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/notes/edit_redirect_test.go

@@ -0,0 +1,36 @@
+package notes
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// hyperguild#188/#173: brain_edit's atomic rename must not be redirected by
+// a symlinked directory inside the brain.
+func TestEditRefusesANoteBehindASymlinkedDirectory(t *testing.T) {
+	b := t.TempDir()
+	// Edit refuses a tree that is not the sync source before any path
+	// check, so the test needs a .git to reach the symlink refusal.
+	require.NoError(t, os.MkdirAll(filepath.Join(b, ".git"), 0o755))
+	victim := filepath.Join(b, "raw", "facts", "v.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
+	require.NoError(t, os.WriteFile(victim, []byte("old text\n"), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w"), 0o755))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(b, "wiki", "w", "alias")))
+	_, err := Edit(b, "wiki/w/alias/v.md", "old text", "new text", ScopeNotes)
+	assert.Error(t, err)
+	got, _ := os.ReadFile(victim)
+	assert.Equal(t, "old text\n", string(got))
+
+	real := filepath.Join(b, "wiki", "w", "facts", "r.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(real), 0o755))
+	require.NoError(t, os.WriteFile(real, []byte("old text\n"), 0o644))
+	_, err = Edit(b, "wiki/w/facts/r.md", "old text", "new text", ScopeNotes)
+	require.NoError(t, err, "positive control: a note in a real directory is edited")
+	got, _ = os.ReadFile(real)
+	assert.Equal(t, "new text\n", string(got))
+}