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/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/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/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/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

@@ -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/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

@@ -136,140 +136,49 @@ 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 {
+// 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 err
+		return nil, 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 err := b.realDir(path.Dir(rel)); err != nil {
+		return nil, err
 	}
 	if fi, err := b.root.Lstat(rel); err == nil && !fi.Mode().IsRegular() {
-		return fmt.Errorf("%s: %w", rel, ErrNotRegular)
+		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
 	} else if err != nil && !errors.Is(err, fs.ErrNotExist) {
-		return err
+		return nil, err
 	}
-	f, err := b.root.OpenFile(rel, os.O_WRONLY|os.O_APPEND|os.O_CREATE|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
+	f, err := b.root.OpenFile(rel, os.O_RDWR|os.O_CREATE|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0o644)
 	if err != nil {
-		return err
+		return nil, 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)
+		_ = f.Close()
+		return nil, fmt.Errorf("%s: changed while opening: %w", rel, ErrNotRegular)
 	}
-	if _, err := f.Write(data); err != nil {
-		return err
-	}
-	return f.Close()
+	return f, nil
 }
 
-// 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 {
+// 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)
 }
 
-// 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) {

ingestion/internal/brainfs/brainfs_test.go

@@ -376,156 +376,3 @@ func TestReadAndWriteRegularRefuseAPathThatIsNotClean(t *testing.T) {
 	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/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/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/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/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/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/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")
-}