Fix packaging: ship the full backend tree (0.1.0:46)

The image COPY'd backend/server.py + a few subdirs but missed core_migrations.py,
backend/migrations/, and the Phase-1 modules (thesis_review/entity_merge/
entity_jobs). On the box the migrations never ran (tables absent) and those
endpoints 503'd ("Jobs unavailable"). Now COPY backend wholesale (.dockerignore
keeps __pycache__/data out). Bump to 0.1.0:46.

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

start9/0.4/Dockerfile

@@ -52,14 +52,13 @@ RUN pip install --no-cache-dir \
       mcp==1.2.0
 
 # ── Application source ──────────────────────────────────────────
-COPY backend/server.py        /app/backend/server.py
-COPY backend/email_integration /app/backend/email_integration
-# Phase-0 substrate: ingest pipeline (entity resolution + backfill) and the
-# CRM MCP server. Shipped alongside the web server so the one-time index build
-# and the (manually-run) MCP server can execute on the box where /data/crm.db
-# lives. See start9/0.4/INGEST_PACKAGING.md.
-COPY backend/ingest           /app/backend/ingest
-COPY backend/mcp              /app/backend/mcp
+# Whole backend tree: server.py + all top-level modules (core_migrations,
+# thesis_review, entity_merge, entity_jobs) + migrations/ + ingest/ + mcp/ +
+# email_integration/. Earlier piecemeal COPYs missed core_migrations.py, the
+# migrations/ dir, and the Phase-1 modules — so the schema migrations never ran
+# and the thesis / index-job endpoints 503'd ("Jobs unavailable") on the box.
+# .dockerignore keeps __pycache__ and data/ out of the context.
+COPY backend                  /app/backend
 COPY frontend                 /app/frontend
 
 # ── StartOS wrapper scripts ─────────────────────────────────────

start9/0.4/startos/utils.ts

@@ -10,8 +10,9 @@ export const PACKAGE_TITLE = 'Ten31 Database'
 //   * 0.1.0:41 (frontend persists auth across refreshes)
 //   * 0.1.0:42 (Gmail integration) / 0.1.0:43 (Gmail POST-body hotfix)
 //   * 0.1.0:44 (Phase-0 ingest + MCP server in image; build-index action)
-//   * Current:        0.1.0:45 (Phase-1 thesis system; dual approval; merge review; in-app index)
-export const PACKAGE_VERSION = '0.1.0:45'
+//   * 0.1.0:45 (Phase-1 thesis system; dual approval; merge review; in-app index)
+//   * Current:        0.1.0:46 (packaging fix: ship full backend so migrations run + endpoints work)
+export const PACKAGE_VERSION = '0.1.0:46'
 
 export const DATA_MOUNT_PATH = '/data'
 export const WEB_PORT = 8080

start9/0.4/startos/versions/index.ts

@@ -6,8 +6,9 @@ import { v_0_1_0_42 } from './v0.1.0.42'
 import { v_0_1_0_43 } from './v0.1.0.43'
 import { v_0_1_0_44 } from './v0.1.0.44'
 import { v_0_1_0_45 } from './v0.1.0.45'
+import { v_0_1_0_46 } from './v0.1.0.46'
 
 export const versionGraph = VersionGraph.of({
-  current: v_0_1_0_45,
-  other: [v_0_1_0_39, v_0_1_0_40, v_0_1_0_41, v_0_1_0_42, v_0_1_0_43, v_0_1_0_44],
+  current: v_0_1_0_46,
+  other: [v_0_1_0_39, v_0_1_0_40, v_0_1_0_41, v_0_1_0_42, v_0_1_0_43, v_0_1_0_44, v_0_1_0_45],
 })

start9/0.4/startos/versions/v0.1.0.46.ts

@@ -0,0 +1,29 @@
+import { VersionInfo } from '@start9labs/start-sdk'
+
+// Packaging fix for 0.1.0:45.
+//
+// 0.1.0:44/:45 shipped a Dockerfile that COPY'd backend/server.py and a few
+// subdirs piecemeal, but MISSED backend/core_migrations.py, the backend/migrations/
+// dir, and the Phase-1 modules (thesis_review/entity_merge/entity_jobs). Result on
+// the box: the in-app schema migrations never ran (the new tables were absent) and
+// the thesis / index-job endpoints returned 503 ("Jobs unavailable"). The index
+// build also could not run (canonical tables missing). This release COPYs the whole
+// backend tree, so the migrations run on boot and all endpoints work. No data
+// migration; the live /data volume is preserved.
+export const v_0_1_0_46 = VersionInfo.of({
+  version: '0.1.0:46',
+  releaseNotes: {
+    en_US: [
+      'Fix: the container image was missing the migration runner, the migrations',
+      'directory, and the Phase-1 backend modules, so the new tables never got',
+      'created and the thesis / index-job features were unavailable on the server.',
+      'The image now ships the full backend; migrations run on boot (additively —',
+      'your data is preserved) and the thesis, duplicate-review, and index actions',
+      'work.',
+    ].join(' '),
+  },
+  migrations: {
+    up: async () => {},
+    down: async () => {},
+  },
+})