fix: creating and generated writes go through the brain root (#188, #158 part A) (#189)

New brainfs PutRegular (create or replace), CreateRegular (create only), AppendRegular, Remove and RealParent: missing parents created one component at a time through the root, every existing component a real directory, new files created with O_EXCL and confirmed before writing. brain_write, promote/reject (O_EXCL create, source kept on refusal), StampProvenanceFile, BuildWingIndex, RebuildIndex, AppendLog and the tunnel candidate log use them; provenance.ApplyFile removed.

Fixes #188. Refs #158. Adversarial review: BLOCKED, BLOCKED, PASS.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.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 +15,61 @@ 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
+}
+
+// createBrainFile creates the file at abs (inside brainDir) through the
+// brain root and fails if anything is already there.
+func createBrainFile(brainDir, abs string, data []byte) 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.CreateRegular(filepath.ToSlash(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))
 }