fix(footnotes): address PR #232 review — fragment-safe canonicalization, plugin placement parity, dead-code removal (#228)

Must-fix:
- Move canonicalizeFootnotes OUT of parseProsemirrorContent. It now runs only
  on FULL writes (createPage, updatePageContent operation==='replace'), never on
  an append/prepend fragment (a fragment would lose definition-only footnotes or
  synthesize a bogus empty list). Add a server binding spec.
- Match the live plugin's list PLACEMENT: a single already-canonical
  footnotesList is left exactly where it sits (the plugin never repositions a
  sole correct list), so the first write no longer reorders content that follows
  the list. Applied to BOTH the editor-ext copy and the MCP mirror; pinned by a
  shared golden corpus case with content after the list.
- Fix MCP tool count 38 -> 39 (README x3, AGENTS.md) and the transformJs param
  help (add canonicalizeFootnotes/insertInlineFootnote).

Simplifications:
- Remove the dead duplicate re-id mechanism (deriveFootnoteId/suffix/occurrence)
  from the PURE canonicalizer in both copies — references are never renamed, so
  the derived ids were never requested; first-wins-drop is the real behaviour.
  This also makes the editor-ext footnote-util note about "no cross-package copy"
  true again.
- Remove the sentinel round-trip in insertInlineFootnote: a generalized
  insertNodesAfterAnchor core inserts the footnoteReference node directly.
- Drop the redundant per-definition deep clone in step 4 (shallow id-normalizing
  copy; out is already deep-cloned).

Docs / architecture:
- Correct the editor-ext copy's "It exists because…" header to its real
  consumers (server import, page.service create/update, client paste).
- Note markdownToProseMirror reuse for create/update comment in collaboration.ts.
- A: shared golden JSON corpus exercised by BOTH the editor-ext copy and the MCP
  mirror (footnote-corpus.ts / .mjs) so "the two copies behave identically" is
  checkable.
- C: split the MCP canonicalizer into a pure mirror + footnote-authoring.ts.
- B: import services persist via a different path, so left one-line consolidation
  comments at the call sites rather than folding (does not fall out cleanly).

Tests: insertFootnote wrapper guards + docmost_transform dryRun auto-canonicalize
(MCP mock), page.service create/update + append/prepend binding (server jest),
shared corpus incl. nested-container reference.

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

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

@@ -504,6 +504,9 @@ export class FileImportTaskService {
             // zip-imported page's footnotes are reference-ordered, deduped, and
             // orphan-free like the editor's invariant (issue #228). Pure +
             // idempotent + shape-safe; a footnote-free doc is unchanged.
+            // (Future consolidation, architecture B: like import.service, this
+            // path persists directly rather than via PageService — a shared
+            // "prepare JSON for persist" helper would centralize this call.)
             const prosemirrorJson = canonicalizeFootnotes(extractedJson);
 
             const insertablePage: InsertablePage = {

apps/server/src/integrations/import/services/import.service.ts

@@ -91,6 +91,10 @@ export class ImportService {
     // retains orphan definitions, and is not deduped. Canonicalize before
     // persisting so the stored page matches the editor's invariant (issue #228).
     // Pure + idempotent + shape-safe: a doc with no footnotes is unchanged.
+    // (Future consolidation, architecture B: this import path persists directly
+    // via pageRepo.insertPage rather than through PageService.createPage, so the
+    // canonicalize call lives here; folding both into one "prepare JSON for
+    // persist" helper is a sensible follow-up.)
     const prosemirrorJson = canonicalizeFootnotes(extracted.prosemirrorJson);
 
     const pageTitle = title || fileName;