an `Authorization: Bearer <plaintext>` header carrying a `UserToken` belonging to the Mnemosyne user the workspace belongs to (minted at `/profile/tokens/`). Workspaces are scoped to their creating user via the `Library.owner_username` property; cross-user access returns 404. Anonymous requests get 401 with `WWW-Authenticate: Bearer`. These endpoints are consumed by the Daedalus FastAPI backend only — not by any frontend.
 
 ### Workspace lifecycle
 
@@ -354,7 +354,7 @@ mnemosyne_s3_operations_total{operation,status}                counter
 - [x] `GET /library/api/jobs/{job_id}/`, `POST .../retry/`, `GET /library/api/jobs/`
 - [x] `library.tasks.ingest_from_daedalus` Celery task with content-hash-aware supersede logic
 - [x] `library.services.daedalus_s3` cross-bucket fetch + copy
-- [x] Per-user DRF token auth (`Authorization: Token <key>`); workspaces scoped to the owning user via `Library.owner_username`
+- [x] Per-user `UserToken` auth (`Authorization: Bearer <plaintext>`, minted at `/profile/tokens/`); workspaces scoped to the owning user via `Library.owner_username`
 
 ### Phase 2 — MCP Server (Mnemosyne roadmap Phase 5)  ✅ Implemented
 - [x] `mcp_server/` module following the [Django MCP Pattern](Pattern_Django-MCP_V1-00.md)

docs/ouranos.md

@@ -1,557 +0,0 @@
-# Ouranos Lab
-
-Infrastructure-as-Code project managing the **Ouranos Lab** — a development sandbox at [ouranos.helu.ca](https://ouranos.helu.ca). Uses **Terraform** for container provisioning and **Ansible** for configuration management, themed around the moons of Uranus.
-
----
-
-## Project Overview
-
-| Component | Purpose |
-|-----------|---------|
-| **Terraform** | Provisions 10 specialised Incus containers (LXC) with DNS-resolved networking, security policies, and resource dependencies |
-| **Ansible** | Deploys Docker, databases (PostgreSQL, Neo4j), observability stack (Prometheus, Grafana, Loki), and application runtimes across all hosts |
-
-> **DNS Domain**: Incus resolves containers via the `.incus` domain suffix (e.g., `oberon.incus`, `portia.incus`). IPv4 addresses are dynamically assigned — always use DNS names, never hardcode IPs.
-
----
-
-## Uranian Host Architecture
-
-All containers are named after moons of Uranus and resolved via the `.incus` DNS suffix.
-
-| Name | Role | Description | Nesting |
-|------|------|-------------|---------|
-| **ariel** | graph_database | Neo4j — Ethereal graph connections | ✔ |
-| **caliban** | agent_automation | Agent S MCP Server with MATE Desktop | ✔ |
-| **miranda** | mcp_docker_host | Dedicated Docker Host for MCP Servers | ✔ |
-| **oberon** | container_orchestration | Docker Host — MCP Switchboard, RabbitMQ, Open WebUI | ✔ |
-| **portia** | database | PostgreSQL — Relational database host | ❌ |
-| **prospero** | observability | PPLG stack — Prometheus, Grafana, Loki, PgAdmin | ❌ |
-| **puck** | application_runtime | Python App Host — JupyterLab, Django apps, Gitea Runner | ✔ |
-| **rosalind** | collaboration | Gitea, LobeChat, Nextcloud, AnythingLLM | ✔ |
-| **sycorax** | language_models | Arke LLM Proxy | ✔ |
-| **titania** | proxy_sso | HAProxy TLS termination + Casdoor SSO | ✔ |
-| **umbriel** | graph_database | Neo4j (Mnemosyne) — dedicated memory graph | ✔ |
-
-### puck — Project Application Runtime
-
-Shape-shifting trickster embodying Python's versatility.
-This is the host that runs Python projects in the Ouranos sandbox.
-It has an RDP server and is generally where application development happens.
-Each project has a number that is used to determine port numbers.
-
-- Docker engine
-- JupyterLab (port 22071 via OAuth2-Proxy)
-- Gitea Runner (CI/CD agent)
-- Django Projects: Zelus (221), Angelia (222), Athena (224), Kairos (225), Icarlos (226), MCP Switchboard (227), Spelunker (228), Peitho (229), Mnemosyne (230)
-- FastAgent Projects: Pallas (240)
-- FastAPI Projects: Daedalus (200), Arke (201) Kernos (202), Rommie (203), Orpheus (204), Periplus (205), Nike (206), Stentor (207)
-
-### caliban — Agent Automation
-
-Autonomous computer agent learning through environmental interaction.
-
-- Docker engine
-- Agent S MCP Server (MATE desktop, AT-SPI automation)
-- Kernos MCP Shell Server (port 22062)
-- Rommie MCP Server (port 22061) — agent-to-agent GUI automation via Agent S
-- FreeCAD Robust MCP Server (port 22063) — CAD automation via FreeCAD XML-RPC
-- GPU passthrough
-- RDP access (port 25521)
-
-### oberon — Container Orchestration & Dockerized Shared Services
-
-King of the Fairies orchestrating containers and managing MCP infrastructure.
-
-- Docker engine
-- MCP Switchboard (port 22781) — Django app routing MCP tool calls
-- RabbitMQ message queue
-- smtp4dev SMTP test server (port 22025)
-
-### portia — Relational Database
-
-Intelligent and resourceful — the reliability of relational databases.
-
-- PostgreSQL 17 (port 5432)
-- Databases: `arke`, `anythingllm`, `gitea`, `hass`, `lobechat`, `mcp_switchboard`, `mnemosyne`, `nextcloud`, `openwebui`, `periplus`, `spelunker`
-
-### ariel — Graph Database
-
-Air spirit — ethereal, interconnected nature mirroring graph relationships.
-
-- Neo4j 5.26.0 (Docker)
-- HTTP API: port 25554
-- Bolt: port 7687 (reached as `ariel.incus:7687` on the internal network)
-
-### umbriel — Graph Database (Mnemosyne)
-
-Dusky melancholy sprite from Pope's *Rape of the Lock* — keeper of the Cave of
-Spleen, naturally paired with Mnemosyne the Titan of memory. Dedicated Neo4j
-instance so Mnemosyne's `Library`/`Collection`/`Item`/`Chunk`/`Concept` labels,
-vector indexes, and schema migrations can't collide with another tenant's
-graph on Ariel.
-
-- Neo4j 5.26.0 (Docker)
-- HTTP Browser: port 25555
-- Bolt: port 7687 (reached as `umbriel.incus:7687` on the internal network)
-
-### miranda — MCP Docker Host
-
-Curious bridge between worlds — hosting MCP server containers.
-
-- Docker engine (API exposed on port 2375 for MCP Switchboard)
-- MCPO OpenAI-compatible MCP proxy 22071
-- Argos MCP Server — web search via SearXNG (port 22062)
-- Grafana MCP Server (port 22063)
-- Neo4j MCP Server (port 22064)
-- Gitea MCP Server (port 22065)
-
-### prospero — Observability Stack
-
-Master magician observing all events.
-
-- PPLG stack via Docker Compose: Prometheus, Loki, Grafana, PgAdmin
-- Internal HAProxy with OAuth2-Proxy for all dashboards
-- AlertManager with Pushover notifications
-- Prometheus metrics collection (`node-exporter`, HAProxy, Loki)
-- Loki log aggregation via Alloy (all hosts)
-- Grafana dashboard suite with Casdoor SSO integration
-
-### rosalind — Third Party Applications for testing and evaluation
-
-Witty and resourceful moon for PHP, Go, and Node.js runtimes.
-
-- SearXNG privacy search (port 22083, behind OAuth2-Proxy)
-- Gitea self-hosted Git (port 22082, SSH on 22022)
-- LobeChat AI chat interface (port 22081)
-- Nextcloud file sharing and collaboration (port 22083)
-- AnythingLLM document AI workspace (port 22084)
-- Nextcloud data on dedicated Incus storage volume
-- Open WebUI LLM interface (port 22088, PostgreSQL backend on Portia
-- Home Assistant (port 8123)
-
-### sycorax — Language Models
-
-Original magical power wielding language magic.
-
-- Arke LLM API Proxy (port 25540)
-- Multi-provider support (OpenAI, Anthropic, etc.)
-- Session management with Memcached
-- Database backend on Portia
-
-### titania — Proxy & SSO Services
-
-Queen of the Fairies managing access control and authentication.
-
-- HAProxy 3.x with TLS termination (port 443)
-- Let's Encrypt wildcard certificate via certbot DNS-01 (Namecheap)
-- HTTP to HTTPS redirect (port 80)
-- Gitea SSH proxy (port 22022)
-- Casdoor SSO (port 22081, local PostgreSQL)
-- Prometheus metrics at `:8404/metrics`
-
----
-
-## Port Numbering
-
-Well-known ports running as a service may be used: Postgresql 5432, Prometheus Metrics 9100.
-
-However inside a docker project, the number plan needs to be followed to avoid port conflicts and confusion:
-XXXYZ
-XXX Project Number or 220 for external project 
-Y Service: 0 reserved, 1-4 flexible, 5 database, 6 MCP, 7 API, 8 Web App, 9 Prometheus metrics
-Z Instance: The running instance of this app on the same host, starting at 1.  May also be used to handle exceptions.
-
-255 Incus port forwarding: Ports in ths range are forwarded from the Incus host to Incus containers (defined in Terraform)
-
-514ZZ is the syslog port.  Docker containers send their syslog to an Alloy syslog collector port.  ZZ is the application instance, they just need to be different on the same host and increment from 01.
-
----
-
-## Application Conventions
-
-Standards that all services deployed in Ouranos MUST follow. For full logging standards and anti-patterns, see [red_panda_standards.md](red_panda_standards.md).
-
-### Health Check Endpoints
-
-All services MUST expose Kubernetes-style health endpoints:
-
-| Endpoint | Purpose | Auth |
-|----------|---------|------|
-| `GET /live` | **Liveness** — process is running and accepting connections | None |
-| `GET /ready` | **Readiness** — process is running AND all dependencies (DB, cache, upstream APIs) are healthy | None |
-| `GET /metrics` | Prometheus metrics (see below) | IP-restricted |
-
-- HAProxy checks `health_path` (typically `/ready/`) for backend health — return HTTP 200 when healthy
-- Health endpoints MUST NOT require authentication (no JWT, no session)
-- Third-party services use their native health paths (e.g., `/api/health`, `/api/healthz`, `/-/healthy`)
-
-### Health Checks in Docker Compose
-
-Use `curl -f` for Docker Compose healthchecks. Install curl in images if needed.
-
-```yaml
-healthcheck:
-  test: ["CMD", "curl", "-f", "http://localhost:8000/live"]
-  interval: 30s
-  timeout: 10s
-  retries: 3
-  start_period: 40s
-```
-
-### Logging Conventions
-
-Log output flows through: **App → syslog (RFC3164) → Alloy → Loki → Grafana**
-
-| Level | Usage |
-|-------|-------|
-| **ERROR** | Broken state requiring human action — always include `exc_info=True`, error type, and context |
-| **WARNING** | Degraded but recovering — client disconnects, performance outliers, client-side exceptions, leaked markup |
-| **INFO** | Lifecycle events — service start/stop, connections, requests completed, jobs finished |
-| **DEBUG** | Diagnostic detail — SSE events, keepalive pings, health check 200 responses, negotiation steps |
-
-**Health check responses MUST be logged at DEBUG only.** HAProxy and Prometheus probe endpoints every 15-30 seconds. Logging these at INFO floods syslog with thousands of identical `200 OK` lines per hour, burying real events.
-
-### Protected vs Unprotected Endpoints
-
-| Protected (require valid JWT) | Unprotected |
-|-------------------------------|-------------|
-| All `/api/v1/*` routes | `GET /live` |
-| | `GET /ready` |
-| | `GET /metrics` (IP-restricted to internal networks) |
-| | `GET /api/auth/login-url` |
-| | `POST /api/auth/token` |
-| | `POST /api/v1/telemetry` (sendBeacon cannot set headers) |
-
-### Prometheus Metrics
-
-All services SHOULD expose `GET /metrics` in Prometheus exposition format, scraped by Prospero's Prometheus (default 15s interval).
-
-- **IP-restricted** to internal networks only (`10.10.0.0/24`, `172.16.0.0/12`, `127.0.0.0/8`)
-- Consider exposing: request counts/durations, error rates, active connections, queue depths, dependency health
-
-### Browser Telemetry
-
-Frontend/browser code MUST send telemetry data and errors back to the application's telemetry API:
-
-- `POST /api/v1/telemetry` — unprotected (browser `sendBeacon` cannot set Authorization headers)
-- Capture and report: JavaScript exceptions, performance metrics, user-facing errors
-- Client-side exceptions should log as **WARNING** on the server (they indicate a problem but not a server-side failure)
-
-### Docker Networking
-
-- Use the **default Docker bridge network** for simple deployments
-- Add additional named networks only when required (e.g., isolating database traffic) or explicitly requested
-- Do not create custom network definitions for single-service Docker Compose stacks
-
----
-
-## External Access via HAProxy
-
-Titania provides TLS termination and reverse proxy for all services.
-
-- **Base domain**: `ouranos.helu.ca`
-- **HTTPS**: port 443 (standard)
-- **HTTP**: port 80 (redirects to HTTPS)
-- **Certificate**: Let's Encrypt wildcard via certbot DNS-01
-
-### Route Table
-
-| Subdomain | Backend | Service |
-|-----------|---------|---------|
-| `ouranos.helu.ca` (root) | puck.incus:22281 | Angelia (Django) |
-| `alertmanager.ouranos.helu.ca` | prospero.incus:443 (SSL) | AlertManager |
-| `angelia.ouranos.helu.ca` | puck.incus:22281 | Angelia (Django) |
-| `anythingllm.ouranos.helu.ca` | rosalind.incus:22084 | AnythingLLM |
-| `arke.ouranos.helu.ca` | sycorax.incus:25540 | Arke LLM Proxy |
-| `athena.ouranos.helu.ca` | puck.incus:22481 | Athena (Django) |
-| `gitea.ouranos.helu.ca` | rosalind.incus:22082 | Gitea |
-| `grafana.ouranos.helu.ca` | prospero.incus:443 (SSL) | Grafana |
-| `hass.ouranos.helu.ca` | oberon.incus:8123 | Home Assistant |
-| `id.ouranos.helu.ca` | titania.incus:22081 | Casdoor SSO |
-| `icarlos.ouranos.helu.ca` | puck.incus:22681 | Icarlos (Django) |
-| `jupyterlab.ouranos.helu.ca` | puck.incus:22071 | JupyterLab (OAuth2-Proxy) |
-| `kairos.ouranos.helu.ca` | puck.incus:22581 | Kairos (Django) |
-| `lobechat.ouranos.helu.ca` | rosalind.incus:22081 | LobeChat |
-| `loki.ouranos.helu.ca` | prospero.incus:443 (SSL) | Loki |
-| `mcp-switchboard.ouranos.helu.ca` | oberon.incus:22781 | MCP Switchboard |
-| `nextcloud.ouranos.helu.ca` | rosalind.incus:22083 | Nextcloud |
-| `openwebui.ouranos.helu.ca` | oberon.incus:22088 | Open WebUI |
-| `peitho.ouranos.helu.ca` | puck.incus:22981 | Peitho (Django) |
-| `periplus.ouranos.helu.ca` | puck.incus:20681 | Periplus (FastAPI + MCP via nginx) |
-| `pgadmin.ouranos.helu.ca` | prospero.incus:443 (SSL) | PgAdmin 4 |
-| `prometheus.ouranos.helu.ca` | prospero.incus:443 (SSL) | Prometheus |
-| `searxng.ouranos.helu.ca` | oberon.incus:22073 | SearXNG (OAuth2-Proxy) |
-| `smtp4dev.ouranos.helu.ca` | oberon.incus:22085 | smtp4dev |
-| `spelunker.ouranos.helu.ca` | puck.incus:22881 | Spelunker (Django) |
-
----
-
-## Infrastructure Management
-
-### Quick Start
-
-```bash
-# Provision containers
-cd terraform
-terraform init
-terraform plan
-terraform apply
-
-# Start all containers
-cd ../ansible
-source ~/env/ouranos/bin/activate
-ansible-playbook sandbox_up.yml
-
-# Deploy all services
-ansible-playbook site.yml
-
-# Stop all containers
-ansible-playbook sandbox_down.yml
-```
-
-### Python Virtual Environment Setup
-
-The Ansible automation requires a Python virtual environment with the `ansible` package installed. Create and activate the environment from the `~` directory:
-
-```bash
-# Create virtual environment
-cd ~
-python3 -m venv env/ouranos
-
-# Activate environment
-source ~/env/ouranos/bin/activate
-
-# Install Ansible
-pip install ansible
-pip install ansible-core
-pip install ansible-community.postgresql
-```
-
-### Ansible Playbook Syntax Check
-
-Before running playbooks, use the `apsc.sh` utility (in PATH) to quickly validate YAML syntax:
-
-```bash
-# From the ansible directory
-apsc.sh
-
-# This will check all YAML files in the current directory for syntax errors
-```
-
-### Terraform Workflow
-
-1. **Define** — Containers, networks, and resources in `*.tf` files
-2. **Plan** — Review changes with `terraform plan`
-3. **Apply** — Provision with `terraform apply`
-4. **Verify** — Check outputs and container status
-
-### Terraform Import
-
-When containers or other resources are created manually (outside Terraform) or need to be re-imported after recreation, use `terraform import` to sync the Terraform state with existing infrastructure.
-
-#### Import Syntax
-
-The correct import format for Incus resources requires quoting resource addresses with `for_each` keys and using the full ID including image fingerprints:
-
-```bash
-# Import a container with correct syntax
-terraform import 'incus_instance.uranian_hosts["<name>"]' ouranos/<name>,image=<fingerprint>
-```
-
-#### Getting Image Fingerprints
-
-First, get the fingerprint of the image resource from Terraform state:
-
-```bash
-cd terraform
-terraform state show incus_image.noble | grep fingerprint
-# Output: fingerprint = "75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644"
-
-terraform state show incus_image.questing | grep fingerprint
-# Output: fingerprint = "e78dd4a406b7fa3592ed0a6048862260b3d2e50c76e32a6169930245c0a13fdf"
-```
-
-#### Importing All Uranian Hosts
-
-Replace containers missing from state (or re-import after manual recreation):
-
-```bash
-# Containers using noble image
-terraform import 'incus_instance.uranian_hosts["ariel"]' ouranos/ariel,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["miranda"]' ouranos/miranda,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["oberon"]' ouranos/oberon,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["portia"]' ouranos/portia,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["prospero"]' ouranos/prospero,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["rosalind"]' ouranos/rosalind,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["sycorax"]' ouranos/sycorax,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["titania"]' ouranos/titania,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-terraform import 'incus_instance.uranian_hosts["umbriel"]' ouranos/umbriel,image=75cde3e755b0e657c05f67e03a42683217b233b0339448be747845747df58644
-
-# Containers using questing image
-terraform import 'incus_instance.uranian_hosts["caliban"]' ouranos/caliban,image=e78dd4a406b7fa3592ed0a6048862260b3d2e50c76e32a6169930245c0a13fdf
-terraform import 'incus_instance.uranian_hosts["puck"]' ouranos/puck,image=e78dd4a406b7fa3592ed0a6048862260b3d2e50c76e32a6169930245c0a13fdf
-```
-
-#### Storage Bucket Import
-
-For storage buckets, use the `<project>/<pool>/<name>` format:
-
-```bash
-terraform import incus_storage_bucket.<name> ouranos/default/<bucket-name>
-```
-
-#### Common Issues
-
-1. **Import ID format errors**: Use quotes around resource addresses with `for_each` keys: `'incus_instance.uranian_hosts["name"]'`
-
-2. **Image replacement on import**: Importing without specifying the image fingerprint will cause Terraform to replace the container on next apply. Always include `image=<fingerprint>` in the import ID.
-
-3. **Tainted state**: If a resource shows "will be created" but already exists, it may be tainted. Remove from state and re-import:
-   ```bash
-   terraform state rm 'incus_instance.uranian_hosts["name"]'
-   terraform import 'incus_instance.uranian_hosts["name"]' ouranos/name,image=<fingerprint>
-   ```
-
-#### Verify Import
-
-After importing, verify with `terraform plan`:
-
-```bash
-terraform plan
-# Should show: Plan: 0 to add, 0 to change, 0 to destroy
-# (Minor "update in-place" changes are normal for state sync of computed attributes)
-```
-
-### Ansible Workflow
-
-1. **Bootstrap** — Update packages, install essentials (`apt_update.yml`)
-2. **Agents** — Deploy Alloy (log/metrics) and Node Exporter on all hosts
-3. **Services** — Configure databases, Docker, applications, observability
-4. **Verify** — Check service health and connectivity
-
-### Vault Management
-
-```bash
-# Edit secrets
-ansible-vault edit inventory/group_vars/all/vault.yml
-
-# View secrets
-ansible-vault view inventory/group_vars/all/vault.yml
-
-# Encrypt a new file
-ansible-vault encrypt new_secrets.yml
-```
-
----
-
-## S3 Storage Provisioning
-
-Terraform provisions Incus S3 buckets for services requiring object storage:
-
-| Service | Host | Purpose |
-|---------|------|---------|
-| **Casdoor** | Titania | User avatars and SSO resource storage |
-| **LobeChat** | Rosalind | File uploads and attachments |
-
-> S3 credentials (access key, secret key, endpoint) are stored as sensitive Terraform outputs and managed in Ansible Vault with the `vault_*_s3_*` prefix.
-
----
-
-## Ansible Automation
-
-### Full Deployment (`site.yml`)
-
-Playbooks run in dependency order:
-
-| Playbook | Hosts | Purpose |
-|----------|-------|---------|
-| `apt_update.yml` | All | Update packages and install essentials |
-| `alloy/deploy.yml` | All | Grafana Alloy log/metrics collection |
-| `prometheus/node_deploy.yml` | All | Node Exporter metrics |
-| `docker/deploy.yml` | Oberon, Ariel, Miranda, Puck, Rosalind, Sycorax, Caliban, Titania | Docker engine |
-| `smtp4dev/deploy.yml` | Oberon | SMTP test server |
-| `pplg/deploy.yml` | Prospero | Full observability stack + HAProxy + OAuth2-Proxy |
-| `postgresql/deploy.yml` | Portia | PostgreSQL with all databases |
-| `postgresql_ssl/deploy.yml` | Titania | Dedicated PostgreSQL for Casdoor |
-| `neo4j/deploy.yml` | Ariel, Umbriel | Neo4j graph database (Umbriel is the dedicated Mnemosyne instance) |
-| `searxng/deploy.yml` | Oberon | SearXNG privacy search |
-| `haproxy/deploy.yml` | Titania | HAProxy TLS termination and routing |
-| `casdoor/deploy.yml` | Titania | Casdoor SSO |
-| `mcpo/deploy.yml` | Miranda | MCPO MCP proxy |
-| `openwebui/deploy.yml` | Oberon | Open WebUI LLM interface |
-| `hass/deploy.yml` | Oberon | Home Assistant |
-| `gitea/deploy.yml` | Rosalind | Gitea self-hosted Git |
-| `nextcloud/deploy.yml` | Rosalind | Nextcloud collaboration |
-
-### Individual Service Deployments
-
-Services with standalone deploy playbooks (not in `site.yml`):
-
-| Playbook | Host | Service |
-|----------|------|---------|
-| `anythingllm/deploy.yml` | Rosalind | AnythingLLM document AI |
-| `arke/deploy.yml` | Sycorax | Arke LLM proxy |
-| `argos/deploy.yml` | Miranda | Argos MCP web search server |
-| `caliban/deploy.yml` | Caliban | Agent S MCP Server |
-| `certbot/deploy.yml` | Titania | Let's Encrypt certificate renewal |
-| `gitea_mcp/deploy.yml` | Miranda | Gitea MCP Server |
-| `gitea_runner/deploy.yml` | Puck | Gitea CI/CD runner |
-| `grafana_mcp/deploy.yml` | Miranda | Grafana MCP Server |
-| `jupyterlab/deploy.yml` | Puck | JupyterLab + OAuth2-Proxy |
-| `kernos/deploy.yml` | Caliban | Kernos MCP shell server |
-| `lobechat/deploy.yml` | Rosalind | LobeChat AI chat |
-| `rommie/deploy.yml` | Caliban | Rommie MCP server (Agent S GUI automation) |
-| `neo4j_mcp/deploy.yml` | Miranda | Neo4j MCP Server |
-| `freecad_mcp/deploy.yml` | Caliban | FreeCAD Robust MCP Server |
-| `rabbitmq/deploy.yml` | Oberon | RabbitMQ message queue |
-
-### Lifecycle Playbooks
-
-| Playbook | Purpose |
-|----------|---------|
-| `sandbox_up.yml` | Start all Uranian host containers |
-| `sandbox_down.yml` | Gracefully stop all containers |
-| `apt_update.yml` | Update packages on all hosts |
-| `site.yml` | Full deployment orchestration |
-
----
-
-## Data Flow Architecture
-
-### Observability Pipeline
-
-```
-All Hosts                      Prospero                         Alerts
-Alloy + Node Exporter     →   Prometheus + Loki + Grafana   →  AlertManager + Pushover
-collect metrics & logs         storage & visualisation           notifications
-```
-
-### Integration Points
-
-| Consumer | Provider | Connection |
-|----------|----------|-----------|
-| All LLM apps | Arke (Sycorax) | `http://sycorax.incus:25540` |
-| Open WebUI, Arke, Gitea, Nextcloud, LobeChat | PostgreSQL (Portia) | `portia.incus:5432` |
-| Neo4j MCP | Neo4j (Ariel) | `ariel.incus:7687` (Bolt) |
-| Mnemosyne | Neo4j (Umbriel) | `umbriel.incus:7687` (Bolt) — dedicated tenant |
-| MCP Switchboard | Docker API (Miranda) | `tcp://miranda.incus:2375` |
-| MCP Switchboard | RabbitMQ (Oberon) | `oberon.incus:5672` |
-| Kairos, Spelunker | RabbitMQ (Oberon) | `oberon.incus:5672` |
-| SMTP (all apps) | smtp4dev (Oberon) | `oberon.incus:22025` |
-| All hosts | Loki (Prospero) | `http://prospero.incus:3100` |
-| All hosts | Prometheus (Prospero) | `http://prospero.incus:9090` |
-
----
-
-## Important Notes
-
-⚠️ **Alloy Host Variables Required** — Every host with `alloy` in its `services` list must define `alloy_log_level` in `inventory/host_vars/<host>.incus.yml`. The playbook will fail with an undefined variable error if this is missing.
-
-⚠️ **Alloy Syslog Listeners Required for Docker Services** — Any Docker Compose service using the syslog logging driver must have a corresponding `loki.source.syslog` listener in the host's Alloy config template (`ansible/alloy/<hostname>/config.alloy.j2`). Missing listeners cause Docker containers to fail on start.
-
-⚠️ **Local Terraform State** — This project uses local Terraform state (no remote backend). Do not run `terraform apply` from multiple machines simultaneously.
-
-⚠️ **Nested Docker** — Docker runs inside Incus containers (nested), requiring `security.nesting = true` and `lxc.apparmor.profile=unconfined` AppArmor override on all Docker-enabled hosts.
-
-⚠️ **Deployment Order** — Prospero (observability) must be fully deployed before other hosts, as Alloy on every host pushes logs and metrics to `prospero.incus`. Run `pplg/deploy.yml` before `site.yml` on a fresh environment.

docs/regenerate_docs.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+# Regenerate Sphinx API reference for every Mnemosyne app, then build HTML.
+# Drives both local development and the CI pipeline.
+set -euo pipefail
+
+cd "$(dirname "$0")"
+
+APPS=(themis library llm_manager mcp_server)
+SOURCE_REF=source/reference/apps
+PACKAGE_ROOT=../mnemosyne
+
+make clean
+
+mkdir -p "$SOURCE_REF"
+
+# Per-app subdir so each app gets its own modules.rst (sphinx-apidoc
+# overwrites the file otherwise, leaving only the last app in the index).
+for app in "${APPS[@]}"; do
+    sphinx-apidoc \
+        --force \
+        --separate \
+        --module-first \
+        --output-dir "$SOURCE_REF/$app" \
+        "$PACKAGE_ROOT/$app" \
+        "$PACKAGE_ROOT/$app/migrations" \
+        "$PACKAGE_ROOT/$app/tests"
+done
+
+# Write a top-level apps.rst that toctree's every app's modules.rst.
+{
+    echo "Applications"
+    echo "============"
+    echo
+    echo ".. toctree::"
+    echo "   :maxdepth: 2"
+    echo
+    for app in "${APPS[@]}"; do
+        echo "   $app/modules"
+    done
+} > "$SOURCE_REF/index.rst"
+
+make html

docs/source/conf.py

@@ -0,0 +1,97 @@
+import os
+import sys
+import tomllib
+
+# The Django package lives at <repo>/mnemosyne/<inner mnemosyne>/. Adding the
+# outer mnemosyne/ directory to sys.path lets autodoc resolve every app
+# (themis, library, llm_manager, mcp_server) and the project settings module.
+sys.path.insert(0, os.path.abspath('../../mnemosyne'))
+
+os.environ.setdefault('DJANGO_SETTINGS_MODULE', 'mnemosyne.settings')
+
+# Load real .env if present (local dev). In CI there is none and that's fine —
+# settings.py provides a default for every env var it reads, so the import
+# succeeds either way.
+_repo_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..', '..'))
+_env_file = os.path.join(_repo_root, 'mnemosyne', '.env')
+if os.path.exists(_env_file):
+    with open(_env_file) as _f:
+        for _line in _f:
+            _line = _line.strip()
+            if not _line or _line.startswith('#') or '=' not in _line:
+                continue
+            _key, _val = _line.split('=', 1)
+            os.environ.setdefault(_key.strip(), _val.strip())
+
+import django  # noqa: E402
+
+django.setup()
+
+# Sphinx autodoc calls repr() on every class attribute it documents. Django's
+# QuerySet.__repr__ executes a SELECT against the database — which doc builds
+# have no business doing. Intercept object_description so QuerySet instances
+# render as a static string instead. Mnemosyne's themis app has at least one
+# DRF viewset with a class-level queryset attribute, so this matters.
+from django.db.models.query import QuerySet  # noqa: E402
+import sphinx.util.inspect as _sphinx_inspect  # noqa: E402
+
+_orig_object_description = _sphinx_inspect.object_description
+
+
+def _safe_object_description(obj, *args, **kwargs):
+    if isinstance(obj, QuerySet):
+        return f'<QuerySet [{obj.model.__name__}]>'
+    return _orig_object_description(obj, *args, **kwargs)
+
+
+_sphinx_inspect.object_description = _safe_object_description
+
+# ── Sphinx configuration ──────────────────────────────────────────────────
+project = 'Mnemosyne'
+copyright = '2026, Mnemosyne Team'
+author = 'Mnemosyne Team'
+
+with open(os.path.join(_repo_root, 'pyproject.toml'), 'rb') as _f:
+    release = tomllib.load(_f)['project']['version']
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.intersphinx',
+    'sphinx_autodoc_typehints',
+    'sphinxcontrib.httpdomain',
+    'sphinxcontrib.mermaid',
+    'myst_parser',
+]
+
+source_suffix = {'.rst': 'restructuredtext', '.md': 'markdown'}
+
+myst_enable_extensions = ['colon_fence', 'deflist', 'tasklist', 'attrs_inline']
+myst_heading_anchors = 4
+
+autodoc_default_options = {
+    'members': True,
+    'member-order': 'bysource',
+    'special-members': '__init__',
+    'undoc-members': True,
+    'exclude-members': '__weakref__',
+}
+autodoc_inherit_docstrings = False
+napoleon_use_ivar = True
+
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'django': ('https://docs.djangoproject.com/en/stable/',
+               'https://docs.djangoproject.com/en/stable/_objects/'),
+}
+
+html_theme = 'sphinx_rtd_theme'
+html_static_path = ['_static']
+html_theme_options = {
+    'navigation_depth': 4,
+    'collapse_navigation': False,
+    'sticky_navigation': True,
+    'includehidden': True,
+    'titles_only': False,
+}

docs/source/index.rst

@@ -0,0 +1,17 @@
+Mnemosyne Documentation
+=======================
+
+Content-type-aware, multimodal personal knowledge management system.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: API Reference
+
+   reference/apps/index
+
+Indices
+-------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/reference/apps/index.rst

@@ -0,0 +1,10 @@
+Applications
+============
+
+.. toctree::
+   :maxdepth: 2
+
+   themis/modules
+   library/modules
+   llm_manager/modules
+   mcp_server/modules

docs/source/reference/apps/library/library.admin.rst

@@ -0,0 +1,7 @@
+library.admin module
+====================
+
+.. automodule:: library.admin
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.api.rst

@@ -0,0 +1,18 @@
+library.api package
+===================
+
+.. automodule:: library.api
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.api.serializers
+   library.api.urls
+   library.api.views
+   library.api.workspaces

docs/source/reference/apps/library/library.api.serializers.rst

@@ -0,0 +1,7 @@
+library.api.serializers module
+==============================
+
+.. automodule:: library.api.serializers
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.api.urls.rst

@@ -0,0 +1,7 @@
+library.api.urls module
+=======================
+
+.. automodule:: library.api.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.api.views.rst

@@ -0,0 +1,7 @@
+library.api.views module
+========================
+
+.. automodule:: library.api.views
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.api.workspaces.rst

@@ -0,0 +1,7 @@
+library.api.workspaces module
+=============================
+
+.. automodule:: library.api.workspaces
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.apps.rst

@@ -0,0 +1,7 @@
+library.apps module
+===================
+
+.. automodule:: library.apps
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.content_types.rst

@@ -0,0 +1,7 @@
+library.content\_types module
+=============================
+
+.. automodule:: library.content_types
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.forms.rst

@@ -0,0 +1,7 @@
+library.forms module
+====================
+
+.. automodule:: library.forms
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.embed_collection.rst

@@ -0,0 +1,7 @@
+library.management.commands.embed\_collection module
+====================================================
+
+.. automodule:: library.management.commands.embed_collection
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.embed_item.rst

@@ -0,0 +1,7 @@
+library.management.commands.embed\_item module
+==============================================
+
+.. automodule:: library.management.commands.embed_item
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.embedding_status.rst

@@ -0,0 +1,7 @@
+library.management.commands.embedding\_status module
+====================================================
+
+.. automodule:: library.management.commands.embedding_status
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.load_library_types.rst

@@ -0,0 +1,7 @@
+library.management.commands.load\_library\_types module
+=======================================================
+
+.. automodule:: library.management.commands.load_library_types
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.rst

@@ -0,0 +1,21 @@
+library.management.commands package
+===================================
+
+.. automodule:: library.management.commands
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.management.commands.embed_collection
+   library.management.commands.embed_item
+   library.management.commands.embedding_status
+   library.management.commands.load_library_types
+   library.management.commands.search
+   library.management.commands.search_stats
+   library.management.commands.setup_neo4j_indexes

docs/source/reference/apps/library/library.management.commands.search.rst

@@ -0,0 +1,7 @@
+library.management.commands.search module
+=========================================
+
+.. automodule:: library.management.commands.search
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.search_stats.rst

@@ -0,0 +1,7 @@
+library.management.commands.search\_stats module
+================================================
+
+.. automodule:: library.management.commands.search_stats
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.commands.setup_neo4j_indexes.rst

@@ -0,0 +1,7 @@
+library.management.commands.setup\_neo4j\_indexes module
+========================================================
+
+.. automodule:: library.management.commands.setup_neo4j_indexes
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.management.rst

@@ -0,0 +1,15 @@
+library.management package
+==========================
+
+.. automodule:: library.management
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.management.commands

docs/source/reference/apps/library/library.metrics.rst

@@ -0,0 +1,7 @@
+library.metrics module
+======================
+
+.. automodule:: library.metrics
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.models.rst

@@ -0,0 +1,7 @@
+library.models module
+=====================
+
+.. automodule:: library.models
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.rst

@@ -0,0 +1,34 @@
+library package
+===============
+
+.. automodule:: library
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.api
+   library.management
+   library.services
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.admin
+   library.apps
+   library.content_types
+   library.forms
+   library.metrics
+   library.models
+   library.tasks
+   library.urls
+   library.utils
+   library.views

docs/source/reference/apps/library/library.services.chunker.rst

@@ -0,0 +1,7 @@
+library.services.chunker module
+===============================
+
+.. automodule:: library.services.chunker
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.concepts.rst

@@ -0,0 +1,7 @@
+library.services.concepts module
+================================
+
+.. automodule:: library.services.concepts
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.daedalus_s3.rst

@@ -0,0 +1,7 @@
+library.services.daedalus\_s3 module
+====================================
+
+.. automodule:: library.services.daedalus_s3
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.embedding_client.rst

@@ -0,0 +1,7 @@
+library.services.embedding\_client module
+=========================================
+
+.. automodule:: library.services.embedding_client
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.fusion.rst

@@ -0,0 +1,7 @@
+library.services.fusion module
+==============================
+
+.. automodule:: library.services.fusion
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.parsers.rst

@@ -0,0 +1,7 @@
+library.services.parsers module
+===============================
+
+.. automodule:: library.services.parsers
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.pipeline.rst

@@ -0,0 +1,7 @@
+library.services.pipeline module
+================================
+
+.. automodule:: library.services.pipeline
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.reranker.rst

@@ -0,0 +1,7 @@
+library.services.reranker module
+================================
+
+.. automodule:: library.services.reranker
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.rst

@@ -0,0 +1,25 @@
+library.services package
+========================
+
+.. automodule:: library.services
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   library.services.chunker
+   library.services.concepts
+   library.services.daedalus_s3
+   library.services.embedding_client
+   library.services.fusion
+   library.services.parsers
+   library.services.pipeline
+   library.services.reranker
+   library.services.search
+   library.services.text_utils
+   library.services.vision

docs/source/reference/apps/library/library.services.search.rst

@@ -0,0 +1,7 @@
+library.services.search module
+==============================
+
+.. automodule:: library.services.search
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.text_utils.rst

@@ -0,0 +1,7 @@
+library.services.text\_utils module
+===================================
+
+.. automodule:: library.services.text_utils
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.services.vision.rst

@@ -0,0 +1,7 @@
+library.services.vision module
+==============================
+
+.. automodule:: library.services.vision
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.tasks.rst

@@ -0,0 +1,7 @@
+library.tasks module
+====================
+
+.. automodule:: library.tasks
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.urls.rst

@@ -0,0 +1,7 @@
+library.urls module
+===================
+
+.. automodule:: library.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.utils.rst

@@ -0,0 +1,7 @@
+library.utils module
+====================
+
+.. automodule:: library.utils
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/library.views.rst

@@ -0,0 +1,7 @@
+library.views module
+====================
+
+.. automodule:: library.views
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/library/modules.rst

@@ -0,0 +1,7 @@
+library
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   library

docs/source/reference/apps/llm_manager/llm_manager.admin.rst

@@ -0,0 +1,7 @@
+llm\_manager.admin module
+=========================
+
+.. automodule:: llm_manager.admin
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.api.rst

@@ -0,0 +1,17 @@
+llm\_manager.api package
+========================
+
+.. automodule:: llm_manager.api
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager.api.serializers
+   llm_manager.api.urls
+   llm_manager.api.views

docs/source/reference/apps/llm_manager/llm_manager.api.serializers.rst

@@ -0,0 +1,7 @@
+llm\_manager.api.serializers module
+===================================
+
+.. automodule:: llm_manager.api.serializers
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.api.urls.rst

@@ -0,0 +1,7 @@
+llm\_manager.api.urls module
+============================
+
+.. automodule:: llm_manager.api.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.api.views.rst

@@ -0,0 +1,7 @@
+llm\_manager.api.views module
+=============================
+
+.. automodule:: llm_manager.api.views
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.apps.rst

@@ -0,0 +1,7 @@
+llm\_manager.apps module
+========================
+
+.. automodule:: llm_manager.apps
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.encryption.rst

@@ -0,0 +1,7 @@
+llm\_manager.encryption module
+==============================
+
+.. automodule:: llm_manager.encryption
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.forms.rst

@@ -0,0 +1,7 @@
+llm\_manager.forms module
+=========================
+
+.. automodule:: llm_manager.forms
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.management.commands.load_default_llm_models.rst

@@ -0,0 +1,7 @@
+llm\_manager.management.commands.load\_default\_llm\_models module
+==================================================================
+
+.. automodule:: llm_manager.management.commands.load_default_llm_models
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.management.commands.rst

@@ -0,0 +1,15 @@
+llm\_manager.management.commands package
+========================================
+
+.. automodule:: llm_manager.management.commands
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager.management.commands.load_default_llm_models

docs/source/reference/apps/llm_manager/llm_manager.management.rst

@@ -0,0 +1,15 @@
+llm\_manager.management package
+===============================
+
+.. automodule:: llm_manager.management
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager.management.commands

docs/source/reference/apps/llm_manager/llm_manager.models.rst

@@ -0,0 +1,7 @@
+llm\_manager.models module
+==========================
+
+.. automodule:: llm_manager.models
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.rst

@@ -0,0 +1,32 @@
+llm\_manager package
+====================
+
+.. automodule:: llm_manager
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager.api
+   llm_manager.management
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager.admin
+   llm_manager.apps
+   llm_manager.encryption
+   llm_manager.forms
+   llm_manager.models
+   llm_manager.services
+   llm_manager.tasks
+   llm_manager.urls
+   llm_manager.views

docs/source/reference/apps/llm_manager/llm_manager.services.rst

@@ -0,0 +1,7 @@
+llm\_manager.services module
+============================
+
+.. automodule:: llm_manager.services
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.tasks.rst

@@ -0,0 +1,7 @@
+llm\_manager.tasks module
+=========================
+
+.. automodule:: llm_manager.tasks
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.urls.rst

@@ -0,0 +1,7 @@
+llm\_manager.urls module
+========================
+
+.. automodule:: llm_manager.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/llm_manager.views.rst

@@ -0,0 +1,7 @@
+llm\_manager.views module
+=========================
+
+.. automodule:: llm_manager.views
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/llm_manager/modules.rst

@@ -0,0 +1,7 @@
+llm_manager
+===========
+
+.. toctree::
+   :maxdepth: 4
+
+   llm_manager

docs/source/reference/apps/mcp_server/mcp_server.admin.rst

@@ -0,0 +1,7 @@
+mcp\_server.admin module
+========================
+
+.. automodule:: mcp_server.admin
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.api.rst

@@ -0,0 +1,17 @@
+mcp\_server.api package
+=======================
+
+.. automodule:: mcp_server.api
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.api.serializers
+   mcp_server.api.teams
+   mcp_server.api.urls

docs/source/reference/apps/mcp_server/mcp_server.api.serializers.rst

@@ -0,0 +1,7 @@
+mcp\_server.api.serializers module
+==================================
+
+.. automodule:: mcp_server.api.serializers
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.api.teams.rst

@@ -0,0 +1,7 @@
+mcp\_server.api.teams module
+============================
+
+.. automodule:: mcp_server.api.teams
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.api.urls.rst

@@ -0,0 +1,7 @@
+mcp\_server.api.urls module
+===========================
+
+.. automodule:: mcp_server.api.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.apps.rst

@@ -0,0 +1,7 @@
+mcp\_server.apps module
+=======================
+
+.. automodule:: mcp_server.apps
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.auth.rst

@@ -0,0 +1,7 @@
+mcp\_server.auth module
+=======================
+
+.. automodule:: mcp_server.auth
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.context.rst

@@ -0,0 +1,7 @@
+mcp\_server.context module
+==========================
+
+.. automodule:: mcp_server.context
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.forms.rst

@@ -0,0 +1,7 @@
+mcp\_server.forms module
+========================
+
+.. automodule:: mcp_server.forms
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.management.commands.backfill_library_memberships.rst

@@ -0,0 +1,7 @@
+mcp\_server.management.commands.backfill\_library\_memberships module
+=====================================================================
+
+.. automodule:: mcp_server.management.commands.backfill_library_memberships
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.management.commands.create_mcp_token.rst

@@ -0,0 +1,7 @@
+mcp\_server.management.commands.create\_mcp\_token module
+=========================================================
+
+.. automodule:: mcp_server.management.commands.create_mcp_token
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.management.commands.rst

@@ -0,0 +1,17 @@
+mcp\_server.management.commands package
+=======================================
+
+.. automodule:: mcp_server.management.commands
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.management.commands.backfill_library_memberships
+   mcp_server.management.commands.create_mcp_token
+   mcp_server.management.commands.seed_signing_key

docs/source/reference/apps/mcp_server/mcp_server.management.commands.seed_signing_key.rst

@@ -0,0 +1,7 @@
+mcp\_server.management.commands.seed\_signing\_key module
+=========================================================
+
+.. automodule:: mcp_server.management.commands.seed_signing_key
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.management.rst

@@ -0,0 +1,15 @@
+mcp\_server.management package
+==============================
+
+.. automodule:: mcp_server.management
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.management.commands

docs/source/reference/apps/mcp_server/mcp_server.metrics.rst

@@ -0,0 +1,7 @@
+mcp\_server.metrics module
+==========================
+
+.. automodule:: mcp_server.metrics
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.models.rst

@@ -0,0 +1,7 @@
+mcp\_server.models module
+=========================
+
+.. automodule:: mcp_server.models
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.rst

@@ -0,0 +1,35 @@
+mcp\_server package
+===================
+
+.. automodule:: mcp_server
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.api
+   mcp_server.management
+   mcp_server.tools
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.admin
+   mcp_server.apps
+   mcp_server.auth
+   mcp_server.context
+   mcp_server.forms
+   mcp_server.metrics
+   mcp_server.models
+   mcp_server.server
+   mcp_server.teams
+   mcp_server.urls
+   mcp_server.views

docs/source/reference/apps/mcp_server/mcp_server.server.rst

@@ -0,0 +1,7 @@
+mcp\_server.server module
+=========================
+
+.. automodule:: mcp_server.server
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.teams.rst

@@ -0,0 +1,7 @@
+mcp\_server.teams module
+========================
+
+.. automodule:: mcp_server.teams
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.tools.discovery.rst

@@ -0,0 +1,7 @@
+mcp\_server.tools.discovery module
+==================================
+
+.. automodule:: mcp_server.tools.discovery
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.tools.health.rst

@@ -0,0 +1,7 @@
+mcp\_server.tools.health module
+===============================
+
+.. automodule:: mcp_server.tools.health
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.tools.rst

@@ -0,0 +1,17 @@
+mcp\_server.tools package
+=========================
+
+.. automodule:: mcp_server.tools
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server.tools.discovery
+   mcp_server.tools.health
+   mcp_server.tools.search

docs/source/reference/apps/mcp_server/mcp_server.tools.search.rst

@@ -0,0 +1,7 @@
+mcp\_server.tools.search module
+===============================
+
+.. automodule:: mcp_server.tools.search
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.urls.rst

@@ -0,0 +1,7 @@
+mcp\_server.urls module
+=======================
+
+.. automodule:: mcp_server.urls
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/mcp_server.views.rst

@@ -0,0 +1,7 @@
+mcp\_server.views module
+========================
+
+.. automodule:: mcp_server.views
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/source/reference/apps/mcp_server/modules.rst

@@ -0,0 +1,7 @@
+mcp_server
+==========
+
+.. toctree::
+   :maxdepth: 4
+
+   mcp_server

docs/source/reference/apps/themis/modules.rst

@@ -0,0 +1,7 @@
+themis
+======
+
+.. toctree::
+   :maxdepth: 4
+
+   themis

docs/source/reference/apps/themis/themis.adapters.rst

@@ -0,0 +1,7 @@
+themis.adapters module
+======================
+
+.. automodule:: themis.adapters
+   :members:
+   :show-inheritance:
+   :undoc-members: