fix: generated and promoted writes go through the brain root (#188, #158)

Writers that created or rewrote brain files by path followed symlinks:
- promote/reject: os.MkdirAll + os.WriteFile of the destination, then
  os.Remove of the raw source. Now PutRegular + brainfs.Remove; the source
  is kept when the write is refused.
- StampProvenanceFile (brain_edit's re-stamp): provenance.ApplyFile read
  and rewrote by path. Now ReadRegular + WriteRegular; ApplyFile, now
  unused, is removed.
- BuildWingIndex (_index.md) and wiki.RebuildIndex (wiki/index.md): now
  PutRegular.
- wiki.AppendLog (log.md) and AutoTunnel's fuzzy-candidate log
  (raw/tunnel-candidates-*.md): now AppendRegular; tunnel's fileExists,
  now unused, is removed.
- New brainfs.Remove: clean path, real parent, removes a final symlink
  itself, never its target.

brain_edit's own atomic rename was already refused behind a symlinked
directory by #187's read check; a guard test pins it.

Pipeline writes, BackfillRefs, the watcher's raw/ markers and the session
archive in cmd/server follow in a separate PR (#158).

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

ingestion/internal/api/provenance.go

@@ -1,6 +1,10 @@
 package api
 
 import (
+	"fmt"
+	"path/filepath"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/provenance"
 )
 
@@ -11,11 +15,62 @@ func StampProvenance(content, origin, writtenBy string) (string, error) {
 	return provenance.Apply(content, provenance.Stamp{Origin: origin, WrittenBy: writtenBy})
 }
 
-// StampProvenanceFile applies StampProvenance to a brain-relative note path.
+// StampProvenanceFile applies StampProvenance to a brain-relative note path,
+// read and rewritten through the brain root (hyperguild#158).
 func StampProvenanceFile(brainDir, relPath, origin, writtenBy string) error {
-	_, abs, err := resolveWithin(brainDir, relPath)
+	rel, _, err := resolveWithin(brainDir, relPath)
 	if err != nil {
 		return err
 	}
-	return provenance.ApplyFile(abs, provenance.Stamp{Origin: origin, WrittenBy: writtenBy})
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	b, err := bfs.ReadRegular(rel)
+	if err != nil {
+		return fmt.Errorf("read for provenance: %w", err)
+	}
+	out, err := provenance.Apply(string(b), provenance.Stamp{Origin: origin, WrittenBy: writtenBy})
+	if err != nil {
+		return err
+	}
+	if out == string(b) {
+		return nil
+	}
+	if err := bfs.WriteRegular(rel, []byte(out)); err != nil {
+		return fmt.Errorf("write provenance: %w", err)
+	}
+	return nil
+}
+
+// putBrainFile creates or replaces the file at abs (inside brainDir) through
+// the brain root, never through a symlinked directory or file (#188).
+func putBrainFile(brainDir, abs string, data []byte) (string, error) {
+	rel, err := filepath.Rel(brainDir, abs)
+	if err != nil {
+		return "", err
+	}
+	rel = filepath.ToSlash(rel)
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return "", fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	return rel, bfs.PutRegular(rel, data)
+}
+
+// removeBrainFile removes the file at abs (inside brainDir) through the
+// brain root.
+func removeBrainFile(brainDir, abs string) error {
+	rel, err := filepath.Rel(brainDir, abs)
+	if err != nil {
+		return err
+	}
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	return bfs.Remove(filepath.ToSlash(rel))
 }