fix(brain_edit): snapshot, rollback and lock file go through the brain root (#192)

brain_edit did its own I/O by path around notes.Edit:
- the pre-edit snapshot used os.ReadFile, which hung on a FIFO note held
  open by a writer;
- the rollback (when the provenance stamp fails) used os.WriteFile;
- the edit lock "<note>.lock" was opened with O_CREATE by path, so a
  planted dangling .lock symlink made a successful edit create a file at
  the link's target, in the brain or outside it.

Snapshot is brainfs ReadRegular, rollback WriteRegular, and the lock is
opened and removed through new brainfs OpenLock/RemoveLock: clean path,
real parent directories, an existing lock must be regular, and the opened
handle must be the file at the path (SameFile).

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

ingestion/cmd/server/symlink_check_test.go

@@ -4,6 +4,7 @@ import (
 	"os"
 	"path/filepath"
 	"strings"
+	"syscall"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -63,3 +64,13 @@ func TestStartupSymlinkCheckRefusesAnUnlistableBrainRoot(t *testing.T) {
 	t.Cleanup(func() { _ = os.Chmod(brain, 0o755) })
 	assert.Error(t, startupSymlinkCheck(brain))
 }
+
+// hyperguild#179: a FIFO in the brain is refused at startup with a clear
+// message, instead of hanging or exiting later in a reader.
+func TestStartupSymlinkCheckRefusesABrainWithAFIFO(t *testing.T) {
+	brain := t.TempDir()
+	require.NoError(t, syscall.Mkfifo(filepath.Join(brain, "classification.yaml"), 0o644))
+	err := startupSymlinkCheck(brain)
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "classification.yaml")
+}

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 // indirect
+	golang.org/x/sys v0.45.0
 	golang.org/x/text v0.39.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1
 )

ingestion/internal/api/readnote_root_test.go

@@ -23,6 +23,13 @@ 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))
@@ -39,5 +46,7 @@ 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

@@ -0,0 +1,36 @@
+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_keeps_learning_test.go

@@ -0,0 +1,34 @@
+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#178: an unreadable directory under wiki/ made the link check
+// fail and brain_write refuse the note, losing the learning. The note is now
+// written with its links as given.
+func TestWriteNoteKeepsTheLearningWhenTheLinkCheckCannotIndex(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	brain := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki", "w", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "w", "facts", "real.md"), []byte("x"), 0o644))
+	locked := filepath.Join(brain, "wiki", "other", "locked")
+	require.NoError(t, os.MkdirAll(locked, 0o755))
+	require.NoError(t, os.Chmod(locked, 0o000))
+	t.Cleanup(func() { _ = os.Chmod(locked, 0o755) })
+
+	rel, err := api.WriteNote(brain, api.WriteNoteOptions{Wing: "w", Hall: "facts", Filename: "n", Content: "learning [[real]] and [[gone]]"})
+	require.NoError(t, err)
+	got, err := os.ReadFile(filepath.Join(brain, filepath.FromSlash(rel)))
+	require.NoError(t, err)
+	assert.Contains(t, string(got), "[[gone]]", "links kept as given when the index is partial")
+}

ingestion/internal/brain/detect_root_test.go

@@ -0,0 +1,125 @@
+package brain_test
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"syscall"
+	"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"
+)
+
+// hyperguild#174 / #157 slice 5b: DetectTunnels walked wiki/ and opened
+// every note with a blocking os.Open, so a FIFO named *.md anywhere under
+// wiki/ hung every brain_write and brain_update (wikiUpkeep -> AutoTunnel),
+// and a symlinked note's title became a tunnel candidate.
+func TestDetectTunnelsReturnsPromptlyWithAFIFOUnderWikiWithAndWithoutAWriter(t *testing.T) {
+	for _, withWriter := range []bool{false, true} {
+		t.Run(fmt.Sprintf("writer=%v", withWriter), func(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 Phrase\n---\n"), 0o644))
+			fifo := filepath.Join(facts, "f.md")
+			require.NoError(t, syscall.Mkfifo(fifo, 0o644))
+			if withWriter {
+				// A writer held open: a reader that opens the FIFO gets no
+				// EOF and parks, unless the FIFO is never opened.
+				w, err := os.OpenFile(fifo, os.O_RDWR, 0)
+				require.NoError(t, err)
+				t.Cleanup(func() { _ = w.Close() })
+			}
+			done := make(chan []brain.TunnelCandidate, 1)
+			go func() {
+				cs, _ := brain.DetectTunnels(b, "text mentioning zqinside phrase here")
+				done <- cs
+			}()
+			select {
+			case cs := <-done:
+				assert.Contains(t, fmt.Sprintf("%+v", cs), "Zqinside Phrase", "positive control")
+			case <-time.After(3 * time.Second):
+				if r, err := os.OpenFile(fifo, os.O_WRONLY|syscall.O_NONBLOCK, 0); err == nil {
+					_ = r.Close()
+				}
+				t.Fatal("DetectTunnels blocked on a FIFO")
+			}
+		})
+	}
+}
+
+func TestDetectTunnelsRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
+	b := t.TempDir()
+	facts := filepath.Join(b, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	// The static note's title differs from the raced note's, so the
+	// harness's "inside was read" floor can only be met by reading r.md.
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "ok.md"), []byte("---\ntitle: Zqstatic Words\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "out.md")))
+	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(b, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "s.md"), filepath.Join(facts, "in.md")))
+	content := "zqstatic words, zqinside phrase and " + brainfstest.Sentinel
+
+	cs, err := brain.DetectTunnels(b, content)
+	require.NoError(t, err)
+	got := fmt.Sprintf("%+v", cs)
+	assert.Contains(t, got, "Zqstatic Words", "positive control")
+	assert.NotContains(t, got, brainfstest.Sentinel)
+
+	p := filepath.Join(facts, "r.md")
+	read := func() string {
+		cs, _ := brain.DetectTunnels(b, content)
+		return fmt.Sprintf("%+v", cs)
+	}
+	brainfstest.AssertNoLeak(t, p, "---\ntitle: Zqinside Phrase\n---\n", 1500*time.Millisecond, read)
+	brainfstest.AssertNoLeakFrom(t, p, "---\ntitle: Zqinside Phrase\n---\n", inBrain, 1500*time.Millisecond, read)
+}
+
+// A wiki/ that is not a real directory yields no candidates and no error:
+// AutoTunnel runs inside brain_write.
+func TestDetectTunnelsSkipsAWikiThatIsNotARealDirectory(t *testing.T) {
+	b := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "w", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(b, "raw", "w", "facts", "r.md"), []byte("---\ntitle: Zqrawonly Phrase\n---\n"), 0o644))
+	require.NoError(t, os.Symlink("raw", filepath.Join(b, "wiki")))
+	cs, err := brain.DetectTunnels(b, "zqrawonly phrase")
+	require.NoError(t, err)
+	assert.Empty(t, cs)
+}
+
+// An unreadable directory under wiki/ is a walk error and DetectTunnels
+// reports it, as filepath.WalkDir did; it is not silently dropped.
+func TestDetectTunnelsReportsAnUnreadableDirectoryUnderWiki(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	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", "ok.md"), []byte("---\ntitle: Zqinside Phrase\n---\n"), 0o644))
+	locked := filepath.Join(b, "wiki", "other", "locked")
+	require.NoError(t, os.MkdirAll(locked, 0o755))
+	require.NoError(t, os.Chmod(locked, 0o000))
+	t.Cleanup(func() { _ = os.Chmod(locked, 0o755) })
+	_, err := brain.DetectTunnels(b, "zqinside phrase")
+	assert.ErrorIs(t, err, os.ErrPermission)
+}
+
+// _index.md files are generated, not notes: their title never becomes a
+// candidate.
+func TestDetectTunnelsSkipsIndexFiles(t *testing.T) {
+	b := t.TempDir()
+	w := filepath.Join(b, "wiki", "w")
+	require.NoError(t, os.MkdirAll(filepath.Join(w, "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(w, "_index.md"), []byte("---\ntitle: Zqindex Words\n---\n"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(w, "facts", "ok.md"), []byte("---\ntitle: Zqinside Phrase\n---\n"), 0o644))
+	cs, err := brain.DetectTunnels(b, "zqindex words and zqinside phrase")
+	require.NoError(t, err)
+	got := fmt.Sprintf("%+v", cs)
+	assert.Contains(t, got, "Zqinside Phrase", "positive control")
+	assert.NotContains(t, got, "Zqindex")
+}

ingestion/internal/brain/index.go

@@ -116,23 +116,6 @@ func collectWingEntries(bfs *brainfs.Brain, wingRel string) ([]noteEntry, error)
 	return out, nil
 }
 
-// readTitleAndCreated reads YAML frontmatter for title + created_at; falls
-// back to slug and file mtime when absent.
-func readTitleAndCreated(path, slug string) (string, string) {
-	f, err := os.Open(path)
-	if err != nil {
-		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
-}
-
 // readTitleAndCreatedIn is readTitleAndCreated through the brain root,
 // regular files only (hyperguild#157).
 func readTitleAndCreatedIn(bfs *brainfs.Brain, rel, slug string) (string, string) {

ingestion/internal/brain/linkcheck.go

@@ -47,7 +47,12 @@ var (
 func StripUnresolvedLinks(brainDir, content string) (string, []string, error) {
 	index, err := entryIndex(brainDir)
 	if err != nil {
-		return "", nil, err
+		// A partial index cannot tell an invented link from one into the
+		// part it could not read, so unwrap nothing, and do not refuse the
+		// write either: this runs before every brain_write, and a refused
+		// write is a lost learning (hyperguild#178).
+		slog.Warn("link check skipped: cannot index the brain", "err", err)
+		return content, nil, nil
 	}
 	if len(index) == 0 {
 		return content, nil, nil

ingestion/internal/brain/linkcheck_fallback_test.go

@@ -0,0 +1,41 @@
+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#178: StripUnresolvedLinks runs before every brain_write and
+// brain_update. An unreadable directory under knowledge/ or wiki/ made it
+// error, the write was refused and the learning lost. When the link index
+// cannot be built, the content is now returned unchanged (no link is
+// unwrapped, none is invented) and no error stops the write.
+func TestStripUnresolvedLinksKeepsContentWhenTheIndexCannotBeBuilt(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	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))
+	locked := filepath.Join(b, "wiki", "other", "locked")
+	require.NoError(t, os.MkdirAll(locked, 0o755))
+	require.NoError(t, os.Chmod(locked, 0o000))
+	t.Cleanup(func() { _ = os.Chmod(locked, 0o755) })
+
+	in := "learning [[real]] and [[gone]]"
+	out, unlinked, err := brain.StripUnresolvedLinks(b, in)
+	require.NoError(t, err)
+	assert.Equal(t, in, out, "content unchanged: no link unwrapped on a partial index")
+	assert.Empty(t, unlinked)
+
+	require.NoError(t, os.Chmod(locked, 0o755))
+	out, _, err = brain.StripUnresolvedLinks(b, in)
+	require.NoError(t, err)
+	assert.NotContains(t, out, "[[gone]]", "positive control: with a readable tree the strip runs")
+}

ingestion/internal/brain/tunnel.go

@@ -2,7 +2,9 @@ package brain
 
 import (
 	"bufio"
+	"errors"
 	"fmt"
+	"io/fs"
 	"os"
 	"path"
 	"path/filepath"
@@ -39,24 +41,29 @@ type TunnelCandidate struct {
 // A note's title is read from YAML frontmatter `title:`; failing that,
 // the filename slug (sans `.md`, hyphens → spaces) is used.
 func DetectTunnels(brainDir, content string) ([]TunnelCandidate, error) {
-	wikiDir := filepath.Join(brainDir, "wiki")
-	if _, err := os.Stat(wikiDir); os.IsNotExist(err) {
+	// Walked and read through the brain root, regular files only
+	// (hyperguild#174, #157): this runs inside every brain_write, so a FIFO
+	// must not block it and a symlinked note's title must not become a
+	// candidate.
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return nil, fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	if _, err := bfs.Lstat("wiki"); errors.Is(err, fs.ErrNotExist) {
 		return nil, nil
-	} else if err != nil {
-		return nil, fmt.Errorf("stat wiki: %w", err)
 	}
 
 	lowerContent := strings.ToLower(content)
 
 	var out []TunnelCandidate
-	err := filepath.WalkDir(wikiDir, func(path string, d os.DirEntry, err error) error {
-		if err != nil {
-			return err
-		}
-		if d.IsDir() || !strings.HasSuffix(path, ".md") || d.Name() == "_index.md" {
+	var walkErr error
+	err = bfs.WalkRegular("wiki", func(rel string) error {
+		name := path.Base(rel)
+		if !strings.HasSuffix(name, ".md") || name == "_index.md" {
 			return nil
 		}
-		title, _ := readTitleAndCreated(path, strings.TrimSuffix(d.Name(), ".md"))
+		title, _ := readTitleAndCreatedIn(bfs, rel, strings.TrimSuffix(name, ".md"))
 		title = strings.TrimSpace(title)
 		if title == "" {
 			return nil
@@ -78,17 +85,25 @@ func DetectTunnels(brainDir, content string) ([]TunnelCandidate, error) {
 		if idx == -1 {
 			return nil
 		}
-		rel, err := filepath.Rel(brainDir, path)
-		if err != nil {
-			return err
-		}
 		out = append(out, TunnelCandidate{
-			TargetPath:  filepath.ToSlash(rel),
+			TargetPath:  rel,
 			MatchedTerm: title,
 			Exact:       isWholeWord(haystack, idx, len(needle)),
 		})
 		return nil
+	}, func(rel string, err error) {
+		// A wiki/ that is not a real directory yields no candidates, as
+		// filepath.WalkDir did; other walk errors still abort.
+		if rel == "wiki" && errors.Is(err, brainfs.ErrNotRegular) {
+			return
+		}
+		if walkErr == nil {
+			walkErr = fmt.Errorf("%s: %w", rel, err)
+		}
 	})
+	if err == nil {
+		err = walkErr
+	}
 	if err != nil {
 		return nil, err
 	}

ingestion/internal/brain/tunnel_redirect_test.go

@@ -0,0 +1,38 @@
+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/brainfs/brainfs.go

@@ -104,6 +104,17 @@ 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.
@@ -125,9 +136,58 @@ func (b *Brain) ReadDirDirs(relDir string) ([]string, error) {
 	return names, nil
 }
 
+// OpenLock opens (creating if absent) a regular lock file at a clean
+// brain-relative path for flock, through the root (hyperguild#192): every
+// directory above it must be real, an existing lock must be a regular file,
+// and the opened handle must be the file at the path (os.Root follows an
+// in-root final symlink even with O_NOFOLLOW). A dangling or swapped-in
+// symlink is refused; nothing is created at its target.
+func (b *Brain) OpenLock(rel string) (*os.File, error) {
+	if err := cleanRel(rel); err != nil {
+		return nil, err
+	}
+	if err := b.realDir(path.Dir(rel)); err != nil {
+		return nil, err
+	}
+	if fi, err := b.root.Lstat(rel); err == nil && !fi.Mode().IsRegular() {
+		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
+	} else if err != nil && !errors.Is(err, fs.ErrNotExist) {
+		return nil, err
+	}
+	f, err := b.root.OpenFile(rel, os.O_RDWR|os.O_CREATE|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
+	if err != nil {
+		return nil, err
+	}
+	hfi, herr := f.Stat()
+	lfi, lerr := b.root.Lstat(rel)
+	if herr != nil || lerr != nil || !lfi.Mode().IsRegular() || !os.SameFile(lfi, hfi) {
+		_ = f.Close()
+		return nil, fmt.Errorf("%s: changed while opening: %w", rel, ErrNotRegular)
+	}
+	return f, nil
+}
+
+// RemoveLock removes the lock file at rel through the root (a symlink there
+// is removed itself, never its target).
+func (b *Brain) RemoveLock(rel string) error {
+	if err := cleanRel(rel); err != nil {
+		return err
+	}
+	if err := b.realDir(path.Dir(rel)); err != nil {
+		return err
+	}
+	return b.root.Remove(rel)
+}
+
 // 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
@@ -154,6 +214,12 @@ 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
@@ -256,10 +322,20 @@ 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. Intermediate in-brain symlinks are still followed (os.Root keeps
-// the write inside the brain; hyperguild#167).
+// 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.
 func (b *Brain) WriteRegular(rel string, data []byte) error {
-	rel = filepath.ToSlash(rel)
+	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
+	}
 	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 TestReadRegularNeverReturnsAnInBrainFileSwappedInBehindASymlink(t *testing.T) {
+func TestReadRegularDoesNotReturnAnInBrainFileSwappedInBehindASymlink(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")
@@ -326,3 +326,53 @@ 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))
+}

ingestion/internal/brainfs/brainfstest/brainfstest.go

@@ -1,8 +1,10 @@
 // Package brainfstest is the shared harness for hyperguild#157's swap-race
-// 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
+// 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
 // hard links, other paths into the reader, or races it does not generate.
 package brainfstest
 
@@ -18,7 +20,7 @@ import (
 	"time"
 )
 
-// Sentinel marks the outside file's contents.
+// Sentinel marks the target file's contents.
 const Sentinel = "zqbrainfssentinelonefiftyseven"
 
 // outsideContent carries Sentinel in every field a reader might extract: the
@@ -141,7 +143,7 @@ func AssertNoLeakFrom(t testing.TB, path, inside, target string, d time.Duration
 		}
 	}
 	if leaks > 0 {
-		t.Fatalf("outside file leaked %d times in %d iterations", leaks, iters)
+		t.Fatalf("symlink target %s leaked %d times in %d iterations", target, 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/mcp/edit_pathio_test.go

@@ -0,0 +1,61 @@
+package mcp_test
+
+import (
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/mcp"
+)
+
+// hyperguild#192: brain_edit snapshotted the note with os.ReadFile by path,
+// which blocks on a FIFO held open by a writer, and hung the call.
+func TestBrainEditReturnsPromptlyOnAFIFONoteWithAWriter(t *testing.T) {
+	dir := newBrainRepo(t)
+	fifo := filepath.Join(dir, "wiki", "homelab", "facts", "f.md")
+	require.NoError(t, syscall.Mkfifo(fifo, 0o644))
+	w, err := os.OpenFile(fifo, os.O_RDWR, 0)
+	require.NoError(t, err)
+	t.Cleanup(func() { _ = w.Close() })
+	srv := mcp.NewServer(dir, nil, nil, nil)
+
+	done := make(chan map[string]any, 1)
+	go func() {
+		done <- call(t, srv, "brain_edit", map[string]any{"path": "wiki/homelab/facts/f.md", "old_str": "a", "new_str": "b"})
+	}()
+	select {
+	case resp := <-done:
+		assert.Contains(t, resp, "error", "a FIFO note is refused")
+	case <-time.After(3 * time.Second):
+		t.Fatal("brain_edit hung on a FIFO note")
+	}
+
+	resp := call(t, srv, "brain_edit", map[string]any{"path": "wiki/homelab/facts/n.md", "old_str": "beta", "new_str": "BETA"})
+	require.NotContains(t, resp, "error", "positive control: a regular note is edited: %v", resp["error"])
+}
+
+// hyperguild#192: the edit lock "<note>.lock" was opened by path with
+// O_CREATE, so a planted dangling .lock symlink made a successful edit create
+// a file at the link's target, outside the brain or elsewhere in it.
+func TestBrainEditDoesNotCreateAFileThroughADanglingLockSymlink(t *testing.T) {
+	for name, target := range map[string]func(t *testing.T, dir string) string{
+		"outside":  func(t *testing.T, _ string) string { return filepath.Join(t.TempDir(), "created") },
+		"in-brain": func(t *testing.T, dir string) string { return filepath.Join(dir, "raw", "created") },
+	} {
+		t.Run(name, func(t *testing.T) {
+			dir := newBrainRepo(t)
+			require.NoError(t, os.MkdirAll(filepath.Join(dir, "raw"), 0o755))
+			tgt := target(t, dir)
+			require.NoError(t, os.Symlink(tgt, filepath.Join(dir, "wiki", "homelab", "facts", "n.md.lock")))
+			srv := mcp.NewServer(dir, nil, nil, nil)
+			_ = call(t, srv, "brain_edit", map[string]any{"path": "wiki/homelab/facts/n.md", "old_str": "beta", "new_str": "BETA"})
+			_, err := os.Lstat(tgt)
+			assert.True(t, os.IsNotExist(err), "a file was created at the lock symlink's target")
+		})
+	}
+}

ingestion/internal/mcp/readexcerpt_root_test.go

@@ -21,6 +21,11 @@ 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))
@@ -28,6 +33,9 @@ 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/mcp/tools_notes.go

@@ -6,8 +6,8 @@ import (
 	"errors"
 	"fmt"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/api"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"log/slog"
-	"os"
 	"strings"
 	"time"
 
@@ -118,7 +118,14 @@ func (s *Server) brainEdit(ctx context.Context, args json.RawMessage) (json.RawM
 		return nil, err
 	}
 	// No snapshot, no edit: without one a failed stamp could not be undone.
-	prior, err := os.ReadFile(target.Abs)
+	// Read through the brain root, regular files only (hyperguild#192): a
+	// FIFO held open by a writer hung os.ReadFile.
+	bfs, err := brainfs.Open(s.brainDir)
+	if err != nil {
+		return nil, fmt.Errorf("snapshot before edit: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	prior, err := bfs.ReadRegular(target.Rel)
 	if err != nil {
 		return nil, fmt.Errorf("snapshot before edit: %w", err)
 	}
@@ -131,7 +138,7 @@ func (s *Server) brainEdit(ctx context.Context, args json.RawMessage) (json.RawM
 	// to the editor after every edit (PR #147 review, escape E1).
 	origin, writtenBy := provenanceFrom(ctx)
 	if serr := api.StampProvenanceFile(s.brainDir, res.Path, origin, writtenBy); serr != nil {
-		if werr := os.WriteFile(target.Abs, prior, 0o644); werr != nil {
+		if werr := bfs.WriteRegular(target.Rel, prior); werr != nil {
 			// Say exactly what state the note is in: edited, unverified.
 			return nil, fmt.Errorf("stamp provenance failed (%v) AND the edit could NOT be rolled back: %w; "+
 				"%s carries the edit under its previous attribution", serr, werr, res.Path)

ingestion/internal/notes/edit.go

@@ -127,7 +127,7 @@ func Edit(brainDir, path, oldStr, newStr string, scope Scope) (Result, error) {
 	mu.Lock()
 	defer mu.Unlock()
 
-	unlock, err := flockFile(t.Abs)
+	unlock, err := flockFile(t)
 	if err != nil {
 		return Result{}, err
 	}
@@ -220,20 +220,32 @@ func lockFor(abs string) *sync.Mutex {
 }
 
 // flockFile takes an advisory lock covering other processes sharing the
-// hostPath — during a RollingUpdate two ingestion pods do.
-func flockFile(abs string) (func(), error) {
-	f, err := os.OpenFile(abs+".lock", os.O_CREATE|os.O_RDWR, 0o644)
+// hostPath — during a RollingUpdate two ingestion pods do. The lock file is
+// opened and removed through the brain root, never through a symlink
+// (hyperguild#192): a planted dangling "<note>.lock" link made a
+// successful edit create a file at its target.
+func flockFile(t Target) (func(), error) {
+	lockRel := t.Rel + ".lock"
+	bfs, err := brainfs.Open(t.Brain)
 	if err != nil {
-		return nil, fmt.Errorf("notes: lock %s: %w", filepath.Base(abs), err)
+		return nil, fmt.Errorf("notes: lock %s: %w", lockRel, err)
+	}
+	f, err := bfs.OpenLock(lockRel)
+	_ = bfs.Close()
+	if err != nil {
+		return nil, fmt.Errorf("notes: lock %s: %w", lockRel, err)
 	}
 	if err := syscall.Flock(int(f.Fd()), syscall.LOCK_EX); err != nil {
 		_ = f.Close()
-		return nil, fmt.Errorf("notes: flock %s: %w", filepath.Base(abs), err)
+		return nil, fmt.Errorf("notes: flock %s: %w", lockRel, err)
 	}
 	return func() {
 		_ = syscall.Flock(int(f.Fd()), syscall.LOCK_UN)
 		_ = f.Close()
-		_ = os.Remove(abs + ".lock")
+		if b, err := brainfs.Open(t.Brain); err == nil {
+			_ = b.RemoveLock(lockRel)
+			_ = b.Close()
+		}
 	}, nil
 }
 

ingestion/internal/notes/read_root_test.go

@@ -38,3 +38,31 @@ 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/search/brainroot_test.go

@@ -12,6 +12,8 @@ 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
@@ -189,3 +191,49 @@ 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

@@ -2,14 +2,17 @@ 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
@@ -90,3 +93,85 @@ 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

@@ -65,14 +65,42 @@ func Append(sessionsDir, sessionID string, entry Entry) error {
 	if err := checkID(sessionID); err != nil {
 		return err
 	}
-	if err := os.MkdirAll(sessionsDir, 0o755); err != nil {
+	// 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) {
 		return fmt.Errorf("create sessions dir: %w", err)
 	}
-	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)
+	// 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)
 	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/symlinkguard/special_test.go

@@ -0,0 +1,104 @@
+package symlinkguard
+
+import (
+	"context"
+	"net"
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// hyperguild#179: the tripwire looked only for symlinks, so a FIFO (or
+// socket) in the brain passed it. A FIFO at classification.yaml then made
+// startup exit; at a note path it could hang readers that skip the handle
+// check.
+func TestScanReportsFIFOsAndSocketsAsSpecialFiles(t *testing.T) {
+	brain := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki", "w"), 0o755))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(brain, "classification.yaml"), 0o644))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(brain, "wiki", "w", "f.md"), 0o644))
+	l, err := net.Listen("unix", filepath.Join(brain, "s.sock"))
+	require.NoError(t, err)
+	defer func() { _ = l.Close() }()
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "w", "n.md"), []byte("n"), 0o644))
+
+	r, err := Scan(brain)
+	require.NoError(t, err)
+	assert.Equal(t, []string{"classification.yaml", "s.sock", "wiki/w/f.md"}, r.Special)
+	assert.False(t, r.Clean())
+	assert.Contains(t, r.String(), "special file")
+}
+
+// Watch removes a FIFO as it removes symlinks, and leaves a regular file
+// (which Scan never reports) alone.
+func TestWatchRemovesAFIFOAndLeavesAnUnreportedRegularFile(t *testing.T) {
+	brain := t.TempDir()
+	fifo := filepath.Join(brain, "f.md")
+	require.NoError(t, syscall.Mkfifo(fifo, 0o644))
+	regular := filepath.Join(brain, "n.md")
+	require.NoError(t, os.WriteFile(regular, []byte("n"), 0o644))
+	n := &recNotifier{}
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+	go Watch(ctx, brain, 10*time.Millisecond, n)
+	require.Eventually(t, func() bool {
+		_, err := os.Lstat(fifo)
+		return os.IsNotExist(err)
+	}, 2*time.Second, 10*time.Millisecond, "the FIFO is removed")
+	require.Eventually(t, func() bool { return n.count() >= 1 }, 2*time.Second, 10*time.Millisecond)
+	b, err := os.ReadFile(regular)
+	require.NoError(t, err)
+	assert.Equal(t, "n", string(b))
+	n.mu.Lock()
+	defer n.mu.Unlock()
+	assert.Contains(t, n.msgs[0], "f.md")
+}
+
+// removeSpecial re-checks the type: a path that is a regular file or a
+// directory at the re-check is not removed. (A swap between the re-check and
+// the unlink can still remove one; Linux has no conditional unlink. The same
+// window exists in removeSymlinks.)
+func TestRemoveSpecialRefusesRegularFilesAndDirectories(t *testing.T) {
+	brain := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "d"), 0o755))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(brain, "f.md"), 0o644))
+	removed, failed := removeSpecial(brain, []string{"n.md", "d", "f.md"})
+	assert.Equal(t, []string{"f.md"}, removed)
+	assert.Equal(t, []string{"n.md", "d"}, failed)
+	_, err := os.Stat(filepath.Join(brain, "n.md"))
+	assert.NoError(t, err)
+}
+
+// A special file Watch cannot remove (its directory is read-only) stays
+// reported: the persistent-finding alert names it.
+func TestWatchReportsASpecialFileItCannotRemove(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	brain := t.TempDir()
+	ro := filepath.Join(brain, "ro")
+	require.NoError(t, os.MkdirAll(ro, 0o755))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(ro, "f.md"), 0o644))
+	require.NoError(t, os.Chmod(ro, 0o555))
+	t.Cleanup(func() { _ = os.Chmod(ro, 0o755) })
+	n := &recNotifier{}
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+	go Watch(ctx, brain, 10*time.Millisecond, n)
+	require.Eventually(t, func() bool { return n.count() >= 1 }, 2*time.Second, 10*time.Millisecond)
+	_, err := os.Lstat(filepath.Join(ro, "f.md"))
+	require.NoError(t, err, "the FIFO could not be removed")
+	n.mu.Lock()
+	defer n.mu.Unlock()
+	assert.Contains(t, n.msgs[0], "ro/f.md")
+	assert.Contains(t, n.msgs[0], "special file")
+	for _, m := range n.msgs {
+		assert.NotContains(t, m, "removed", "a file it could not remove was reported as removed")
+	}
+}

ingestion/internal/symlinkguard/symlinkguard.go

@@ -46,10 +46,16 @@ type Notifier interface {
 type Result struct {
 	Symlinks   []string
 	Unreadable []string
+	// Special holds FIFOs, sockets and devices (hyperguild#179): a reader
+	// that opens one by path can hang, and a FIFO at classification.yaml
+	// stops startup.
+	Special []string
 }
 
 // Clean reports whether the scan found nothing to act on.
-func (r Result) Clean() bool { return len(r.Symlinks) == 0 && len(r.Unreadable) == 0 }
+func (r Result) Clean() bool {
+	return len(r.Symlinks) == 0 && len(r.Unreadable) == 0 && len(r.Special) == 0
+}
 
 // String describes the findings for a log line or alert. Paths are quoted, so
 // a name containing a newline cannot blur two findings together.
@@ -59,6 +65,9 @@ func (r Result) String() string {
 	if len(r.Symlinks) > 0 {
 		parts = append(parts, fmt.Sprintf("%d symlink(s): %s", len(r.Symlinks), q(r.Symlinks)))
 	}
+	if len(r.Special) > 0 {
+		parts = append(parts, fmt.Sprintf("%d special file(s) (FIFO, socket or device; delete them): %s", len(r.Special), q(r.Special)))
+	}
 	if len(r.Unreadable) > 0 {
 		parts = append(parts, fmt.Sprintf("%d unreadable dir(s): %s", len(r.Unreadable), q(r.Unreadable)))
 	}
@@ -113,12 +122,16 @@ func Scan(brainDir string) (Result, error) {
 		if d.IsDir() && p == rootGit {
 			return filepath.SkipDir
 		}
-		if d.Type()&os.ModeSymlink != 0 {
+		switch {
+		case d.Type()&os.ModeSymlink != 0:
 			r.Symlinks = append(r.Symlinks, rel)
+		case !d.IsDir() && !d.Type().IsRegular():
+			r.Special = append(r.Special, rel)
 		}
 		return nil
 	})
 	sort.Strings(r.Symlinks)
+	sort.Strings(r.Special)
 	sort.Strings(r.Unreadable)
 	if walkErr != nil {
 		// Only the root's own error reaches here (deeper errors are recorded
@@ -182,14 +195,20 @@ func Watch(ctx context.Context, brainDir string, interval time.Duration, n Notif
 				q.push(fmt.Sprintf("brain symlink tripwire (hyperguild#157): removed %d symlink(s) from the brain dir: %s",
 					len(removed), Result{}.quoted(removed)))
 			}
-			key = Result{Symlinks: failed, Unreadable: r.Unreadable}.String()
+			sRemoved, sFailed := removeSpecial(brainDir, r.Special)
+			if len(sRemoved) > 0 {
+				slog.Error("brain symlink tripwire removed special files", "count", len(sRemoved))
+				q.push(fmt.Sprintf("brain symlink tripwire (hyperguild#179): removed %d special file(s) (FIFO, socket or device) from the brain dir: %s",
+					len(sRemoved), Result{}.quoted(sRemoved)))
+			}
+			key = Result{Symlinks: failed, Unreadable: r.Unreadable, Special: sFailed}.String()
 		}
 		if key != reported {
 			reported = key
 			if key != "" {
 				slog.Error("brain symlink tripwire", "finding", key)
-				q.push("brain symlink tripwire (hyperguild#157): " + key +
-					". Readers may follow symlinks out of the brain; fix them.")
+				q.push("brain symlink tripwire (hyperguild#157, #179): " + key +
+					". Symlinks can lead readers out of the brain and special files can hang them; remove them.")
 			}
 		}
 	}
@@ -322,6 +341,40 @@ func permanent(err error) bool {
 	return errors.As(err, &p) && p.Permanent()
 }
 
+// removeSpecial unlinks each brain-relative FIFO, socket or device through
+// an os.Root on the brain dir, after re-checking that it is still one: a
+// path that is a regular file, a directory or a symlink at the re-check is
+// left alone and reported as failed. The re-check narrows, but cannot close,
+// the window before the unlink (Linux has no conditional unlink); the same
+// window exists in removeSymlinks, and only a local writer can use it.
+func removeSpecial(brainDir string, rels []string) (removed, failed []string) {
+	if len(rels) == 0 {
+		return nil, nil
+	}
+	resolved, err := filepath.EvalSymlinks(brainDir)
+	if err != nil {
+		return nil, rels
+	}
+	root, err := os.OpenRoot(resolved)
+	if err != nil {
+		return nil, rels
+	}
+	defer func() { _ = root.Close() }()
+	for _, rel := range rels {
+		fi, err := root.Lstat(rel)
+		if err != nil || fi.IsDir() || fi.Mode().IsRegular() || fi.Mode()&os.ModeSymlink != 0 {
+			failed = append(failed, rel)
+			continue
+		}
+		if err := root.Remove(rel); err != nil {
+			failed = append(failed, rel)
+			continue
+		}
+		removed = append(removed, rel)
+	}
+	return removed, failed
+}
+
 // removeSymlinks unlinks each brain-relative symlink through an os.Root on
 // the brain dir, after re-checking it is still a symlink. Removing a symlink
 // never touches its target. It returns what was removed and what was not.

ingestion/internal/vectorstore/sync_root_test.go

@@ -42,6 +42,11 @@ 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{}
@@ -51,6 +56,7 @@ 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")
@@ -61,6 +67,7 @@ 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() })
 }