fix(footnotes): strip bare definitions on rebuild; MCP full-doc + zip-import canonicalize tests (#228)

Review #6 (approve-with-comments) follow-ups:
1. canonicalize step 7 now strips bare footnoteDefinitions at ANY depth
   (stripFootnoteDefinitionsDeep), not just footnotesList, in BOTH copies. A
   definition hand-authored outside a list (e.g. nested in a callout via a
   raw-JSON write path) was left in place while a copy was also added to the
   rebuilt list -> duplicate, idempotent, self-perpetuating. Runs only in the
   rebuild path (after the lists are stripped); the fast-path / placement-keep
   branch is untouched. Added a shared-corpus case (bare def nested in a callout)
   to pin it in both mirrors.
2. markdown-clipboard: removed the dead top-level footnoteReference check in
   canonicalizePastedFootnotes (an inline atom is never a top-level slice child;
   only the descendants scan can find it).

Test coverage:
4. New MCP binding tests (full-doc-write-canonicalize.test.mjs): update_page_json
   and copy_page_content canonicalize the persisted full doc, asserted via a new
   `replacePage` seam (symmetric to the existing `mutatePage` seam) so no live
   collab socket is needed. Routed both writers through the seam.
5. New server spec (file-import-task.service.footnote-canonicalize.spec.ts): the
   zip-import path (processGenericImport) canonicalizes footnotes — real
   markdown->HTML->JSON via a real ImportService over a temp-dir .md file, DB trx
   stubbed to capture the persisted page content. FileImportTaskService had no
   spec before.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

apps/server/src/integrations/import/services/file-import-task.service.footnote-canonicalize.spec.ts

@@ -0,0 +1,150 @@
+// Importing FileImportTaskService transitively loads import-formatter.ts, which
+// imports the ESM-only @sindresorhus/slugify package (not in jest's transform
+// allowlist). slugify is irrelevant to the path under test, so it is mocked out
+// to keep the module graph loadable under ts-jest (mirrors the import.service spec).
+jest.mock('@sindresorhus/slugify', () => ({
+  __esModule: true,
+  default: (input: string) => String(input),
+}));
+// import-attachment.service.ts (loaded transitively for DI typing) imports the
+// ESM-only `p-limit` / `image-dimensions`; neither is exercised on the path under
+// test, so stub them so the module graph loads under ts-jest.
+jest.mock('p-limit', () => ({
+  __esModule: true,
+  default: () => (fn: any) => fn(),
+}));
+jest.mock('image-dimensions', () => ({
+  __esModule: true,
+  imageDimensionsFromData: () => undefined,
+}));
+
+import { promises as fs } from 'fs';
+import * as os from 'os';
+import * as path from 'path';
+import { FileImportTaskService } from './file-import-task.service';
+import { ImportService } from './import.service';
+
+/**
+ * Binding test for issue #228 / review #5: FileImportTaskService.processGenericImport
+ * is a NON-editor write path (markdownToHtml -> processHTML -> JSON, never runs
+ * footnoteSyncPlugin), so it canonicalizes footnotes before persisting. This pins
+ * that binding — the same one import.service has a spec for — which previously had
+ * NO spec at all.
+ *
+ * The markdown -> HTML -> ProseMirror conversion is REAL (a real ImportService,
+ * its createYdoc stubbed); the filesystem is a real temp dir with one .md file;
+ * the DB transaction is stubbed to capture the persisted page content.
+ */
+
+// Out-of-order references (c, a, b), a REUSED reference ([^a] twice), and an
+// ORPHAN definition ([^z], never referenced).
+const MARKDOWN = [
+  '# Title',
+  '',
+  'Body refs [^c] and [^a] and [^b] and again [^a].',
+  '',
+  '[^a]: note A',
+  '[^b]: note B',
+  '[^c]: note C',
+  '[^z]: orphan note',
+].join('\n');
+
+function footnoteListIds(content: any): string[] {
+  const list = (content?.content ?? []).find(
+    (n: any) => n.type === 'footnotesList',
+  );
+  return (list?.content ?? [])
+    .filter((n: any) => n.type === 'footnoteDefinition')
+    .map((n: any) => n.attrs?.id);
+}
+
+// A permissive chainable stub for the spaces lookup (selectFrom(...).select(...)
+// .where(...).executeTakeFirst()).
+function chainable(result: any): any {
+  const proxy: any = new Proxy(function () {}, {
+    get: (_t, prop) => {
+      if (prop === 'executeTakeFirst') return async () => result;
+      if (prop === 'execute') return async () => [];
+      return () => proxy;
+    },
+  });
+  return proxy;
+}
+
+describe('FileImportTaskService.processGenericImport — footnote canonicalization (#228)', () => {
+  it('orders footnotes by first reference, dedupes reuse, and drops orphans on zip import', async () => {
+    const extractDir = await fs.mkdtemp(path.join(os.tmpdir(), 'fit-canon-'));
+    await fs.writeFile(path.join(extractDir, 'note.md'), MARKDOWN, 'utf-8');
+
+    // Real ImportService for the html -> JSON conversion; stub the yjs encode.
+    const importService = new ImportService(
+      {} as any,
+      {} as any,
+      {} as any,
+      {} as any,
+    );
+    jest
+      .spyOn(importService as any, 'createYdoc')
+      .mockResolvedValue(Buffer.from([]) as any);
+
+    let captured: any = null;
+    const trx = {
+      insertInto: (table: string) => ({
+        values: (v: any) => {
+          if (table === 'pages') captured = v;
+          return { execute: async () => {} };
+        },
+      }),
+    };
+    const db: any = {
+      selectFrom: () => chainable({ slug: 'space-slug' }),
+      transaction: () => ({ execute: (fn: any) => fn(trx) }),
+    };
+
+    const importAttachmentService = {
+      processAttachments: async ({ html }: any) => html,
+    };
+    const backlinkRepo = { insertBacklink: jest.fn() };
+    const eventEmitter = { emit: jest.fn() };
+    const auditService = { logBatchWithContext: jest.fn() };
+
+    const pageService = { nextPagePosition: async () => 'a0' };
+
+    const service = new FileImportTaskService(
+      {} as any, // storageService
+      importService as any,
+      pageService as any,
+      backlinkRepo as any,
+      db,
+      importAttachmentService as any,
+      eventEmitter as any,
+      auditService as any,
+    );
+
+    const fileTask: any = {
+      id: 'task-1',
+      source: 'generic',
+      spaceId: 'space-1',
+      workspaceId: 'ws-1',
+      creatorId: 'user-1',
+    };
+
+    try {
+      await service.processGenericImport({ extractDir, fileTask });
+
+      expect(captured).toBeTruthy();
+      const content = captured.content;
+      // Reference order is c, a, b (NOT the markdown definition order a, b, c).
+      expect(footnoteListIds(content)).toEqual(['c', 'a', 'b']);
+      // Orphan [^z] dropped; reused [^a] collapses to one definition; one list.
+      expect(footnoteListIds(content)).not.toContain('z');
+      const lists = (content.content ?? []).filter(
+        (n: any) => n.type === 'footnotesList',
+      );
+      expect(lists).toHaveLength(1);
+      expect(footnoteListIds(content).filter((id) => id === 'a')).toHaveLength(1);
+    } finally {
+      await fs.rm(extractDir, { recursive: true, force: true });
+    }
+  });
+});