fix(git-sync): kill spurious marker-leaking conflict, concurrent-edit loss, flapping HEAD

Three more git-sync QA defects from the 2nd live pass on PR #119, plus a
callout-fidelity nit:

1. SPURIOUS conflict leaked raw markers into canonical main (root cause). On an
   ordinary round-trip the only difference between the docmost mirror (normalize-
   on-write) and a user's raw push is trailing/empty-line normalization, which made
   git's line-based docmost->main merge CONFLICT, and the wedge fix then committed
   the file WITH literal <<<<<<< / ======= / >>>>>>> markers onto main (git and the
   DB silently diverged for cycles). Fix: on a conflict, normalize trailing/empty
   lines on BOTH sides (showStage :2:/:3:) before comparing — a trailing-only diff
   is recognized as spurious and resolved to the clean normalized form. A GENUINE
   same-block conflict is auto-resolved to OURS (git wins, mirroring the live-doc
   3-way rule); the docmost side stays on the `docmost` branch + page history. Raw
   markers NEVER reach main again.

2. Concurrent UI<->git edit silently lost the UI side. The git->Docmost 3-way merge
   ran against a live Y.Doc that hadn't yet received the user's debounced in-flight
   edit, so git clean-applied (no conflict detected) and the edit vanished even on a
   different block. Fix: flush the pending debounced store before the merge so the
   in-flight edit is drained into the live doc first — a different-block edit is
   merged, a same-block one is detected and pinned to history (recoverable).

3. Smart-HTTP HEAD flapped to the read-only `docmost` mirror (~1/4 of clones). The
   engine transiently checks out `docmost` mid-pull and the host advertises whatever
   HEAD resolves to. Fix: VaultGit.pinHeadToMain(); the cycle restores HEAD->main in
   a finally; and the upload-pack ref advertisement is served HEAD-pinned under the
   per-space lock so it can never observe a mid-cycle HEAD.

4. (callout) clampCalloutType now mirrors the editor's GITHUB_ALERT_TYPE_MAP for
   non-schema aliases (tip->success, caution->danger, important->info) instead of
   flatly collapsing to info. The editor schema genuinely supports only the six
   banner types, so unknown types still fall back to info (by design).

Tests: deterministic real-git trailing-blank round-trip (no conflict, no markers,
in sync over 2 cycles) + genuine-conflict no-marker-leak; HEAD advertisement
stability; pre/post-flush concurrent-edit survival; serveReadAdvertisement lock
pin; widened callout-alias coverage. Engine vitest + server tsc + collaboration /
git-http / orchestrator specs all green.

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

apps/server/src/collaboration/collaboration.handler.git-sync.spec.ts

@@ -147,6 +147,86 @@ describe('CollaborationHandler.gitSyncWriteBody (owner-routed body write)', () =
     ]);
   });
 
+  it('FLUSHES the pending debounced store BEFORE merging so an in-flight edit survives (finding #2)', async () => {
+    // QA #119 finding #2: the 3-way merge must run against the latest live-doc
+    // state. A concurrent UI edit that is still in-flight (the store is debounced)
+    // must be drained into the live doc BEFORE git merges, or git clean-applies and
+    // the edit is silently dropped — even on a DIFFERENT block. Model the drain via
+    // the pending-store flush: when it runs, the in-flight block-0 edit lands.
+    const shared = new Y.Doc();
+    const frag = shared.getXmlFragment('default');
+    shared.transact(() => {
+      frag.insert(
+        0,
+        [
+          { text: 'alpha', id: 'p1' },
+          { text: 'beta', id: 'p2' },
+        ].map((s) => {
+          const el = new Y.XmlElement('paragraph');
+          el.setAttribute('id', s.id);
+          const t = new Y.XmlText();
+          t.insert(0, s.text);
+          el.insert(0, [t]);
+          return el;
+        }),
+      );
+    });
+
+    const order: string[] = [];
+    const debouncer = {
+      isDebounced: jest.fn(() => true),
+      executeNow: jest.fn(async () => {
+        order.push('flush');
+        // The in-flight client edit to block 0 only lands once the pending store
+        // is flushed (i.e. the event loop is drained) — BEFORE the merge.
+        shared.transact(() =>
+          ((frag.get(0) as Y.XmlElement).get(0) as Y.XmlText).insert(5, ' EDIT'),
+        );
+      }),
+    };
+    const openDirectConnection = jest.fn(async () => ({
+      transact: async (fn: (doc: Y.Doc) => void) => {
+        order.push('merge');
+        fn(shared);
+      },
+      disconnect: jest.fn(async () => undefined),
+    }));
+    const hocuspocus = { openDirectConnection, debouncer } as any;
+
+    const handler = new CollaborationHandler();
+    await handler.getHandlers(hocuspocus).gitSyncWriteBody('page.x', {
+      prosemirrorJson: pmDoc('alpha', 'beta2'), // git changes block 1
+      baseProsemirrorJson: pmDoc('alpha', 'beta'),
+      userId: 'svc-user',
+    });
+
+    // The flush ran, and it ran BEFORE the merge transaction.
+    expect(debouncer.executeNow).toHaveBeenCalledTimes(1);
+    expect(order).toEqual(['flush', 'merge']);
+    // Both the in-flight block-0 edit and git's block-1 change survive — the
+    // pre-flush bug would have produced ['alpha', 'beta2'] (UI edit dropped).
+    expect(texts(shared.getXmlFragment('default'))).toEqual([
+      'alpha EDIT',
+      'beta2',
+    ]);
+  });
+
+  it('does not flush when no store is pending (isDebounced false)', async () => {
+    const { hocuspocus, shared } = fakeHocuspocus([{ text: 'a', id: 'p1' }]);
+    const executeNow = jest.fn();
+    (hocuspocus as any).debouncer = {
+      isDebounced: jest.fn(() => false),
+      executeNow,
+    };
+    const handler = new CollaborationHandler();
+    await handler.getHandlers(hocuspocus).gitSyncWriteBody('page.x', {
+      prosemirrorJson: pmDoc('a', 'b'),
+      userId: 'svc-user',
+    });
+    expect(executeNow).not.toHaveBeenCalled();
+    expect(texts(shared.getXmlFragment('default'))).toEqual(['a', 'b']);
+  });
+
   it('crash-safe: a transform failure never opens the connection or mutates the live doc', async () => {
     const { hocuspocus, shared } = fakeHocuspocus([{ text: 'alpha', id: 'p1' }]);
     const before = texts(shared.getXmlFragment('default'));

apps/server/src/collaboration/collaboration.handler.ts

@@ -158,6 +158,24 @@ export class CollaborationHandler {
               )
             : null;
 
+        // CONCURRENT-EDIT FLUSH (QA #119, finding #2). The 3-way merge below runs
+        // against the LIVE Y.Doc, so a concurrent UI edit is only preserved if it
+        // is already part of that doc. A user's edit is debounced before it lands
+        // (the editor batches; the collab store is debounced up to 10s), so the
+        // merge could otherwise run against a PRE-EDIT doc: git would then
+        // clean-apply (no same-block conflict detected) and the in-flight UI edit
+        // — even on a DIFFERENT block — would be silently dropped.
+        //
+        // Flushing the pending debounced store here (a) drains the event loop so a
+        // just-arrived client Yjs update is applied to the live doc BEFORE we
+        // merge, and (b) persists the live doc so the merge baseline is current
+        // even on the doc-reload-from-DB path. After the flush the merge sees the
+        // latest state, so an edit on a different block is MERGED (not overwritten)
+        // and a genuine same-block edit is detected as a conflict -> the
+        // boundary-snapshot in PersistenceExtension pins it to page history
+        // (recoverable) instead of vanishing silently.
+        await this.flushPendingStore(hocuspocus, documentName);
+
         // actor:'git-sync' + the service user flow into PersistenceExtension
         // (lastUpdatedSource='git-sync', lastUpdatedById=userId).
         await this.withYdocConnection(
@@ -195,6 +213,33 @@ export class CollaborationHandler {
     };
   }
 
+  /**
+   * Flush any pending DEBOUNCED store for `documentName` so the live Y.Doc and the
+   * DB are current BEFORE a git-sync merge reads them (QA #119, finding #2 —
+   * concurrent UI edit silently lost). Mirrors the PersistenceExtension.onDisconnect
+   * flush: only acts when a store is actually pending (`isDebounced`), runs the
+   * SAME scheduled payload (`executeNow`, preserving the edit's context/actor), and
+   * never throws — a flush failure must not abort the git-sync write. Awaiting it
+   * also drains the event loop, so a client Yjs update sitting in the socket buffer
+   * is applied to the live doc before the merge transaction runs.
+   */
+  private async flushPendingStore(
+    hocuspocus: Hocuspocus,
+    documentName: string,
+  ): Promise<void> {
+    const debounceId = `onStoreDocument-${documentName}`;
+    try {
+      const debouncer = (hocuspocus as any)?.debouncer;
+      if (!debouncer?.isDebounced?.(debounceId)) return;
+      await debouncer.executeNow(debounceId);
+    } catch (err) {
+      this.logger.warn(
+        `git-sync pre-merge flush failed for ${documentName}: ` +
+          (err instanceof Error ? err.message : String(err)),
+      );
+    }
+  }
+
   async withYdocConnection(
     hocuspocus: Hocuspocus,
     documentName: string,

apps/server/src/collaboration/merge/yjs-body-merge.callout.spec.ts

@@ -152,8 +152,18 @@ describe('git-sync callout type fidelity (QA "callout type -> [!info]")', () =>
     });
   }
 
+  it('maps a known GitHub/Obsidian alias to the editor banner (tip -> success)', async () => {
+    // `tip` is not a schema callout type — it is an input alias the editor itself
+    // maps onto the supported set (GITHUB_ALERT_TYPE_MAP: tip -> success). git-sync
+    // mirrors that so the ingest lands on the closest banner instead of flatly info.
+    const content = editorPage('tip');
+    const gitContent = await gitRoundTrip(content);
+    const co = gitContent.find((b: any) => b.type === 'callout');
+    expect(co?.attrs?.type).toBe('success');
+  });
+
   it('flattens a genuinely unknown callout type to info', async () => {
-    const content = editorPage('tip'); // not an editor-canonical type
+    const content = editorPage('banana'); // not a type and not a known alias
     const gitContent = await gitRoundTrip(content);
     const co = gitContent.find((b: any) => b.type === 'callout');
     expect(co?.attrs?.type).toBe('info');