test(tunnel): pin the raced read, the walk error and the _index.md skip (#174)

Review round 1 on PR #186:

- The swap test's static note had the same title as the raced note, so
  the harness's "inside was read" floor passed without reading r.md
  (skipping r.md stayed green). The static note now has its own title.
- An unreadable directory under wiki/ reaches the walk-error path, and
  swallowing that error stayed green. New test asserts the error.
- The FIFO test now runs with and without a writer held open.
- _index.md skip had no test; new test.
- index.go: the double blank line left by removing readTitleAndCreated.

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

ingestion/go.mod

@@ -68,7 +68,7 @@ require (
 	github.com/segmentio/asm v1.2.0 // indirect
 	golang.org/x/crypto v0.51.0 // indirect
 	golang.org/x/sync v0.21.0 // indirect
-	golang.org/x/sys v0.45.0
+	golang.org/x/sys v0.45.0 // indirect
 	golang.org/x/text v0.39.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1
 )

ingestion/internal/api/handler.go

@@ -12,7 +12,6 @@ import (
 	"time"
 
 	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/claim"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/pipeline"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/search"
@@ -228,22 +227,14 @@ func writeHallNote(brainDir string, opts WriteNoteOptions) (string, error) {
 	// The directory is created only once the note is known to be writable:
 	// a refused write leaves nothing behind, not even an empty hall dir
 	// (brain#21; provenance refusal joins the envelope refusal here).
-	// Created through the brain root, never through a symlinked wing or
-	// hall directory (hyperguild#188).
-	rel, err := filepath.Rel(brainDir, dest)
-	if err != nil {
-		return "", fmt.Errorf("note path: %w", err)
+	if err := os.MkdirAll(filepath.Dir(dest), 0o755); err != nil {
+		return "", fmt.Errorf("create hall dir: %w", err)
 	}
-	rel = filepath.ToSlash(rel)
-	bfs, err := brainfs.Open(brainDir)
-	if err != nil {
-		return "", fmt.Errorf("open brain: %w", err)
-	}
-	defer func() { _ = bfs.Close() }()
-	if err := bfs.PutRegular(rel, []byte(final)); err != nil {
+	if err := os.WriteFile(dest, []byte(final), 0o644); err != nil {
 		return "", fmt.Errorf("write: %w", err)
 	}
-	return rel, nil
+	rel, _ := filepath.Rel(brainDir, dest)
+	return filepath.ToSlash(rel), nil
 }
 
 // scalarValues flattens frontmatter fields to key -> scalar value for

ingestion/internal/api/promote.go

@@ -127,18 +127,18 @@ func PromoteNote(brainDir string, opts PromoteOptions) (string, error) {
 	}
 	fm.set("promoted_at", now)
 
-	// Write-then-delete: the source survives any write failure. Both go
-	// through the brain root (hyperguild#188).
+	if err := os.MkdirAll(filepath.Dir(dest), 0o755); err != nil {
+		return "", fmt.Errorf("create wing dir: %w", err)
+	}
+	// Write-then-delete: the source survives any write failure.
 	promoted, err := StampProvenance(fm.render()+body, opts.Origin, opts.WrittenBy)
 	if err != nil {
 		return "", err
 	}
-	// Created with O_EXCL: a note that appeared after the collision check
-	// above is never overwritten.
-	if err := createBrainFile(brainDir, dest, []byte(promoted)); err != nil {
+	if err := os.WriteFile(dest, []byte(promoted), 0o644); err != nil {
 		return "", fmt.Errorf("write promoted note: %w", err)
 	}
-	if err := removeBrainFile(brainDir, src); err != nil {
+	if err := os.Remove(src); err != nil {
 		return "", fmt.Errorf("promoted note written but source removal failed: %w", err)
 	}
 
@@ -196,12 +196,14 @@ func RejectNote(brainDir string, opts RejectOptions) (string, error) {
 		fm.set("reject_reason", opts.Reason)
 	}
 
-	// Write-then-delete: the source survives any write failure. Both go
-	// through the brain root (hyperguild#188).
-	if err := createBrainFile(brainDir, dest, []byte(fm.render()+body)); err != nil {
+	if err := os.MkdirAll(filepath.Dir(dest), 0o755); err != nil {
+		return "", fmt.Errorf("create rejected dir: %w", err)
+	}
+	// Write-then-delete: the source survives any write failure.
+	if err := os.WriteFile(dest, []byte(fm.render()+body), 0o644); err != nil {
 		return "", fmt.Errorf("write rejected note: %w", err)
 	}
-	if err := removeBrainFile(brainDir, src); err != nil {
+	if err := os.Remove(src); err != nil {
 		return "", fmt.Errorf("rejected note written but source removal failed: %w", err)
 	}
 

ingestion/internal/api/promote_redirect_test.go

@@ -1,87 +0,0 @@
-package api_test
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/api"
-)
-
-// hyperguild#188: promote and reject wrote the destination with
-// os.MkdirAll + os.WriteFile by path, so a symlinked wing (promote) or a
-// symlinked raw/rejected (reject) redirected the note; the raw source was
-// then removed.
-func TestPromoteAndRejectRefuseASymlinkedDestinationDirectory(t *testing.T) {
-	brain := t.TempDir()
-	outside := t.TempDir()
-	raw := filepath.Join(brain, "raw")
-	require.NoError(t, os.MkdirAll(raw, 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(raw, "2026-10-05-n.md"), []byte("---\ntitle: n\n---\nbody\n"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(outside, filepath.Join(brain, "wiki", "lw")))
-	require.NoError(t, os.Symlink(outside, filepath.Join(raw, "rejected")))
-
-	_, err := api.PromoteNote(brain, api.PromoteOptions{Filename: "2026-10-05-n.md", Wing: "lw", Hall: "facts"})
-	assert.Error(t, err)
-	_, err = api.RejectNote(brain, api.RejectOptions{Filename: "2026-10-05-n.md"})
-	assert.Error(t, err)
-	ents, _ := os.ReadDir(outside)
-	assert.Empty(t, ents, "a note was written outside the brain")
-	_, err = os.Stat(filepath.Join(raw, "2026-10-05-n.md"))
-	assert.NoError(t, err, "the raw source is kept when the write is refused")
-
-	require.NoError(t, os.Remove(filepath.Join(raw, "rejected")))
-	_, err = api.PromoteNote(brain, api.PromoteOptions{Filename: "2026-10-05-n.md", Wing: "w", Hall: "facts"})
-	require.NoError(t, err, "positive control: promote into a real wing")
-}
-
-// StampProvenanceFile read and rewrote the note by path (provenance.ApplyFile).
-func TestStampProvenanceFileRefusesANoteBehindASymlinkedDirectory(t *testing.T) {
-	brain := t.TempDir()
-	victim := filepath.Join(brain, "raw", "facts", "v.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
-	require.NoError(t, os.WriteFile(victim, []byte("---\ntitle: v\n---\nuntouched\n"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki", "w"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(brain, "wiki", "w", "alias")))
-	assert.Error(t, api.StampProvenanceFile(brain, "wiki/w/alias/v.md", "static", "x"))
-	got, _ := os.ReadFile(victim)
-	assert.Equal(t, "---\ntitle: v\n---\nuntouched\n", string(got))
-
-	real := filepath.Join(brain, "wiki", "w", "facts", "r.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(real), 0o755))
-	require.NoError(t, os.WriteFile(real, []byte("---\ntitle: r\n---\nbody\n"), 0o644))
-	require.NoError(t, api.StampProvenanceFile(brain, "wiki/w/facts/r.md", "static", "x"), "positive control")
-	got, _ = os.ReadFile(real)
-	assert.Contains(t, string(got), "written_by: x")
-}
-
-// The same through an in-brain symlinked wing and raw/rejected, which
-// os.Root alone would follow.
-func TestPromoteAndRejectRefuseAnInBrainSymlinkedDestinationDirectory(t *testing.T) {
-	brain := t.TempDir()
-	raw := filepath.Join(brain, "raw")
-	require.NoError(t, os.MkdirAll(raw, 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(raw, "2026-10-05-n.md"), []byte("---\ntitle: n\n---\nbody\n"), 0o644))
-	target := filepath.Join(brain, "archive")
-	require.NoError(t, os.MkdirAll(target, 0o755))
-	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "archive"), filepath.Join(brain, "wiki", "lw")))
-	require.NoError(t, os.Symlink(filepath.Join("..", "archive"), filepath.Join(raw, "rejected")))
-
-	_, err := api.PromoteNote(brain, api.PromoteOptions{Filename: "2026-10-05-n.md", Wing: "lw", Hall: "facts"})
-	assert.Error(t, err)
-	_, err = api.RejectNote(brain, api.RejectOptions{Filename: "2026-10-05-n.md"})
-	assert.Error(t, err)
-	ents, _ := os.ReadDir(target)
-	assert.Empty(t, ents, "a note was written at the in-brain link's target")
-	_, err = os.Stat(filepath.Join(raw, "2026-10-05-n.md"))
-	assert.NoError(t, err, "the raw source is kept")
-
-	require.NoError(t, os.Remove(filepath.Join(raw, "rejected")))
-	_, err = api.RejectNote(brain, api.RejectOptions{Filename: "2026-10-05-n.md"})
-	require.NoError(t, err, "positive control: reject into a real raw/rejected")
-}

ingestion/internal/api/provenance.go

@@ -1,10 +1,6 @@
 package api
 
 import (
-	"fmt"
-	"path/filepath"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/provenance"
 )
 
@@ -15,61 +11,11 @@ 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,
-// read and rewritten through the brain root (hyperguild#158).
+// StampProvenanceFile applies StampProvenance to a brain-relative note path.
 func StampProvenanceFile(brainDir, relPath, origin, writtenBy string) error {
-	rel, _, err := resolveWithin(brainDir, relPath)
+	_, abs, err := resolveWithin(brainDir, relPath)
 	if err != nil {
 		return err
 	}
-	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))
+	return provenance.ApplyFile(abs, provenance.Stamp{Origin: origin, WrittenBy: writtenBy})
 }

ingestion/internal/api/readnote_root_test.go

@@ -23,13 +23,6 @@ func TestReadNoteRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
 	_, body, _, err := api.ReadNote(brain, "wiki/w/facts/leak.md")
 	assert.Error(t, err)
 	assert.NotContains(t, body, brainfstest.Sentinel)
-	// A link to a file elsewhere in the brain: os.Root allows it, only the
-	// regular-file check refuses it (hyperguild#171).
-	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
-	_, body, _, err = api.ReadNote(brain, "wiki/w/facts/inlink.md")
-	assert.Error(t, err)
-	assert.NotContains(t, body, brainfstest.Sentinel)
 
 	p := filepath.Join(facts, "r.md")
 	require.NoError(t, os.WriteFile(p, []byte("---\nx: y\n---\ninside"), 0o644))
@@ -46,7 +39,5 @@ func TestReadNoteRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
 		return s
 	}
 	brainfstest.AssertNoLeak(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, read)
-	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	brainfstest.AssertNoLeakFrom(t, p, "---\nx: y\n---\ninside", inBrain, 1500*time.Millisecond, read)
 	brainfstest.AssertNoHang(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
 }

ingestion/internal/api/update_redirect_test.go

@@ -1,36 +0,0 @@
-package api_test
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/api"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
-)
-
-// hyperguild#173: a directory symlink inside wiki/ that points elsewhere in
-// the brain redirected brain_update's write (os.Root follows in-root
-// intermediate symlinks). Every directory above the note must be real.
-func TestUpdateNoteRefusesANoteBehindASymlinkedDirectory(t *testing.T) {
-	brain := t.TempDir()
-	victim := filepath.Join(brain, "raw", "facts", "v.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
-	require.NoError(t, os.WriteFile(victim, []byte("---\ntitle: v\n---\nuntouched\n"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki", "w"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(brain, "wiki", "w", "alias")))
-
-	_, _, _, err := api.UpdateNote(brain, api.UpdateNoteOptions{Path: "wiki/w/alias/v.md", Content: "replaced"})
-	assert.ErrorIs(t, err, brainfs.ErrNotRegular)
-	got, _ := os.ReadFile(victim)
-	assert.Contains(t, string(got), "untouched")
-
-	real := filepath.Join(brain, "wiki", "w", "facts", "r.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(real), 0o755))
-	require.NoError(t, os.WriteFile(real, []byte("---\ntitle: r\n---\nold\n"), 0o644))
-	_, _, _, err = api.UpdateNote(brain, api.UpdateNoteOptions{Path: "wiki/w/facts/r.md", Content: "new"})
-	require.NoError(t, err, "positive control: a note in a real directory is updated")
-}

ingestion/internal/api/write_redirect_test.go

@@ -1,43 +0,0 @@
-package api_test
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/api"
-)
-
-// hyperguild#188: brain_write created a new note with os.MkdirAll +
-// os.WriteFile by path, so a symlinked wing directory redirected the note
-// elsewhere in the brain or outside it.
-func TestWriteNoteRefusesASymlinkedWing(t *testing.T) {
-	for name, target := range map[string]func(t *testing.T, brain string) string{
-		"in-brain": func(t *testing.T, brain string) string {
-			require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw"), 0o755))
-			return filepath.Join("..", "raw")
-		},
-		"outside": func(t *testing.T, _ string) string { return t.TempDir() },
-	} {
-		t.Run(name, func(t *testing.T) {
-			brain := t.TempDir()
-			require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki"), 0o755))
-			link := target(t, brain)
-			require.NoError(t, os.Symlink(link, filepath.Join(brain, "wiki", "lw")))
-			_, err := api.WriteNote(brain, api.WriteNoteOptions{Wing: "lw", Hall: "facts", Filename: "n", Content: "learning"})
-			assert.Error(t, err)
-			resolved := link
-			if !filepath.IsAbs(resolved) {
-				resolved = filepath.Join(brain, "wiki", link)
-			}
-			_, serr := os.Stat(filepath.Join(resolved, "facts"))
-			assert.True(t, os.IsNotExist(serr), "a hall was created at the link's target")
-
-			_, err = api.WriteNote(brain, api.WriteNoteOptions{Wing: "w", Hall: "facts", Filename: "n", Content: "learning"})
-			require.NoError(t, err, "positive control: a real wing is written")
-		})
-	}
-}

ingestion/internal/brain/index.go

@@ -7,6 +7,8 @@ import (
 	"fmt"
 	"io"
 	"io/fs"
+	"os"
+	"path/filepath"
 	"sort"
 	"strings"
 	"time"
@@ -30,6 +32,7 @@ func BuildWingIndex(brainDir, wing string) error {
 	if w == "" {
 		return fmt.Errorf("invalid wing %q", wing)
 	}
+	wingDir := filepath.Join(brainDir, "wiki", w)
 	// Listed and read through the brain root (hyperguild#157): a wing or
 	// hall that is a symlink is not followed, and notes are regular files.
 	bfs, err := brainfs.Open(brainDir)
@@ -60,9 +63,8 @@ func BuildWingIndex(brainDir, wing string) error {
 		fmt.Fprintf(&b, "| %s | [%s](%s/%s.md) | %s |\n", e.Hall, e.Title, e.Hall, e.Slug, e.Created)
 	}
 
-	// Written through the brain root, never through a symlinked _index.md
-	// (hyperguild#158).
-	return bfs.PutRegular("wiki/"+w+"/_index.md", []byte(b.String()))
+	dest := filepath.Join(wingDir, "_index.md")
+	return os.WriteFile(dest, []byte(b.String()), 0o644)
 }
 
 // BuildAllWingIndexes regenerates _index.md for every wing under brain/wiki/.

ingestion/internal/brain/tunnel.go

@@ -5,6 +5,7 @@ import (
 	"errors"
 	"fmt"
 	"io/fs"
+	"os"
 	"path"
 	"path/filepath"
 	"strings"
@@ -175,23 +176,35 @@ func logFuzzyCandidates(brainDir, sourcePath string, cs []TunnelCandidate) error
 	if len(cs) == 0 {
 		return nil
 	}
-	// Appended through the brain root, never through a symlinked raw/ or
-	// log file (hyperguild#158).
-	bfs, err := brainfs.Open(brainDir)
-	if err != nil {
-		return fmt.Errorf("open brain: %w", err)
+	rawDir := filepath.Join(brainDir, "raw")
+	if err := os.MkdirAll(rawDir, 0o755); err != nil {
+		return err
 	}
-	defer func() { _ = bfs.Close() }()
 	stamp := time.Now().UTC().Format("2006-01-02")
-	rel := "raw/tunnel-candidates-" + stamp + ".md"
-	var buf strings.Builder
-	if _, err := bfs.Lstat(rel); errors.Is(err, fs.ErrNotExist) {
-		buf.WriteString("# Tunnel candidates " + stamp + "\n\nFuzzy cross-wing matches surfaced by AutoTunnel. Review and promote to a tunnel via `brain_tunnel` if relevant.\n\n")
+	path := filepath.Join(rawDir, "tunnel-candidates-"+stamp+".md")
+	existed := fileExists(path)
+	f, err := os.OpenFile(path, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0o644)
+	if err != nil {
+		return err
+	}
+	defer func() { _ = f.Close() }()
+	if !existed {
+		if _, err := f.WriteString("# Tunnel candidates " + stamp + "\n\nFuzzy cross-wing matches surfaced by AutoTunnel. Review and promote to a tunnel via `brain_tunnel` if relevant.\n\n"); err != nil {
+			return err
+		}
 	}
 	for _, c := range cs {
-		fmt.Fprintf(&buf, "- `%s` ↔ `%s` (term: %q)\n", sourcePath, c.TargetPath, c.MatchedTerm)
+		line := fmt.Sprintf("- `%s` ↔ `%s` (term: %q)\n", sourcePath, c.TargetPath, c.MatchedTerm)
+		if _, err := f.WriteString(line); err != nil {
+			return err
 		}
-	return bfs.AppendRegular(rel, []byte(buf.String()))
+	}
+	return nil
+}
+
+func fileExists(p string) bool {
+	_, err := os.Stat(p)
+	return err == nil
 }
 
 // WriteTunnel appends a bidirectional wikilink between sourcePath and

ingestion/internal/brain/tunnel_redirect_test.go

@@ -1,38 +0,0 @@
-package brain_test
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
-)
-
-// hyperguild#173: brain_tunnel's write followed a directory symlink inside
-// wiki/ that points elsewhere in the brain.
-func TestWriteTunnelRefusesATargetBehindASymlinkedDirectory(t *testing.T) {
-	b := t.TempDir()
-	src := filepath.Join(b, "wiki", "a", "facts", "s.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(src), 0o755))
-	require.NoError(t, os.WriteFile(src, []byte("x\n"), 0o644))
-	victim := filepath.Join(b, "raw", "facts", "v.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
-	require.NoError(t, os.WriteFile(victim, []byte("untouched\n"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "b"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(b, "wiki", "b", "facts")))
-
-	assert.ErrorIs(t, brain.WriteTunnel(b, "wiki/a/facts/s.md", "wiki/b/facts/v.md"), brainfs.ErrNotRegular)
-	got, _ := os.ReadFile(victim)
-	assert.Equal(t, "untouched\n", string(got))
-	got, _ = os.ReadFile(src)
-	assert.Equal(t, "x\n", string(got), "the source is not rewritten either")
-
-	real := filepath.Join(b, "wiki", "c", "facts", "t.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(real), 0o755))
-	require.NoError(t, os.WriteFile(real, []byte("t\n"), 0o644))
-	require.NoError(t, brain.WriteTunnel(b, "wiki/a/facts/s.md", "wiki/c/facts/t.md"), "positive control: a tunnel between real directories is written")
-}

ingestion/internal/brain/writers_redirect_test.go

@@ -1,52 +0,0 @@
-package brain_test
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
-)
-
-// hyperguild#158: BuildWingIndex wrote wiki/<wing>/_index.md with
-// os.WriteFile, so a symlinked _index.md was written through.
-func TestBuildWingIndexDoesNotWriteThroughASymlinkedIndex(t *testing.T) {
-	b := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w", "facts"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "w", "facts", "n.md"), []byte("---\ntitle: zqn\n---\n"), 0o644))
-	victim := filepath.Join(b, "raw", "v.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
-	require.NoError(t, os.WriteFile(victim, []byte("untouched"), 0o644))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "v.md"), filepath.Join(b, "wiki", "w", "_index.md")))
-	assert.Error(t, brain.BuildWingIndex(b, "w"))
-	got, _ := os.ReadFile(victim)
-	assert.Equal(t, "untouched", string(got))
-
-	require.NoError(t, os.Remove(filepath.Join(b, "wiki", "w", "_index.md")))
-	require.NoError(t, brain.BuildWingIndex(b, "w"), "positive control")
-	idx, _ := os.ReadFile(filepath.Join(b, "wiki", "w", "_index.md"))
-	assert.Contains(t, string(idx), "zqn")
-}
-
-// AutoTunnel's fuzzy-candidate log appended to raw/tunnel-candidates-*.md
-// with os.OpenFile, so a symlinked raw/ (or log file) was written through.
-func TestAutoTunnelDoesNotAppendTheCandidateLogThroughASymlinkedRaw(t *testing.T) {
-	b := t.TempDir()
-	outside := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "a", "facts"), 0o755))
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "b", "facts"), 0o755))
-	// "zq widget" matches as a substring of "zq widgets", a fuzzy candidate.
-	require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "b", "facts", "t.md"), []byte("---\ntitle: Zq Widget\n---\n"), 0o644))
-	require.NoError(t, os.Symlink(outside, filepath.Join(b, "raw")))
-	_ = brain.AutoTunnel(b, "wiki/a/facts/s.md", "about zq widgets")
-	ents, _ := os.ReadDir(outside)
-	assert.Empty(t, ents, "the candidate log was written outside the brain")
-
-	require.NoError(t, os.Remove(filepath.Join(b, "raw")))
-	require.NoError(t, brain.AutoTunnel(b, "wiki/a/facts/s.md", "about zq widgets"))
-	logs, _ := filepath.Glob(filepath.Join(b, "raw", "tunnel-candidates-*.md"))
-	assert.Len(t, logs, 1, "positive control: the fuzzy candidate is logged in the real raw/")
-}

ingestion/internal/brainfs/brainfs.go

@@ -104,17 +104,6 @@ func (b *Brain) ReadDirRegular(relDir string) ([]string, error) {
 	return names, nil
 }
 
-// cleanRel refuses a path that is not clean and local. realDir checks the
-// cleaned parent, so the I/O must use that same path: os.Root resolves ".."
-// after following a symlink, and a ".." after a symlinked directory would
-// otherwise pass the check and redirect the read or write.
-func cleanRel(rel string) error {
-	if rel == "" || path.Clean(rel) != rel || !filepath.IsLocal(rel) || strings.Contains(rel, "\\") {
-		return fmt.Errorf("%q: not a clean brain-relative path: %w", rel, ErrNotRegular)
-	}
-	return nil
-}
-
 // ReadDirDirs lists the real subdirectories directly in a brain-relative
 // directory, by name. Every component of relDir must be a real directory
 // (ErrNotRegular otherwise); symlinks to directories are left out.
@@ -136,149 +125,9 @@ func (b *Brain) ReadDirDirs(relDir string) ([]string, error) {
 	return names, nil
 }
 
-// PutRegular creates or replaces a regular file at a brain-relative path,
-// for creating writes (hyperguild#188, #158). Missing parent directories are
-// created one component at a time through the root, and every existing
-// component must be a real directory, so a symlinked directory cannot
-// redirect the write elsewhere in the brain or outside it. An existing file
-// is replaced only if it is regular (WriteRegular's checks); a new file is
-// created with O_EXCL and confirmed to be the file that was opened. A
-// directory swapped in after the checks is the #167 residual.
-func (b *Brain) PutRegular(rel string, data []byte) error {
-	if err := cleanRel(rel); err != nil {
-		return err
-	}
-	if err := b.mkdirReal(path.Dir(rel)); err != nil {
-		return err
-	}
-	if _, err := b.root.Lstat(rel); err == nil {
-		return b.WriteRegular(rel, data)
-	} else if !errors.Is(err, fs.ErrNotExist) {
-		return err
-	}
-	return b.createNew(rel, data)
-}
-
-// CreateRegular creates a new regular file at a brain-relative path, with
-// PutRegular's parent rules, and fails with fs.ErrExist if anything is
-// already there: for writers that must never overwrite (promote, reject).
-func (b *Brain) CreateRegular(rel string, data []byte) error {
-	if err := cleanRel(rel); err != nil {
-		return err
-	}
-	if err := b.mkdirReal(path.Dir(rel)); err != nil {
-		return err
-	}
-	return b.createNew(rel, data)
-}
-
-// createNew creates rel with O_EXCL and writes data only after confirming
-// the path is the regular file it created.
-func (b *Brain) createNew(rel string, data []byte) error {
-	f, err := b.root.OpenFile(rel, os.O_WRONLY|os.O_CREATE|os.O_EXCL|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
-	if err != nil {
-		return err
-	}
-	defer func() { _ = f.Close() }()
-	hfi, herr := f.Stat()
-	lfi, lerr := b.root.Lstat(rel)
-	if herr != nil || lerr != nil || !lfi.Mode().IsRegular() || !os.SameFile(lfi, hfi) {
-		return fmt.Errorf("%s: changed while creating: %w", rel, ErrNotRegular)
-	}
-	if _, err := f.Write(data); err != nil {
-		return err
-	}
-	return f.Close()
-}
-
-// AppendRegular appends data to a regular file at a brain-relative path,
-// creating it (and missing parent directories, as PutRegular does) if it is
-// absent. It writes only after confirming the path is the regular file it
-// opened, so a final symlink or special file, or one swapped in, is refused.
-func (b *Brain) AppendRegular(rel string, data []byte) error {
-	if err := cleanRel(rel); err != nil {
-		return err
-	}
-	if err := b.mkdirReal(path.Dir(rel)); err != nil {
-		return err
-	}
-	if fi, err := b.root.Lstat(rel); err == nil && !fi.Mode().IsRegular() {
-		return fmt.Errorf("%s: %w", rel, ErrNotRegular)
-	} else if err != nil && !errors.Is(err, fs.ErrNotExist) {
-		return err
-	}
-	f, err := b.root.OpenFile(rel, os.O_WRONLY|os.O_APPEND|os.O_CREATE|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
-	if err != nil {
-		return err
-	}
-	defer func() { _ = f.Close() }()
-	hfi, herr := f.Stat()
-	lfi, lerr := b.root.Lstat(rel)
-	if herr != nil || lerr != nil || !lfi.Mode().IsRegular() || !os.SameFile(lfi, hfi) {
-		return fmt.Errorf("%s: changed while opening: %w", rel, ErrNotRegular)
-	}
-	if _, err := f.Write(data); err != nil {
-		return err
-	}
-	return f.Close()
-}
-
-// Remove removes the file at a clean brain-relative path through the root,
-// refusing a path behind a symlinked directory. A final symlink is removed
-// itself, never its target.
-func (b *Brain) Remove(rel string) error {
-	if err := b.RealParent(rel); err != nil {
-		return err
-	}
-	return b.root.Remove(rel)
-}
-
-// RealParent returns ErrNotRegular unless rel is clean and every directory
-// above it is a real directory, for writers that do their own I/O (an atomic
-// rename) but must not be redirected by a symlinked directory.
-func (b *Brain) RealParent(rel string) error {
-	if err := cleanRel(rel); err != nil {
-		return err
-	}
-	return b.realDir(path.Dir(rel))
-}
-
-// mkdirReal makes sure every component of rel exists as a real directory,
-// creating missing ones through the root; an existing component that is
-// not a real directory is ErrNotRegular.
-func (b *Brain) mkdirReal(rel string) error {
-	if rel == "." {
-		return nil
-	}
-	prefix := ""
-	for _, part := range strings.Split(rel, "/") {
-		prefix = path.Join(prefix, part)
-		fi, err := b.root.Lstat(prefix)
-		if errors.Is(err, fs.ErrNotExist) {
-			if err := b.root.Mkdir(prefix, 0o755); err != nil && !errors.Is(err, fs.ErrExist) {
-				return err
-			}
-			fi, err = b.root.Lstat(prefix)
-		}
-		if err != nil {
-			return err
-		}
-		if !fi.IsDir() {
-			return fmt.Errorf("%s: component %s is not a directory: %w", rel, prefix, ErrNotRegular)
-		}
-	}
-	return nil
-}
-
 // ReadRegular reads a brain-relative path, refusing anything that is not a
 // regular file, both before the open and on the opened handle.
 func (b *Brain) ReadRegular(rel string) ([]byte, error) {
-	if err := cleanRel(rel); err != nil {
-		return nil, err
-	}
-	if err := b.realDir(path.Dir(rel)); err != nil {
-		return nil, err
-	}
 	fi, err := b.root.Lstat(rel)
 	if err != nil {
 		return nil, err
@@ -305,12 +154,6 @@ func (b *Brain) readOpened(rel string) ([]byte, error) { return b.readOpenedMax(
 // ReadRegularMax is ReadRegular with a size limit, checked on the opened
 // handle before reading (max < 0 means no limit).
 func (b *Brain) ReadRegularMax(rel string, max int64) ([]byte, error) {
-	if err := cleanRel(rel); err != nil {
-		return nil, err
-	}
-	if err := b.realDir(path.Dir(rel)); err != nil {
-		return nil, err
-	}
 	fi, err := b.root.Lstat(rel)
 	if err != nil {
 		return nil, err
@@ -413,20 +256,10 @@ func (b *Brain) WalkRegular(relDir string, fn func(rel string) error, onErr func
 // O_NOFOLLOW (verified on go1.27), so the path is Lstat-ed through the root
 // first and the opened handle must be that same file (os.SameFile), which
 // also catches a swap between the two. O_NONBLOCK keeps a FIFO from blocking
-// the open. Every directory above the file must be a real directory
-// (hyperguild#173); a directory swapped in after that check is the #167
-// residual.
+// the open. Intermediate in-brain symlinks are still followed (os.Root keeps
+// the write inside the brain; hyperguild#167).
 func (b *Brain) WriteRegular(rel string, data []byte) error {
-	if err := cleanRel(rel); err != nil {
-		return err
-	}
-	// Every directory above the file must be real: os.Root follows an
-	// in-brain intermediate symlink, which would redirect the write
-	// elsewhere in the brain (hyperguild#173). A swap after this check is
-	// the #167 residual.
-	if err := b.realDir(path.Dir(rel)); err != nil {
-		return err
-	}
+	rel = filepath.ToSlash(rel)
 	lfi, err := b.root.Lstat(rel)
 	if err != nil {
 		return err

ingestion/internal/brainfs/brainfs_test.go

@@ -218,7 +218,7 @@ func TestReadDirRegularListsOnlyRegularFilesAndRefusesSymlinkedComponents(t *tes
 // A final component swapped for a symlink to another regular file in the
 // brain between the Lstat and the open: os.Root follows in-root links, so
 // only comparing the two (os.SameFile) refuses it.
-func TestReadRegularDoesNotReturnAnInBrainFileSwappedInBehindASymlink(t *testing.T) {
+func TestReadRegularNeverReturnsAnInBrainFileSwappedInBehindASymlink(t *testing.T) {
 	dir := t.TempDir()
 	require.NoError(t, os.WriteFile(filepath.Join(dir, "s.md"), []byte("zqsamefilesentinel"), 0o644))
 	p := filepath.Join(dir, "r.md")
@@ -326,206 +326,3 @@ func TestReadDirDirsListsOnlyRealSubdirsAndRefusesSymlinkedComponents(t *testing
 	_, err = b.ReadDirDirs("alias")
 	assert.ErrorIs(t, err, ErrNotRegular)
 }
-
-// hyperguild#173: a file reached through a symlinked directory inside the
-// brain is refused for reads and writes, so a caller-supplied path cannot be
-// redirected to another part of the brain.
-func TestReadAndWriteRegularRefuseAFileBehindASymlinkedDirectory(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(dir, "wiki", "alias")))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	_, err = b.ReadRegular("wiki/alias/v.md")
-	assert.ErrorIs(t, err, ErrNotRegular)
-	_, err = b.ReadRegularMax("wiki/alias/v.md", 100)
-	assert.ErrorIs(t, err, ErrNotRegular)
-	assert.ErrorIs(t, b.WriteRegular("wiki/alias/v.md", []byte("x")), ErrNotRegular)
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-	got, err = b.ReadRegular("raw/v.md")
-	require.NoError(t, err, "positive control: the real path still reads")
-	assert.Equal(t, "untouched", string(got))
-}
-
-// realDir checks the cleaned parent, so the I/O must use that same clean
-// path: os.Root resolves ".." after following a symlink, and a ".." placed
-// after a symlinked directory would otherwise pass the check and redirect.
-func TestReadAndWriteRegularRefuseAPathThatIsNotClean(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw", "facts"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw", "facts"), filepath.Join(dir, "wiki", "alias")))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	for _, rel := range []string{"wiki/alias/../v.md", "./raw/v.md", "raw//v.md", "/raw/v.md"} {
-		got, err := b.ReadRegular(rel)
-		assert.ErrorIs(t, err, ErrNotRegular, rel)
-		assert.NotContains(t, string(got), "untouched", rel)
-		_, err = b.ReadRegularMax(rel, 100)
-		assert.ErrorIs(t, err, ErrNotRegular, rel)
-		assert.ErrorIs(t, b.WriteRegular(rel, []byte("OVERWRITTEN")), ErrNotRegular, rel)
-	}
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-}
-
-// hyperguild#188: PutRegular creates or replaces a regular file through the
-// root. Missing parent directories are created; an existing component that
-// is not a real directory, a final symlink or special file, and an unclean
-// path are refused, and nothing is created at a link's target.
-func TestPutRegularCreatesOrReplacesOnlyThroughRealDirectories(t *testing.T) {
-	dir := t.TempDir()
-	outside := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(dir, "wiki", "inwing")))
-	require.NoError(t, os.Symlink(outside, filepath.Join(dir, "wiki", "outwing")))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki", "w"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "v.md"), filepath.Join(dir, "wiki", "w", "link.md")))
-	require.NoError(t, syscall.Mkfifo(filepath.Join(dir, "wiki", "w", "f.md"), 0o644))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	for _, rel := range []string{"wiki/inwing/facts/n.md", "wiki/outwing/facts/n.md", "wiki/w/link.md", "wiki/w/f.md", "wiki/w/../../raw/v.md", "/abs.md"} {
-		assert.ErrorIs(t, b.PutRegular(rel, []byte("x")), ErrNotRegular, rel)
-	}
-	ents, _ := os.ReadDir(outside)
-	assert.Empty(t, ents, "nothing created outside the brain")
-	_, err = os.Stat(filepath.Join(dir, "raw", "facts"))
-	assert.True(t, os.IsNotExist(err), "nothing created through the in-brain link")
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-
-	require.NoError(t, b.PutRegular("wiki/new/facts/n.md", []byte("one")), "positive control: create with missing parents")
-	got, _ = os.ReadFile(filepath.Join(dir, "wiki", "new", "facts", "n.md"))
-	assert.Equal(t, "one", string(got))
-	require.NoError(t, b.PutRegular("wiki/new/facts/n.md", []byte("two")), "positive control: replace")
-	got, _ = os.ReadFile(filepath.Join(dir, "wiki", "new", "facts", "n.md"))
-	assert.Equal(t, "two", string(got))
-}
-
-func TestAppendRegularCreatesOrAppendsOnlyThroughRealDirectories(t *testing.T) {
-	dir := t.TempDir()
-	outside := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.Symlink(outside, filepath.Join(dir, "outdir")))
-	require.NoError(t, os.Symlink("raw", filepath.Join(dir, "indir")))
-	require.NoError(t, os.Symlink(filepath.Join("raw", "v.md"), filepath.Join(dir, "log.md")))
-	require.NoError(t, syscall.Mkfifo(filepath.Join(dir, "f.md"), 0o644))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	for _, rel := range []string{"outdir/l.md", "indir/v.md", "log.md", "f.md", "raw/../log.md"} {
-		assert.ErrorIs(t, b.AppendRegular(rel, []byte("x")), ErrNotRegular, rel)
-	}
-	ents, _ := os.ReadDir(outside)
-	assert.Empty(t, ents)
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-
-	require.NoError(t, b.AppendRegular("logs/a.md", []byte("one\n")), "positive control: create")
-	require.NoError(t, b.AppendRegular("logs/a.md", []byte("two\n")), "positive control: append")
-	got, _ = os.ReadFile(filepath.Join(dir, "logs", "a.md"))
-	assert.Equal(t, "one\ntwo\n", string(got))
-}
-
-func TestRealParentRefusesASymlinkedDirectoryOrUncleanPath(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(dir, "wiki", "alias")))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-	assert.ErrorIs(t, b.RealParent("wiki/alias/x.md"), ErrNotRegular)
-	assert.ErrorIs(t, b.RealParent("wiki/../raw/x.md"), ErrNotRegular)
-	assert.NoError(t, b.RealParent("wiki/x.md"), "positive control")
-}
-
-// cleanRel must refuse an unclean path on its own: here the ".." resolves,
-// after a symlinked directory, to a real regular file, so only the clean
-// check stands between the call and that file.
-func TestAppendRegularRefusesAnUncleanPathThatResolvesToARealFile(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw", "keep"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.Symlink(filepath.Join("raw", "keep"), filepath.Join(dir, "indir")))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-	assert.ErrorIs(t, b.AppendRegular("indir/../v.md", []byte("x")), ErrNotRegular)
-	assert.ErrorIs(t, b.PutRegular("indir/../v.md", []byte("x")), ErrNotRegular)
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-}
-
-func TestRemoveRefusesAPathBehindASymlinkedDirectoryAndRemovesOnlyTheLink(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("keep"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(dir, "wiki", "alias")))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw", "v.md"), filepath.Join(dir, "wiki", "link.md")))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "wiki", "n.md"), []byte("n"), 0o644))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	assert.ErrorIs(t, b.Remove("wiki/alias/v.md"), ErrNotRegular)
-	_, err = os.Stat(filepath.Join(dir, "raw", "v.md"))
-	assert.NoError(t, err, "the file behind the symlinked directory is kept")
-	require.NoError(t, b.Remove("wiki/link.md"))
-	_, err = os.Stat(filepath.Join(dir, "raw", "v.md"))
-	assert.NoError(t, err, "removing a final symlink never removes its target")
-	require.NoError(t, b.Remove("wiki/n.md"), "positive control")
-	_, err = os.Stat(filepath.Join(dir, "wiki", "n.md"))
-	assert.True(t, os.IsNotExist(err))
-}
-
-// CreateRegular is the only write path for promote and reject: it creates
-// missing parents through the root, refuses an in-brain symlinked parent and
-// an unclean path, and never replaces anything already there (fs.ErrExist,
-// content unchanged), including a dangling link.
-func TestCreateRegularCreatesOnlyNewFilesThroughRealDirectories(t *testing.T) {
-	dir := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw", "keep"), 0o755))
-	require.NoError(t, os.MkdirAll(filepath.Join(dir, "wiki"), 0o755))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(dir, "wiki", "inwing")))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "raw", "v.md"), []byte("untouched"), 0o644))
-	require.NoError(t, os.Symlink(filepath.Join("raw", "keep"), filepath.Join(dir, "indir")))
-	require.NoError(t, os.WriteFile(filepath.Join(dir, "wiki", "exists.md"), []byte("original"), 0o644))
-	require.NoError(t, os.Symlink("nowhere.md", filepath.Join(dir, "wiki", "dangling.md")))
-	b, err := Open(dir)
-	require.NoError(t, err)
-	defer func() { _ = b.Close() }()
-
-	assert.ErrorIs(t, b.CreateRegular("wiki/inwing/facts/n.md", []byte("x")), ErrNotRegular)
-	_, err = os.Stat(filepath.Join(dir, "raw", "facts"))
-	assert.True(t, os.IsNotExist(err), "nothing created through the in-brain link")
-	assert.ErrorIs(t, b.CreateRegular("indir/../v.md", []byte("x")), ErrNotRegular)
-	got, _ := os.ReadFile(filepath.Join(dir, "raw", "v.md"))
-	assert.Equal(t, "untouched", string(got))
-
-	assert.ErrorIs(t, b.CreateRegular("wiki/exists.md", []byte("x")), fs.ErrExist)
-	got, _ = os.ReadFile(filepath.Join(dir, "wiki", "exists.md"))
-	assert.Equal(t, "original", string(got))
-	assert.ErrorIs(t, b.CreateRegular("wiki/dangling.md", []byte("x")), fs.ErrExist)
-	_, err = os.Stat(filepath.Join(dir, "wiki", "nowhere.md"))
-	assert.True(t, os.IsNotExist(err), "nothing created at the dangling link's target")
-
-	require.NoError(t, b.CreateRegular("wiki/new/facts/n.md", []byte("one")), "positive control: create with missing parents")
-	got, _ = os.ReadFile(filepath.Join(dir, "wiki", "new", "facts", "n.md"))
-	assert.Equal(t, "one", string(got))
-}

ingestion/internal/brainfs/brainfstest/brainfstest.go

@@ -1,10 +1,8 @@
 // Package brainfstest is the shared harness for hyperguild#157's swap-race
-// tests: it keeps swapping a regular note, a symlink to a sentinel target file
-// (outside the brain, or inside it for hyperguild#171), or a FIFO (with a
-// writer held open) into a path while a reader under test loops.
-// It observes two things, over a sampled window only: no sentinel byte from
-// the target reaches the reader's output, and the reader returns within a
-// timeout. It does not cover
+// tests: it keeps swapping a regular note, a symlink to an outside file, or a
+// FIFO (with a writer held open) into a path while a reader under test loops.
+// It observes two things: no sentinel byte from the outside file reaches the
+// reader's output, and the reader returns within a timeout. It does not cover
 // hard links, other paths into the reader, or races it does not generate.
 package brainfstest
 
@@ -20,7 +18,7 @@ import (
 	"time"
 )
 
-// Sentinel marks the target file's contents.
+// Sentinel marks the outside file's contents.
 const Sentinel = "zqbrainfssentinelonefiftyseven"
 
 // outsideContent carries Sentinel in every field a reader might extract: the
@@ -143,7 +141,7 @@ func AssertNoLeakFrom(t testing.TB, path, inside, target string, d time.Duration
 		}
 	}
 	if leaks > 0 {
-		t.Fatalf("symlink target %s leaked %d times in %d iterations", target, leaks, iters)
+		t.Fatalf("outside file leaked %d times in %d iterations", leaks, iters)
 	}
 	if n := swaps.Load(); n == 0 {
 		t.Fatalf("no symlink was swapped into %s in %d iterations: the race did not run", path, iters)

ingestion/internal/classification/classification.go

@@ -16,10 +16,9 @@
 package classification
 
 import (
-	"errors"
 	"fmt"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
-	"io/fs"
+	"os"
+	"path/filepath"
 	"strings"
 
 	"gopkg.in/yaml.v3"
@@ -111,20 +110,9 @@ type rawConfig struct {
 func Load(brainDir string) (*Config, error) {
 	cfg := &Config{wings: map[string]Level{}, repos: map[string]Level{}}
 
-	// Read through the brain root, regular files only (hyperguild#157): a
-	// symlinked or special file is not trusted as the config, which is a hard
-	// error like a malformed one.
-	bfs, err := brainfs.Open(brainDir)
-	if errors.Is(err, fs.ErrNotExist) {
-		return cfg, nil
-	}
+	data, err := os.ReadFile(filepath.Join(brainDir, "classification.yaml"))
 	if err != nil {
-		return nil, fmt.Errorf("open brain: %w", err)
-	}
-	defer func() { _ = bfs.Close() }()
-	data, err := bfs.ReadRegular("classification.yaml")
-	if err != nil {
-		if errors.Is(err, fs.ErrNotExist) {
+		if os.IsNotExist(err) {
 			return cfg, nil
 		}
 		return nil, fmt.Errorf("read classification.yaml: %w", err)

ingestion/internal/classification/root_test.go

@@ -1,46 +0,0 @@
-package classification
-
-import (
-	"os"
-	"path/filepath"
-	"syscall"
-	"testing"
-	"time"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// hyperguild#157 slice 6: Load read classification.yaml with os.ReadFile. It
-// sets the I1 sovereignty levels; a symlinked file must not be trusted as the
-// config (a hard error, as for a malformed file), and a FIFO must not hang
-// startup.
-func TestLoadRefusesASymlinkedOrFIFOClassificationFile(t *testing.T) {
-	ok := t.TempDir()
-	require.NoError(t, os.WriteFile(filepath.Join(ok, "classification.yaml"), []byte("wings:\n  w: confidential\n"), 0o644))
-	_, err := Load(ok)
-	require.NoError(t, err, "positive control")
-
-	linked := t.TempDir()
-	require.NoError(t, os.WriteFile(filepath.Join(linked, "real.yaml"), []byte("wings:\n  w: public\n"), 0o644))
-	require.NoError(t, os.Symlink("real.yaml", filepath.Join(linked, "classification.yaml")))
-	_, err = Load(linked)
-	assert.Error(t, err, "an in-brain symlink is not trusted as the config")
-
-	fifo := t.TempDir()
-	require.NoError(t, syscall.Mkfifo(filepath.Join(fifo, "classification.yaml"), 0o644))
-	w, err := os.OpenFile(filepath.Join(fifo, "classification.yaml"), os.O_RDWR, 0)
-	require.NoError(t, err)
-	defer func() { _ = w.Close() }()
-	done := make(chan error, 1)
-	go func() { _, err := Load(fifo); done <- err }()
-	select {
-	case err := <-done:
-		assert.Error(t, err)
-	case <-time.After(3 * time.Second):
-		t.Fatal("Load hung on a FIFO")
-	}
-
-	_, err = Load(t.TempDir())
-	assert.NoError(t, err, "an absent file is still not an error")
-}

ingestion/internal/mcp/readexcerpt_root_test.go

@@ -21,11 +21,6 @@ func TestReadExcerptRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
 	require.NoError(t, os.MkdirAll(facts, 0o755))
 	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
 	assert.NotContains(t, readExcerpt(brain, "wiki/w/facts/leak.md", 500), brainfstest.Sentinel)
-	// A link to a file elsewhere in the brain: os.Root allows it, only the
-	// regular-file check refuses it (hyperguild#171).
-	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
-	assert.NotContains(t, readExcerpt(brain, "wiki/w/facts/inlink.md", 500), brainfstest.Sentinel)
 
 	p := filepath.Join(facts, "r.md")
 	require.NoError(t, os.WriteFile(p, []byte("---\nx: y\n---\ninside"), 0o644))
@@ -33,9 +28,6 @@ func TestReadExcerptRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
 	brainfstest.AssertNoLeak(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, func() string {
 		return readExcerpt(brain, "wiki/w/facts/r.md", 500)
 	})
-	brainfstest.AssertNoLeakFrom(t, p, "---\nx: y\n---\ninside", inBrain, 1500*time.Millisecond, func() string {
-		return readExcerpt(brain, "wiki/w/facts/r.md", 500)
-	})
 	brainfstest.AssertNoHang(t, p, "---\nx: y\n---\ninside", 1500*time.Millisecond, 6*time.Second, func() {
 		_ = readExcerpt(brain, "wiki/w/facts/r.md", 500)
 	})

ingestion/internal/notes/edit_redirect_test.go

@@ -1,36 +0,0 @@
-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))
-}

ingestion/internal/notes/read_root_test.go

@@ -38,31 +38,3 @@ func TestReadScopedRefusesANoteOverMaxNoteBytes(t *testing.T) {
 	_, err := ReadScoped(brain, "wiki/w/facts/big.md", ScopeNotes)
 	assert.ErrorIs(t, err, ErrTooLarge)
 }
-
-// hyperguild#171 (review of #172, finding 1): os.Root alone refuses links that
-// leave the brain, so the outside-target race above stays green for a reader
-// that skips brainfs's Lstat and SameFile checks. An in-brain target (raw/,
-// outside ScopeNotes) is what tells them apart.
-func TestReadScopedDoesNotReturnAnInBrainSymlinkTargetStaticallyOrDuringASampledSwapRace(t *testing.T) {
-	brain := t.TempDir()
-	facts := filepath.Join(brain, "wiki", "w", "facts")
-	require.NoError(t, os.MkdirAll(facts, 0o755))
-	target := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
-	b, err := ReadScoped(brain, "wiki/w/facts/inlink.md", ScopeNotes)
-	assert.Error(t, err, "static in-brain link")
-	assert.NotContains(t, string(b), brainfstest.Sentinel, "static in-brain link")
-
-	p := filepath.Join(facts, "r.md")
-	require.NoError(t, os.WriteFile(p, []byte("inside"), 0o644))
-	b, err = ReadScoped(brain, "wiki/w/facts/r.md", ScopeNotes)
-	require.NoError(t, err)
-	assert.Equal(t, "inside", string(b), "positive control: a regular note reads")
-
-	read := func() string {
-		b, _ := ReadScoped(brain, "wiki/w/facts/r.md", ScopeNotes)
-		return string(b)
-	}
-	brainfstest.AssertNoLeakFrom(t, p, "inside", target, 1500*time.Millisecond, read)
-}

ingestion/internal/pipeline/backfill.go

@@ -3,10 +3,7 @@ package pipeline
 
 import (
 	"context"
-	"errors"
 	"fmt"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
-	"io/fs"
 	"os"
 	"path/filepath"
 	"strings"
@@ -26,16 +23,10 @@ func BackfillRefs(ctx context.Context, brainDir string) (int, error) {
 		return 0, fmt.Errorf("load inventory: %w", err)
 	}
 
-	// Listed and read through the brain root, regular files only
-	// (hyperguild#157).
-	bfs, err := brainfs.Open(brainDir)
+	sourcesDir := filepath.Join(brainDir, "wiki", "sources")
+	entries, err := os.ReadDir(sourcesDir)
 	if err != nil {
-		return 0, fmt.Errorf("open brain: %w", err)
-	}
-	defer func() { _ = bfs.Close() }()
-	names, err := bfs.ReadDirRegular("wiki/sources")
-	if err != nil {
-		if errors.Is(err, fs.ErrNotExist) {
+		if os.IsNotExist(err) {
 			return 0, nil
 		}
 		return 0, fmt.Errorf("read sources dir: %w", err)
@@ -46,20 +37,20 @@ func BackfillRefs(ctx context.Context, brainDir string) (int, error) {
 	// get both refs merged before a single write.
 	pending := make(map[string]wiki.Page)
 
-	for _, name := range names {
+	for _, e := range entries {
 		if ctx.Err() != nil {
 			return 0, ctx.Err()
 		}
-		if !strings.HasSuffix(name, ".md") {
+		if e.IsDir() || !strings.HasSuffix(e.Name(), ".md") {
 			continue
 		}
 
-		b, err := bfs.ReadRegular("wiki/sources/" + name)
+		b, err := os.ReadFile(filepath.Join(sourcesDir, e.Name()))
 		if err != nil {
 			continue
 		}
 		sourceContent := string(b)
-		sourceSlug := strings.TrimSuffix(name, ".md")
+		sourceSlug := strings.TrimSuffix(e.Name(), ".md")
 		sourceTitle := extractTitle(sourceContent)
 		if sourceTitle == "" {
 			sourceTitle = sourceSlug
@@ -79,7 +70,7 @@ func BackfillRefs(ctx context.Context, brainDir string) (int, error) {
 			// Start from already-accumulated version if we've seen this page.
 			page, seen := pending[relPath]
 			if !seen {
-				raw, err := bfs.ReadRegular(relPath)
+				raw, err := os.ReadFile(filepath.Join(brainDir, filepath.FromSlash(relPath)))
 				if err != nil {
 					continue
 				}

ingestion/internal/pipeline/pipeline.go

@@ -5,10 +5,7 @@ import (
 	"context"
 	"crypto/sha256"
 	"encoding/hex"
-	"errors"
 	"fmt"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
-	"io/fs"
 	"os"
 	"path/filepath"
 	"strings"
@@ -132,7 +129,7 @@ func buildAndWrite(ctx context.Context, rawPages []RawPage, sourceSlug, date, br
 			if err := os.MkdirAll(filepath.Dir(dest), 0o755); err != nil {
 				return Result{}, fmt.Errorf("mkdir for %s: %w", page.Path, err)
 			}
-			content, conflicts, err := reviseOrCreate(brainDir, page)
+			content, conflicts, err := reviseOrCreate(dest, page)
 			if err != nil {
 				return Result{}, err
 			}
@@ -191,27 +188,14 @@ func hashBody(content string) string {
 
 // readSourcePage returns the full on-disk content of the source page at
 // wiki/sources/<sourceSlug>.md, or "" when it doesn't exist yet.
-// It reads through the brain root, regular files only (hyperguild#157): the
-// content goes into the LLM prompt.
 func readSourcePage(brainDir, sourceSlug string) string {
-	raw, err := readBrainFile(brainDir, "wiki/sources/"+sourceSlug+".md")
+	raw, err := os.ReadFile(filepath.Join(brainDir, "wiki", "sources", sourceSlug+".md"))
 	if err != nil {
 		return ""
 	}
 	return string(raw)
 }
 
-// readBrainFile reads one brain-relative file through the brain root,
-// regular files only (hyperguild#157).
-func readBrainFile(brainDir, rel string) ([]byte, error) {
-	bfs, err := brainfs.Open(brainDir)
-	if err != nil {
-		return nil, err
-	}
-	defer func() { _ = bfs.Close() }()
-	return bfs.ReadRegular(rel)
-}
-
 // storedSourceHash reads source_hash from the source page a previous ingest
 // wrote, or "" when there is no such page or no such field.
 //
@@ -246,10 +230,10 @@ func storedSourceHash(brainDir, sourceSlug string) string {
 // its first-ingest date on a revised page. Left deliberately — the alternative
 // is this function editing frontmatter it does not own, and no lint reads that
 // field today.
-func reviseOrCreate(brainDir string, page wiki.Page) (string, []string, error) {
-	existing, err := readBrainFile(brainDir, page.Path)
+func reviseOrCreate(dest string, page wiki.Page) (string, []string, error) {
+	existing, err := os.ReadFile(dest)
 	switch {
-	case errors.Is(err, fs.ErrNotExist):
+	case os.IsNotExist(err):
 		return page.Content, nil, nil
 	case err != nil:
 		return "", nil, fmt.Errorf("read existing %s: %w", page.Path, err)
@@ -283,7 +267,7 @@ See brain/schema.md for the full schema.
 `
 
 func loadSchema(brainDir string) string {
-	b, err := readBrainFile(brainDir, "schema.md")
+	b, err := os.ReadFile(filepath.Join(brainDir, "schema.md"))
 	if err != nil {
 		return defaultSchema
 	}

ingestion/internal/pipeline/refs.go

@@ -2,6 +2,7 @@
 package pipeline
 
 import (
+	"os"
 	"path/filepath"
 	"regexp"
 	"strings"
@@ -52,7 +53,8 @@ func injectSourceRefs(pages []wiki.Page, inventory map[wiki.PageType][]wiki.Entr
 		if !ok {
 			continue
 		}
-		b, err := readBrainFile(brainDir, "wiki/"+string(pt)+"/"+slug+".md")
+		diskPath := filepath.Join(brainDir, "wiki", string(pt), slug+".md")
+		b, err := os.ReadFile(diskPath)
 		if err != nil {
 			continue
 		}

ingestion/internal/pipeline/root_test.go

@@ -1,167 +0,0 @@
-package pipeline
-
-import (
-	"context"
-	"fmt"
-	"io"
-	"os"
-	"path/filepath"
-	"syscall"
-	"testing"
-	"time"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/wiki"
-)
-
-// hyperguild#157 slice 6: the pipeline read the source page, schema.md, the
-// pages it revises and the pages it adds source refs to with os.ReadFile, so
-// a symlinked file's content reached the LLM prompt and the written pages,
-// and a FIFO hung the ingest.
-
-func mkdirs(t *testing.T, brain string, dirs ...string) {
-	t.Helper()
-	for _, d := range dirs {
-		require.NoError(t, os.MkdirAll(filepath.Join(brain, filepath.FromSlash(d)), 0o755))
-	}
-}
-
-func TestReadSourcePageAndSchemaRefuseSymlinksAndSurviveSwapRaces(t *testing.T) {
-	brain := t.TempDir()
-	mkdirs(t, brain, "wiki/sources")
-	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok.md"), []byte("zqinside source"), 0o644))
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "schema.md"), []byte("zqinside schema"), 0o644))
-	assert.Equal(t, "zqinside source", readSourcePage(brain, "ok"), "positive control")
-	assert.Equal(t, "zqinside schema", loadSchema(brain), "positive control")
-
-	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(brain, "wiki", "sources", "out.md")))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "sources", "in.md")))
-	assert.NotContains(t, readSourcePage(brain, "out"), brainfstest.Sentinel)
-	assert.NotContains(t, readSourcePage(brain, "in"), brainfstest.Sentinel)
-	assert.NotContains(t, storedSourceHash(brain, "in"), brainfstest.Sentinel)
-
-	src := filepath.Join(brain, "wiki", "sources", "r.md")
-	read := func() string { return readSourcePage(brain, "r") }
-	brainfstest.AssertNoLeak(t, src, "zqinside", 1500*time.Millisecond, read)
-	brainfstest.AssertNoLeakFrom(t, src, "zqinside", inBrain, 1500*time.Millisecond, read)
-	brainfstest.AssertNoHang(t, src, "zqinside", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
-
-	schema := filepath.Join(brain, "schema.md")
-	rs := func() string { return loadSchema(brain) }
-	brainfstest.AssertNoLeakFrom(t, schema, "zqinside schema", inBrain, 1500*time.Millisecond, rs)
-	brainfstest.AssertNoHang(t, schema, "zqinside schema", 1500*time.Millisecond, 6*time.Second, func() { _ = rs() })
-}
-
-func TestReviseOrCreateRefusesASymlinkedExistingPage(t *testing.T) {
-	brain := t.TempDir()
-	mkdirs(t, brain, "wiki/concepts")
-	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "concepts", "c.md")))
-	page := wiki.Page{Path: "wiki/concepts/c.md", Content: "---\ntitle: C\n---\nnew\n"}
-	out, _, err := reviseOrCreate(brain, page)
-	assert.Error(t, err)
-	assert.NotContains(t, out, brainfstest.Sentinel)
-
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "d.md"), []byte("---\ntitle: D\n---\nzqold\n"), 0o644))
-	out, _, err = reviseOrCreate(brain, wiki.Page{Path: "wiki/concepts/d.md", Content: "---\ntitle: D\n---\nnew\n"})
-	require.NoError(t, err)
-	assert.Contains(t, out, "zqold", "positive control: the existing page is read")
-	out, _, err = reviseOrCreate(brain, wiki.Page{Path: "wiki/concepts/new.md", Content: "fresh"})
-	require.NoError(t, err)
-	assert.Equal(t, "fresh", out, "positive control: a missing page is created")
-}
-
-func TestInjectSourceRefsDoesNotReadASymlinkedPage(t *testing.T) {
-	brain := t.TempDir()
-	mkdirs(t, brain, "wiki/concepts")
-	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "concepts", "c.md")))
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "d.md"), []byte("zqinside d"), 0o644))
-	inv := map[wiki.PageType][]wiki.Entry{wiki.PageTypeConcept: {
-		{Slug: "c", Type: wiki.PageTypeConcept}, {Slug: "d", Type: wiki.PageTypeConcept},
-	}}
-	src := wiki.Page{Path: "wiki/sources/src.md", Content: "---\ntitle: Src\n---\nsee [[c|C]] and [[d|D]]\n"}
-	out := injectSourceRefs([]wiki.Page{src}, inv, brain)
-	got := fmt.Sprintf("%+v", out)
-	assert.Contains(t, got, "zqinside d", "positive control")
-	assert.NotContains(t, got, brainfstest.Sentinel)
-}
-
-func TestBackfillRefsSkipsSymlinkedSourcesAndPages(t *testing.T) {
-	brain := t.TempDir()
-	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "real.md"), []byte("---\ntitle: R\n---\nbody\n"), 0o644))
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok.md"), []byte("---\ntitle: zqinside\n---\n[[real|R]]\n"), 0o644))
-	// A source elsewhere in the brain whose title is the sentinel and which
-	// links the real concept with the [[slug|title]] form the pipeline follows.
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "src.md"),
-		[]byte("---\ntitle: "+brainfstest.Sentinel+"\n---\n[[real|R]]\n"), 0o644))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "src.md"), filepath.Join(brain, "wiki", "sources", "in.md")))
-	// A concept page linked by the regular source that is itself a symlink.
-	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok2.md"), []byte("---\ntitle: Two\n---\n[[lnk|L]]\n"), 0o644))
-	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "page.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "page.md"), filepath.Join(brain, "wiki", "concepts", "lnk.md")))
-
-	_, err := BackfillRefs(context.Background(), brain)
-	require.NoError(t, err)
-	b, _ := os.ReadFile(filepath.Join(brain, "wiki", "concepts", "real.md"))
-	assert.Contains(t, string(b), "zqinside", "positive control: the regular source's ref is added")
-	assert.NotContains(t, string(b), brainfstest.Sentinel, "a symlinked source's title was written as a ref")
-	raw, _ := os.ReadFile(filepath.Join(brain, "raw", "page.md"))
-	assert.NotContains(t, string(raw), "[[ok2", "the symlinked concept page's target was rewritten")
-}
-
-// A source swapped between a regular file and a symlink to an in-brain source
-// whose title is the sentinel: the read refuses the swapped-in link, so the
-// sentinel never lands in the concept page as a ref.
-func TestBackfillRefsDoesNotWriteARefFromASourceSwappedInBehindASymlink(t *testing.T) {
-	brain := t.TempDir()
-	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
-	realPage := filepath.Join(brain, "wiki", "concepts", "real.md")
-	target := filepath.Join(brain, "raw", "src.md")
-	require.NoError(t, os.WriteFile(target, []byte("---\ntitle: "+brainfstest.Sentinel+"\n---\n[[real|R]]\n"), 0o644))
-	src := filepath.Join(brain, "wiki", "sources", "r.md")
-	inside := "---\ntitle: zqinside\n---\n[[real|R]]\n"
-	read := func() string {
-		_ = os.WriteFile(realPage, []byte("---\ntitle: R\n---\nbody\n"), 0o644)
-		_, _ = BackfillRefs(context.Background(), brain)
-		b, _ := os.ReadFile(realPage)
-		return string(b)
-	}
-	require.NoError(t, os.WriteFile(src, []byte(inside), 0o644))
-	require.Contains(t, read(), "zqinside", "positive control")
-	brainfstest.AssertNoLeakFrom(t, src, inside, target, 1500*time.Millisecond, read)
-}
-
-// A concept page that is regular when the inventory lists it, then swapped
-// for a symlink to an in-brain file before BackfillRefs reads it: only the
-// page read's own check refuses it (a static symlink never gets this far,
-// because LoadInventory does not list it).
-func TestBackfillRefsDoesNotCopyAPageSwappedInBehindASymlink(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")
-	inside := "---\ntitle: C\n---\nzqinside\n"
-	read := func() string {
-		// The write path still follows a swapped-in link (#158) and can
-		// overwrite the target, so restore it each round.
-		_ = os.WriteFile(target, []byte("---\ntitle: X\n---\n"+brainfstest.Sentinel+"\n"), 0o644)
-		_, _ = BackfillRefs(context.Background(), brain)
-		f, err := os.OpenFile(page, os.O_RDONLY|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0)
-		if err != nil {
-			return ""
-		}
-		defer func() { _ = f.Close() }()
-		b, _ := io.ReadAll(f)
-		return string(b)
-	}
-	require.NoError(t, os.WriteFile(page, []byte(inside), 0o644))
-	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)
-}

ingestion/internal/provenance/provenance.go

@@ -28,6 +28,7 @@ import (
 	"context"
 	"errors"
 	"fmt"
+	"os"
 	"regexp"
 	"strings"
 
@@ -101,6 +102,25 @@ func Apply(content string, s Stamp) (string, error) {
 	return out, nil
 }
 
+// ApplyFile applies the stamp to the note at absPath in place.
+func ApplyFile(absPath string, s Stamp) error {
+	b, err := os.ReadFile(absPath)
+	if err != nil {
+		return fmt.Errorf("read for provenance: %w", err)
+	}
+	out, err := Apply(string(b), s)
+	if err != nil {
+		return err
+	}
+	if out == string(b) {
+		return nil
+	}
+	if err := os.WriteFile(absPath, []byte(out), 0o644); err != nil {
+		return fmt.Errorf("write provenance: %w", err)
+	}
+	return nil
+}
+
 // plainGroups keeps the provably plain key groups of a frontmatter block.
 func plainGroups(block string) string {
 	lines := strings.Split(strings.TrimSuffix(block, "\n"), "\n")

ingestion/internal/search/brainroot_test.go

@@ -12,8 +12,6 @@ import (
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
 )
 
 // hyperguild#157 option 1: search walked and read the brain by path, so a
@@ -191,49 +189,3 @@ func TestHydrateRefusesASymlink(t *testing.T) {
 	assert.Error(t, err)
 	assert.NotContains(t, r.Excerpt, sentinel157)
 }
-
-// hyperguild#171: os.Root refuses links that leave the brain on its own, so
-// the outside-target cases above would stay green for a caller that read
-// without brainfs's Lstat and SameFile checks. These targets are inside the
-// brain (raw/, which is not a search root).
-func inBrainTarget(t *testing.T, brain string) string {
-	t.Helper()
-	return brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-}
-
-func TestQueryDoesNotReturnAnInBrainSymlinkTargetDuringASampledSwapRace(t *testing.T) {
-	brain, facts, _ := searchBrain(t)
-	target := inBrainTarget(t, brain)
-	read := func() string {
-		// Both terms, so the regular note is a possible hit: a reader that
-		// never returns the inside note would pass vacuously (#177 floor).
-		rs, _ := Query(brain, QueryOptions{Query: brainfstest.Sentinel + " zqinside", Limit: 10})
-		s := ""
-		for _, r := range rs {
-			s += r.Title + r.Excerpt
-		}
-		return s
-	}
-	brainfstest.AssertNoLeakFrom(t, filepath.Join(facts, "r.md"), "# r\n\nzqinside", target, 1500*time.Millisecond, read)
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
-	assert.NotContains(t, read(), brainfstest.Sentinel, "static in-brain link")
-}
-
-func TestHydrateRefusesAnInBrainSymlinkAndDoesNotReturnItsTargetDuringASampledSwapRace(t *testing.T) {
-	brain, facts, _ := searchBrain(t)
-	target := inBrainTarget(t, brain)
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
-	r, err := hydrate(brain, "wiki/w/facts/inlink.md")
-	assert.Error(t, err)
-	assert.NotContains(t, r.Excerpt+r.Title, brainfstest.Sentinel)
-
-	p := filepath.Join(facts, "r.md")
-	require.NoError(t, os.WriteFile(p, []byte("# r\n\nzqinside"), 0o644))
-	r, err = hydrate(brain, "wiki/w/facts/r.md")
-	require.NoError(t, err)
-	assert.Contains(t, r.Excerpt, "zqinside", "positive control: a regular note hydrates")
-	brainfstest.AssertNoLeakFrom(t, p, "# r\n\nzqinside", target, 1500*time.Millisecond, func() string {
-		r, _ := hydrate(brain, "wiki/w/facts/r.md")
-		return r.Title + r.Excerpt
-	})
-}

ingestion/internal/session/id_test.go

@@ -2,17 +2,14 @@ package session
 
 import (
 	"errors"
-	"fmt"
 	"os"
 	"path/filepath"
-	"sync/atomic"
 	"syscall"
 	"testing"
 	"time"
 
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
-	"golang.org/x/sys/unix"
 )
 
 // session_log passed the caller's session_id straight into
@@ -93,85 +90,3 @@ func TestAppendReturnsPromptlyOnAFIFOLogWithNoReader(t *testing.T) {
 		t.Fatal("Append blocked on a FIFO log with no reader")
 	}
 }
-
-// hyperguild#173: session_log followed a symlinked sessions dir.
-func TestAppendRefusesASymlinkedSessionsDir(t *testing.T) {
-	root := t.TempDir()
-	elsewhere := filepath.Join(root, "elsewhere")
-	require.NoError(t, os.MkdirAll(elsewhere, 0o755))
-	dir := filepath.Join(root, "sessions")
-	require.NoError(t, os.Symlink("elsewhere", dir))
-	assert.Error(t, Append(dir, "s", Entry{SessionID: "s"}))
-	ents, _ := os.ReadDir(elsewhere)
-	assert.Empty(t, ents, "a log was created through the symlinked dir")
-}
-
-// The sessions dir is swapped (RENAME_EXCHANGE) with a symlink to a
-// directory outside the brain while Append runs. Append opens through an
-// os.Root on the sessions dir's parent, so a swap can redirect it only
-// inside that parent (the #167 residual), never outside it.
-func TestAppendNeverCreatesALogOutsideTheParentUnderADirSwapRace(t *testing.T) {
-	brain := t.TempDir()
-	outside := t.TempDir()
-	dir := filepath.Join(brain, "sessions")
-	other := filepath.Join(brain, "sessions.link")
-	require.NoError(t, os.MkdirAll(dir, 0o755))
-	require.NoError(t, os.Symlink(outside, other))
-	var stop atomic.Bool
-	done := make(chan struct{})
-	go func() {
-		defer close(done)
-		for !stop.Load() {
-			_ = unix.Renameat2(unix.AT_FDCWD, dir, unix.AT_FDCWD, other, unix.RENAME_EXCHANGE)
-		}
-	}()
-	ok := 0
-	for i := 0; i < 20000; i++ {
-		if Append(dir, fmt.Sprintf("s%d", i), Entry{SessionID: "s"}) == nil {
-			ok++
-		}
-	}
-	stop.Store(true)
-	<-done
-	ents, _ := os.ReadDir(outside)
-	assert.Empty(t, ents, "logs were created outside the brain")
-	assert.Positive(t, ok, "positive control: appends to the real dir succeed")
-}
-
-// The log file is swapped between a regular file and a symlink to another
-// file in the brain while Append runs: Append writes only after confirming
-// the path is the regular file it opened, so the other file never grows.
-func TestAppendNeverWritesThroughALogSwappedForASymlink(t *testing.T) {
-	brain := t.TempDir()
-	dir := filepath.Join(brain, "sessions")
-	require.NoError(t, os.MkdirAll(dir, 0o755))
-	victim := filepath.Join(brain, "victim.md")
-	require.NoError(t, os.WriteFile(victim, []byte("untouched\n"), 0o644))
-	log := filepath.Join(dir, "s.jsonl")
-	var stop atomic.Bool
-	done := make(chan struct{})
-	go func() {
-		defer close(done)
-		tmp := log + ".swap"
-		for i := 0; !stop.Load(); i++ {
-			_ = os.Remove(tmp)
-			if i%2 == 0 {
-				_ = os.WriteFile(tmp, nil, 0o644)
-			} else {
-				_ = os.Symlink(filepath.Join("..", "victim.md"), tmp)
-			}
-			_ = os.Rename(tmp, log)
-		}
-	}()
-	ok := 0
-	for i := 0; i < 20000; i++ {
-		if Append(dir, "s", Entry{SessionID: "s"}) == nil {
-			ok++
-		}
-	}
-	stop.Store(true)
-	<-done
-	got, _ := os.ReadFile(victim)
-	assert.Equal(t, "untouched\n", string(got), "a log line was written through the swapped-in symlink")
-	assert.Positive(t, ok, "positive control: appends to the regular log succeed")
-}

ingestion/internal/session/session.go

@@ -65,42 +65,14 @@ func Append(sessionsDir, sessionID string, entry Entry) error {
 	if err := checkID(sessionID); err != nil {
 		return err
 	}
-	// Opened through an os.Root on the sessions dir's parent (the brain dir),
-	// so a sessions dir swapped for a symlink after the check below can
-	// redirect the log only inside that parent, never outside it (#173; the
-	// in-brain swap is the #167 residual).
-	parentDir, name := filepath.Dir(sessionsDir), filepath.Base(sessionsDir)
-	if err := os.MkdirAll(parentDir, 0o755); err != nil {
-		return fmt.Errorf("create sessions parent: %w", err)
-	}
-	root, err := os.OpenRoot(parentDir)
-	if err != nil {
-		return fmt.Errorf("open sessions parent: %w", err)
-	}
-	defer func() { _ = root.Close() }()
-	if err := root.Mkdir(name, 0o755); err != nil && !errors.Is(err, fs.ErrExist) {
+	if err := os.MkdirAll(sessionsDir, 0o755); err != nil {
 		return fmt.Errorf("create sessions dir: %w", err)
 	}
-	// The sessions dir itself must be a real directory, not a symlink that
-	// redirects the log elsewhere (hyperguild#173).
-	if fi, err := root.Lstat(name); err != nil {
-		return fmt.Errorf("stat sessions dir: %w", err)
-	} else if !fi.IsDir() {
-		return fmt.Errorf("sessions dir %s is not a real directory", sessionsDir)
-	}
-	logRel := name + "/" + sessionID + ".jsonl"
-	f, err := root.OpenFile(logRel, os.O_CREATE|os.O_APPEND|os.O_WRONLY|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
+	path := filepath.Join(sessionsDir, sessionID+".jsonl")
+	f, err := os.OpenFile(path, os.O_CREATE|os.O_APPEND|os.O_WRONLY|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
 	if err != nil {
 		return fmt.Errorf("open session log: %w", err)
 	}
-	// os.Root follows an in-root final symlink even with O_NOFOLLOW, so
-	// confirm, before writing, that the path is the regular file we opened.
-	hfi, herr := f.Stat()
-	lfi, lerr := root.Lstat(logRel)
-	if herr != nil || lerr != nil || !lfi.Mode().IsRegular() || !os.SameFile(lfi, hfi) {
-		_ = f.Close()
-		return fmt.Errorf("session log %s is not a regular file", logRel)
-	}
 
 	line, err := json.Marshal(entry)
 	if err != nil {

ingestion/internal/vectorstore/sync_root_test.go

@@ -42,11 +42,6 @@ func TestSyncRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
 	brain := t.TempDir()
 	writeNote(t, brain, "wiki/w/facts/ok.md", "inside note")
 	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(brain, "wiki", "w", "facts", "leak.md")))
-	// A link to a file elsewhere in the brain: os.Root allows it, only the
-	// regular-file checks refuse it (hyperguild#171). raw/ is not a scan root,
-	// so its sentinel can only arrive through the link.
-	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
-	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "w", "facts", "inlink.md")))
 
 	emb := &recordingEmbedder{}
 	store := &stubStore{}
@@ -56,7 +51,6 @@ func TestSyncRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
 	assert.NotContains(t, emb.all(), brainfstest.Sentinel)
 	for p := range store.upserts {
 		assert.NotContains(t, p, "leak.md")
-		assert.NotContains(t, p, "inlink.md")
 	}
 
 	p := filepath.Join(brain, "knowledge", "r.md")
@@ -67,7 +61,6 @@ func TestSyncRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
 		return e.all()
 	}
 	brainfstest.AssertNoLeak(t, p, "inside", 1500*time.Millisecond, sync)
-	brainfstest.AssertNoLeakFrom(t, p, "inside", inBrain, 1500*time.Millisecond, sync)
 	brainfstest.AssertNoHang(t, p, "inside", 1500*time.Millisecond, 6*time.Second, func() { _ = sync() })
 }
 

ingestion/internal/wiki/index.go

@@ -3,6 +3,8 @@ package wiki
 
 import (
 	"fmt"
+	"os"
+	"path/filepath"
 	"strings"
 
 	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
@@ -48,8 +50,8 @@ func RebuildIndex(brainDir, date string) error {
 		sb.WriteString("\n")
 	}
 
-	// Written through the brain root, never through a symlink (#158).
-	return bfs.PutRegular("wiki/index.md", []byte(sb.String()))
+	dest := filepath.Join(brainDir, "wiki", "index.md")
+	return os.WriteFile(dest, []byte(sb.String()), 0o644)
 }
 
 // pageFirstSentence reads the page through the brain root, regular files

ingestion/internal/wiki/log.go

@@ -3,7 +3,8 @@ package wiki
 
 import (
 	"fmt"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
+	"os"
+	"path/filepath"
 	"strings"
 )
 
@@ -26,14 +27,14 @@ func AppendLog(brainDir, source string, pages, warnings []string, date string) e
 	}
 	sb.WriteString("\n")
 
-	// Appended through the brain root, never through a symlink (#158).
-	bfs, err := brainfs.Open(brainDir)
+	logPath := filepath.Join(brainDir, "log.md")
+	f, err := os.OpenFile(logPath, os.O_APPEND|os.O_CREATE|os.O_WRONLY, 0o644)
 	if err != nil {
-		return fmt.Errorf("open brain: %w", err)
+		return fmt.Errorf("open log: %w", err)
 	}
-	defer func() { _ = bfs.Close() }()
-	if err := bfs.AppendRegular("log.md", []byte(sb.String())); err != nil {
+	if _, err = f.WriteString(sb.String()); err != nil {
+		f.Close() //nolint:errcheck
 		return fmt.Errorf("write log: %w", err)
 	}
-	return nil
+	return f.Close()
 }

ingestion/internal/wiki/writers_redirect_test.go

@@ -1,35 +0,0 @@
-package wiki
-
-import (
-	"os"
-	"path/filepath"
-	"testing"
-
-	"github.com/stretchr/testify/assert"
-	"github.com/stretchr/testify/require"
-)
-
-// hyperguild#158: RebuildIndex wrote wiki/index.md and AppendLog appended
-// log.md with os.WriteFile / os.OpenFile, so a symlinked file was written
-// through.
-func TestRebuildIndexAndAppendLogDoNotWriteThroughSymlinks(t *testing.T) {
-	b := t.TempDir()
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "concepts"), 0o755))
-	victim := filepath.Join(b, "raw", "v.md")
-	require.NoError(t, os.MkdirAll(filepath.Dir(victim), 0o755))
-	require.NoError(t, os.WriteFile(victim, []byte("untouched"), 0o644))
-	require.NoError(t, os.Symlink(filepath.Join("..", "raw", "v.md"), filepath.Join(b, "wiki", "index.md")))
-	require.NoError(t, os.Symlink(filepath.Join("raw", "v.md"), filepath.Join(b, "log.md")))
-
-	assert.Error(t, RebuildIndex(b, "2026-10-05"))
-	assert.Error(t, AppendLog(b, "src", []string{"p"}, nil, "2026-10-05"))
-	got, _ := os.ReadFile(victim)
-	assert.Equal(t, "untouched", string(got))
-
-	require.NoError(t, os.Remove(filepath.Join(b, "wiki", "index.md")))
-	require.NoError(t, os.Remove(filepath.Join(b, "log.md")))
-	require.NoError(t, RebuildIndex(b, "2026-10-05"), "positive control")
-	require.NoError(t, AppendLog(b, "src", []string{"p"}, nil, "2026-10-05"), "positive control")
-	l, _ := os.ReadFile(filepath.Join(b, "log.md"))
-	assert.Contains(t, string(l), "src")
-}