fix: bootstrap fresh alpha silo

hub/package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "@paradigm/hub",
-  "version": "0.0.3",
+  "version": "0.0.4",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@paradigm/hub",
-      "version": "0.0.3",
+      "version": "0.0.4",
       "dependencies": {
         "@anthropic-ai/claude-agent-sdk": "^0.3.202",
         "@fastify/cookie": "^11.0.2",

hub/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@paradigm/hub",
-  "version": "0.0.3",
+  "version": "0.0.4",
   "private": true,
   "type": "module",
   "engines": {

hub/src/deployment/bootstrap-silo.ts

@@ -49,6 +49,7 @@ export async function bootstrapAlphaSilo(
   } = {},
 ): Promise<AlphaSiloBootstrapResult> {
   const normalized = validateInput(input);
+  await removePristineLegacyMigrationOrganization(prisma);
   const existing = await loadExistingSilo(prisma, normalized.organization.id, normalized.owner.openId);
   let initialized = false;
   let ownerUserId: string;
@@ -113,6 +114,63 @@ export async function bootstrapAlphaSilo(
   };
 }
 
+const LEGACY_MIGRATION_ORGANIZATION = {
+  id: "org_default",
+  slug: "legacy-default",
+  name: "Legacy Default Organization",
+  inboxId: "folder_inbox_2b99350e0db97ad0cbcb55c20ee8bafa",
+} as const;
+
+/**
+ * A fresh database still receives the compatibility Organization inserted by
+ * the tenant-root migration, plus its later default settings and Inbox. An
+ * Alpha Silo bootstrap may replace only that exact, otherwise-unused scaffold.
+ * Any tenant data or shape drift remains a hard manual-repair error.
+ */
+async function removePristineLegacyMigrationOrganization(prisma: PrismaClient): Promise<void> {
+  await prisma.$transaction(async (tx) => {
+    const organization = await tx.organization.findUnique({
+      where: { id: LEGACY_MIGRATION_ORGANIZATION.id },
+      include: {
+        memberships: { take: 1, select: { id: true } },
+        projects: { take: 1, select: { id: true } },
+        teams: { take: 1, select: { id: true } },
+        externalDirectoryConnections: { take: 1, select: { id: true } },
+        providerConnections: { take: 1, select: { id: true } },
+        feishuApplicationConnection: { select: { id: true } },
+        auditEntries: { take: 1, select: { id: true } },
+        projectSettings: true,
+        folders: {
+          take: 2,
+          select: { id: true, parentId: true, name: true, sortKey: true, archivedAt: true },
+        },
+      },
+    });
+    if (organization === null) return;
+    const pristine =
+      organization.slug === LEGACY_MIGRATION_ORGANIZATION.slug &&
+      organization.name === LEGACY_MIGRATION_ORGANIZATION.name &&
+      organization.status === "ACTIVE" &&
+      organization.memberships.length === 0 &&
+      organization.projects.length === 0 &&
+      organization.teams.length === 0 &&
+      organization.externalDirectoryConnections.length === 0 &&
+      organization.providerConnections.length === 0 &&
+      organization.feishuApplicationConnection === null &&
+      organization.auditEntries.length === 0 &&
+      organization.projectSettings?.membersCanCreateProjects === true &&
+      organization.folders.length === 1 &&
+      organization.folders[0]?.id === LEGACY_MIGRATION_ORGANIZATION.inboxId &&
+      organization.folders[0].parentId === null &&
+      organization.folders[0].name === "Inbox" &&
+      organization.folders[0].sortKey === "000000" &&
+      organization.folders[0].archivedAt === null;
+    if (pristine) {
+      await tx.organization.delete({ where: { id: organization.id } });
+    }
+  });
+}
+
 async function ensureBootstrapTeams(
   prisma: PrismaClient,
   organizationId: string,

hub/test/integration/silo-bootstrap.test.ts

@@ -18,6 +18,21 @@ const input = {
 describe("Alpha Silo bootstrap", () => {
   beforeEach(async () => {
     await prisma.$executeRawUnsafe(`TRUNCATE TABLE "Organization" RESTART IDENTITY CASCADE`);
+    await prisma.organization.create({
+      data: {
+        id: "org_default",
+        slug: "legacy-default",
+        name: "Legacy Default Organization",
+        projectSettings: { create: { membersCanCreateProjects: true } },
+        folders: {
+          create: {
+            id: "folder_inbox_2b99350e0db97ad0cbcb55c20ee8bafa",
+            name: "Inbox",
+            sortKey: "000000",
+          },
+        },
+      },
+    });
   });
 
   afterAll(async () => {
@@ -54,4 +69,21 @@ describe("Alpha Silo bootstrap", () => {
     });
     await expect(requireSiloOrganization(prisma, "org_other")).rejects.toThrow("Silo Organization mismatch");
   });
+
+  it("does not delete a legacy migration Organization that contains tenant data", async () => {
+    await prisma.project.create({
+      data: {
+        organizationId: "org_default",
+        folderId: "folder_inbox_2b99350e0db97ad0cbcb55c20ee8bafa",
+        name: "Legacy Project",
+        workspaceDir: "legacy-project",
+      },
+    });
+
+    await expect(bootstrapAlphaSilo(prisma, testSecretEnvelope, input, {
+      feishu: async () => {},
+      provider: async () => {},
+    })).rejects.toThrow("bootstrap database is not the configured single-Organization Silo");
+    await expect(prisma.organization.findUnique({ where: { id: "org_default" } })).resolves.not.toBeNull();
+  });
 });