fix(linkcheck): skip a linked tree that is not a real directory (#157)

Review round 1 on PR #175:

- entryIndex returned WalkRegular's walk-root ErrNotRegular as an error,
  and StripUnresolvedLinks runs before every brain_write: a symlinked,
  dangling or regular-file knowledge/ (or wiki/) made every write fail
  and lose the learning. main's filepath.WalkDir skipped such a root. It
  is now skipped with a warning; other walk errors still abort, as on
  main. New table test over the three shapes.
- The symlinked-hall assertion passed with no index written at all. It
  now indexes a real hall next to the symlinked one and asserts no
  error, the index exists and lists the real note; a new test does the
  same for BuildAllWingIndexes with a symlinked wing next to a real one.
- The test comment no longer says this PR fixed the FIFO hang on every
  brain_write: that path is tunnel.DetectTunnels (slice 5b).

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

ingestion/internal/brain/index.go

@@ -2,12 +2,18 @@ package brain
 
 import (
 	"bufio"
+	"bytes"
+	"errors"
 	"fmt"
+	"io"
+	"io/fs"
 	"os"
 	"path/filepath"
 	"sort"
 	"strings"
 	"time"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 )
 
 // noteEntry is one row in a Wing _index.md.
@@ -27,13 +33,18 @@ func BuildWingIndex(brainDir, wing string) error {
 		return fmt.Errorf("invalid wing %q", wing)
 	}
 	wingDir := filepath.Join(brainDir, "wiki", w)
-	if _, err := os.Stat(wingDir); os.IsNotExist(err) {
+	// 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)
+	if err != nil {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	if _, err := bfs.Lstat("wiki/" + w); errors.Is(err, fs.ErrNotExist) {
 		return nil
-	} else if err != nil {
-		return fmt.Errorf("stat wing: %w", err)
 	}
 
-	entries, err := collectWingEntries(wingDir)
+	entries, err := collectWingEntries(bfs, "wiki/"+w)
 	if err != nil {
 		return err
 	}
@@ -58,51 +69,47 @@ func BuildWingIndex(brainDir, wing string) error {
 
 // BuildAllWingIndexes regenerates _index.md for every wing under brain/wiki/.
 func BuildAllWingIndexes(brainDir string) error {
-	wikiDir := filepath.Join(brainDir, "wiki")
+	bfs, err := brainfs.Open(brainDir)
-	ents, err := os.ReadDir(wikiDir)
+	if err != nil {
-	if os.IsNotExist(err) {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	wings, err := bfs.ReadDirDirs("wiki")
+	_ = bfs.Close()
+	if errors.Is(err, fs.ErrNotExist) {
 		return nil
 	}
 	if err != nil {
 		return fmt.Errorf("read wiki: %w", err)
 	}
-	for _, e := range ents {
+	for _, w := range wings {
-		if !e.IsDir() {
+		if err := BuildWingIndex(brainDir, w); err != nil {
-			continue
+			return fmt.Errorf("index %s: %w", w, err)
-		}
-		if err := BuildWingIndex(brainDir, e.Name()); err != nil {
-			return fmt.Errorf("index %s: %w", e.Name(), err)
 		}
 	}
 	return nil
 }
 
-func collectWingEntries(wingDir string) ([]noteEntry, error) {
+func collectWingEntries(bfs *brainfs.Brain, wingRel string) ([]noteEntry, error) {
 	var out []noteEntry
-	ents, err := os.ReadDir(wingDir)
+	halls, err := bfs.ReadDirDirs(wingRel)
 	if err != nil {
 		return nil, fmt.Errorf("read wing: %w", err)
 	}
-	for _, hallEnt := range ents {
+	for _, hall := range halls {
-		if !hallEnt.IsDir() {
-			continue
-		}
-		hall := hallEnt.Name()
 		if !IsValidHall(hall) {
 			continue
 		}
-		hallDir := filepath.Join(wingDir, hall)
+		hallRel := wingRel + "/" + hall
-		notes, err := os.ReadDir(hallDir)
+		names, err := bfs.ReadDirRegular(hallRel)
 		if err != nil {
 			return nil, fmt.Errorf("read hall %s: %w", hall, err)
 		}
-		for _, n := range notes {
+		for _, name := range names {
-			if n.IsDir() || !strings.HasSuffix(n.Name(), ".md") || n.Name() == "_index.md" {
+			if !strings.HasSuffix(name, ".md") || name == "_index.md" {
 				continue
 			}
-			slug := strings.TrimSuffix(n.Name(), ".md")
+			slug := strings.TrimSuffix(name, ".md")
-			full := filepath.Join(hallDir, n.Name())
+			title, created := readTitleAndCreatedIn(bfs, hallRel+"/"+name, slug)
-			title, created := readTitleAndCreated(full, slug)
 			out = append(out, noteEntry{Hall: hall, Slug: slug, Title: title, Created: created})
 		}
 	}
@@ -117,9 +124,40 @@ func readTitleAndCreated(path, slug string) (string, string) {
 		return slug, ""
 	}
 	defer func() { _ = f.Close() }()
+	title, created := parseTitleAndCreated(f)
+	if created == "" {
+		if info, err := os.Stat(path); err == nil {
+			created = info.ModTime().UTC().Format("2006-01-02")
+		}
+	}
+	return titleOrSlug(title, slug), created
+}
 
-	title, created := "", ""
+// readTitleAndCreatedIn is readTitleAndCreated through the brain root,
-	scanner := bufio.NewScanner(f)
+// regular files only (hyperguild#157).
+func readTitleAndCreatedIn(bfs *brainfs.Brain, rel, slug string) (string, string) {
+	content, err := bfs.ReadRegular(rel)
+	if err != nil {
+		return slug, ""
+	}
+	title, created := parseTitleAndCreated(bytes.NewReader(content))
+	if created == "" {
+		if info, err := bfs.Lstat(rel); err == nil {
+			created = info.ModTime().UTC().Format("2006-01-02")
+		}
+	}
+	return titleOrSlug(title, slug), created
+}
+
+func titleOrSlug(title, slug string) string {
+	if title == "" {
+		return strings.ReplaceAll(slug, "-", " ")
+	}
+	return title
+}
+
+func parseTitleAndCreated(r io.Reader) (title, created string) {
+	scanner := bufio.NewScanner(r)
 	inFrontmatter := false
 	for scanner.Scan() {
 		line := scanner.Text()
@@ -149,13 +187,5 @@ func readTitleAndCreated(path, slug string) (string, string) {
 			}
 		}
 	}
-	if title == "" {
-		title = strings.ReplaceAll(slug, "-", " ")
-	}
-	if created == "" {
-		if info, err := os.Stat(path); err == nil {
-			created = info.ModTime().UTC().Format("2006-01-02")
-		}
-	}
 	return title, created
 }

ingestion/internal/brain/index_root_test.go

@@ -0,0 +1,132 @@
+package brain_test
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+func readIndex(t *testing.T, brainDir, wing string) string {
+	t.Helper()
+	b, _ := os.ReadFile(filepath.Join(brainDir, "wiki", wing, "_index.md"))
+	return string(b)
+}
+
+// hyperguild#157 slice 5: BuildWingIndex listed wiki/<wing>/<hall>/ with
+// os.ReadDir and opened each note by path, so a symlinked note put the
+// target's title into _index.md, and a FIFO hung the index build.
+func TestBuildWingIndexRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
+	b := t.TempDir()
+	facts := filepath.Join(b, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "ok.md"), []byte("---\ntitle: zqinside\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
+	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(b, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "inlink.md")))
+
+	require.NoError(t, brain.BuildWingIndex(b, "w"))
+	idx := readIndex(t, b, "w")
+	assert.Contains(t, idx, "zqinside", "positive control")
+	assert.NotContains(t, idx, brainfstest.Sentinel)
+	assert.NotContains(t, idx, "leak")
+	assert.NotContains(t, idx, "inlink")
+
+	p := filepath.Join(facts, "r.md")
+	read := func() string {
+		_ = brain.BuildWingIndex(b, "w")
+		return readIndex(t, b, "w")
+	}
+	brainfstest.AssertNoLeak(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, read)
+	brainfstest.AssertNoLeakFrom(t, p, "---\ntitle: zqinside\n---\n", inBrain, 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}
+
+// A symlinked hall is skipped while a real hall next to it is indexed; a
+// symlinked wing is refused and nothing is written into its target.
+func TestBuildWingIndexSkipsASymlinkedHallAndRefusesASymlinkedWing(t *testing.T) {
+	b := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(b, "raw", "facts", "r.md"), []byte("---\ntitle: zqrawonly\n---\n"), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w", "decisions"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "w", "decisions", "d.md"), []byte("---\ntitle: zqrealhall\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(b, "wiki", "w", "facts")))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(b, "wiki", "alias")))
+
+	require.NoError(t, brain.BuildWingIndex(b, "w"))
+	idx, err := os.ReadFile(filepath.Join(b, "wiki", "w", "_index.md"))
+	require.NoError(t, err, "the wing index is written")
+	assert.Contains(t, string(idx), "zqrealhall", "the real hall is indexed")
+	assert.NotContains(t, string(idx), "zqrawonly", "the symlinked hall is not")
+
+	assert.Error(t, brain.BuildWingIndex(b, "alias"))
+	_, err = os.Stat(filepath.Join(b, "raw", "_index.md"))
+	assert.True(t, os.IsNotExist(err), "an index was written into the symlinked wing's target")
+}
+
+// BuildAllWingIndexes indexes the real wings and skips a symlinked one.
+func TestBuildAllWingIndexesSkipsASymlinkedWing(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: zqrealwing\n---\n"), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "facts"), 0o755))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(b, "wiki", "alias")))
+
+	require.NoError(t, brain.BuildAllWingIndexes(b))
+	idx, err := os.ReadFile(filepath.Join(b, "wiki", "w", "_index.md"))
+	require.NoError(t, err)
+	assert.Contains(t, string(idx), "zqrealwing")
+	_, err = os.Stat(filepath.Join(b, "raw", "_index.md"))
+	assert.True(t, os.IsNotExist(err))
+}
+
+// A link to a symlinked note does not resolve: only regular files count as
+// entries, so StripUnresolvedLinks unwraps it.
+func TestStripUnresolvedLinksDoesNotCountASymlinkedNoteAsAnEntry(t *testing.T) {
+	b := t.TempDir()
+	facts := filepath.Join(b, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "real.md"), []byte("x"), 0o644))
+	brainfstest.WriteSentinelAt(t, filepath.Join(b, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "ghost.md")))
+	out, unlinked, err := brain.StripUnresolvedLinks(b, "see [[real]] and [[ghost]]")
+	require.NoError(t, err)
+	assert.Contains(t, out, "[[real]]", "positive control")
+	assert.NotContains(t, out, "[[ghost]]")
+	assert.Contains(t, unlinked, "ghost")
+}
+
+// A linked tree (knowledge/ or wiki/) that is not a real directory is
+// skipped, not an error: StripUnresolvedLinks runs before every brain_write,
+// and an error there loses the learning.
+func TestStripUnresolvedLinksSkipsALinkedTreeThatIsNotARealDirectory(t *testing.T) {
+	for name, mk := range map[string]func(t *testing.T, b string){
+		"symlink to an in-brain dir": func(t *testing.T, b string) {
+			require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "k"), 0o755))
+			require.NoError(t, os.Symlink(filepath.Join("raw", "k"), filepath.Join(b, "knowledge")))
+		},
+		"dangling symlink": func(t *testing.T, b string) {
+			require.NoError(t, os.Symlink("nowhere", filepath.Join(b, "knowledge")))
+		},
+		"regular file": func(t *testing.T, b string) {
+			require.NoError(t, os.WriteFile(filepath.Join(b, "knowledge"), []byte("x"), 0o644))
+		},
+	} {
+		t.Run(name, func(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", "real.md"), []byte("x"), 0o644))
+			mk(t, b)
+			out, _, err := brain.StripUnresolvedLinks(b, "learning [[real]] and [[gone]]")
+			require.NoError(t, err)
+			assert.Contains(t, out, "[[real]]", "links into wiki/ still resolve")
+			assert.NotContains(t, out, "[[gone]]")
+		})
+	}
+}

ingestion/internal/brain/linkcheck.go

@@ -1,12 +1,16 @@
 package brain
 
 import (
+	"errors"
 	"fmt"
-	"os"
+	"io/fs"
-	"path/filepath"
+	"log/slog"
+	"path"
 	"regexp"
 	"sort"
 	"strings"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 )
 
 // wikilinkRE matches [[target]] and [[target|Display Text]].
@@ -98,29 +102,40 @@ var linkedTrees = []string{"knowledge", "wiki"}
 // one the audit will also resolve.
 func entryIndex(brainDir string) (map[string]struct{}, error) {
 	index := map[string]struct{}{}
-	for _, dir := range linkedTrees {
+	// Walked through the brain root (hyperguild#157): only regular files
-		root := filepath.Join(brainDir, dir)
+	// count as entries, so a symlinked .md name cannot make a link resolve.
-		if _, err := os.Stat(root); os.IsNotExist(err) {
+	bfs, err := brainfs.Open(brainDir)
-			continue
-		} else if err != nil {
-			return nil, fmt.Errorf("stat %s: %w", dir, err)
-		}
-		err := filepath.WalkDir(root, func(path string, d os.DirEntry, err error) error {
 	if err != nil {
-				return err
+		return nil, fmt.Errorf("open brain: %w", err)
 	}
-			if d.IsDir() || !strings.HasSuffix(path, ".md") {
+	defer func() { _ = bfs.Close() }()
+	for _, dir := range linkedTrees {
+		if _, err := bfs.Lstat(dir); errors.Is(err, fs.ErrNotExist) {
+			continue
+		}
+		var walkErr error
+		err := bfs.WalkRegular(dir, func(rel string) error {
+			if !strings.HasSuffix(rel, ".md") {
 				return nil
 			}
-			rel, err := filepath.Rel(brainDir, path)
+			index[strings.TrimSuffix(path.Base(rel), ".md")] = struct{}{}
-			if err != nil {
-				return err
-			}
-			rel = filepath.ToSlash(rel)
-			index[strings.TrimSuffix(filepath.Base(rel), ".md")] = struct{}{}
 			index[strings.TrimPrefix(strings.TrimSuffix(rel, ".md"), "wiki/")] = struct{}{}
 			return nil
+		}, func(rel string, err error) {
+			// A linked tree that is not a real directory (a symlink, a
+			// file) is skipped, as filepath.WalkDir did: this runs before
+			// every brain_write, and an error here loses the learning.
+			if rel == dir && errors.Is(err, brainfs.ErrNotRegular) {
+				slog.Warn("link check: skipping a linked tree that is not a real directory", "dir", dir)
+				return
+			}
+			if walkErr == nil {
+				walkErr = fmt.Errorf("%s: %w", rel, err)
+			}
 		})
+		if err == nil {
+			err = walkErr
+		}
 		if err != nil {
 			return nil, fmt.Errorf("walk %s: %w", dir, err)
 		}

ingestion/internal/brainfs/brainfs.go

@@ -104,6 +104,27 @@ func (b *Brain) ReadDirRegular(relDir string) ([]string, error) {
 	return names, 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.
+func (b *Brain) ReadDirDirs(relDir string) ([]string, error) {
+	relDir = filepath.ToSlash(relDir)
+	if err := b.realDir(relDir); err != nil {
+		return nil, err
+	}
+	ents, err := fs.ReadDir(b.root.FS(), relDir)
+	if err != nil {
+		return nil, err
+	}
+	var names []string
+	for _, e := range ents {
+		if e.Type().IsDir() {
+			names = append(names, e.Name())
+		}
+	}
+	return names, 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) {

ingestion/internal/brainfs/brainfs_test.go

@@ -262,3 +262,21 @@ func TestReadRegularNeverReturnsAnInBrainFileSwappedInBehindASymlink(t *testing.
 	assert.Zero(t, leaks)
 	assert.Positive(t, ok, "positive control: the regular file is read")
 }
+
+func TestReadDirDirsListsOnlyRealSubdirsAndRefusesSymlinkedComponents(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "a", "real"), 0o755))
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "other"), 0o755))
+	require.NoError(t, os.Symlink(filepath.Join("..", "other"), filepath.Join(dir, "a", "linked")))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "a", "f.md"), []byte("f"), 0o644))
+	require.NoError(t, os.Symlink("a", filepath.Join(dir, "alias")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+
+	names, err := b.ReadDirDirs("a")
+	require.NoError(t, err)
+	assert.Equal(t, []string{"real"}, names)
+	_, err = b.ReadDirDirs("alias")
+	assert.ErrorIs(t, err, ErrNotRegular)
+}

ingestion/internal/classification/classification.go

@@ -16,10 +16,9 @@
 package classification
 
 import (
-	"errors"
 	"fmt"
-	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
+	"os"
-	"io/fs"
+	"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
+	data, err := os.ReadFile(filepath.Join(brainDir, "classification.yaml"))
-	// 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
-	}
 	if err != nil {
-		return nil, fmt.Errorf("open brain: %w", err)
+		if os.IsNotExist(err) {
-	}
-	defer func() { _ = bfs.Close() }()
-	data, err := bfs.ReadRegular("classification.yaml")
-	if err != nil {
-		if errors.Is(err, fs.ErrNotExist) {
 			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/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
+	sourcesDir := filepath.Join(brainDir, "wiki", "sources")
-	// (hyperguild#157).
+	entries, err := os.ReadDir(sourcesDir)
-	bfs, err := brainfs.Open(brainDir)
 	if err != nil {
-		return 0, fmt.Errorf("open brain: %w", err)
+		if os.IsNotExist(err) {
-	}
-	defer func() { _ = bfs.Close() }()
-	names, err := bfs.ReadDirRegular("wiki/sources")
-	if err != nil {
-		if errors.Is(err, fs.ErrNotExist) {
 			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) {
+func reviseOrCreate(dest string, page wiki.Page) (string, []string, error) {
-	existing, err := readBrainFile(brainDir, page.Path)
+	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(), "zqinside", "positive control: the regular page gets the ref")
-	brainfstest.AssertNoLeakFrom(t, page, inside, target, 3*time.Second, read)
-}