fix: pipeline, backfill, watcher and archive writes go through the brain root (#158 part B)

The remaining writers created or rewrote brain files by path:
- pipeline buildAndWrite: os.MkdirAll + os.WriteFile of every page.
- BackfillRefs: os.WriteFile of each concept page; a page swapped for a
  symlink after the read was written through (the race test overwrote an
  in-brain target before this change).
- watcher: the raw/processed and raw/failed archive copies (os.Create),
  the .processed/.failed markers and the log.md entry (os.OpenFile).
- cmd/server: the claude-session archive.

All now go through brainfs PutRegular/AppendRegular (new package-level
PutFile/AppendFile for one-off writers: the watcher's call-site lint bans
.Open calls in that file so raw/ reads stay on OpenRegular).

Stacked on #189 (needs PutRegular/AppendRegular).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

ingestion/internal/pipeline/root_test.go

@@ -165,3 +165,28 @@ func TestBackfillRefsDoesNotCopyAPageSwappedInBehindASymlink(t *testing.T) {
 	require.Contains(t, read(), "[[s|S]]", "positive control: the regular page gets the source ref")
 	brainfstest.AssertNoLeakFrom(t, page, inside, target, 3*time.Second, read)
 }
+
+// hyperguild#158: BackfillRefs read a regular concept page, a symlink could
+// be swapped in, and os.WriteFile then followed it and overwrote the link's
+// target. The target is not restored between rounds here, so any
+// write-through shows.
+func TestBackfillRefsNeverWritesThroughAPageSwappedForASymlink(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "s.md"), []byte("---\ntitle: S\n---\n[[c|C]]\n"), 0o644))
+	page := filepath.Join(brain, "wiki", "concepts", "c.md")
+	target := filepath.Join(brain, "raw", "secret.md")
+	require.NoError(t, os.WriteFile(target, []byte("untouched"), 0o644))
+	inside := "---\ntitle: C\n---\nbody\n"
+	require.NoError(t, os.WriteFile(page, []byte(inside), 0o644))
+	brainfstest.StartSwap(t, page, inside, target, false)
+	ok := 0
+	for deadline := time.Now().Add(2 * time.Second); time.Now().Before(deadline); {
+		if _, err := BackfillRefs(context.Background(), brain); err == nil {
+			ok++
+		}
+	}
+	got, _ := os.ReadFile(target)
+	assert.Equal(t, "untouched", string(got), "BackfillRefs wrote through a swapped-in symlink")
+	assert.Positive(t, ok, "positive control: some backfills ran")
+}