test(pipeline): pin BackfillRefs' page read with a swap race (#157)

Review round 1 on PR #176: reverting the BackfillRefs concept-page read
to os.ReadFile left every test green. The static symlinked page never
reaches that read, because LoadInventory does not list it; the read is
reachable only when a page listed as regular is swapped for a symlink
before it is read. New test does that against an in-brain target and
reads the page back with O_NOFOLLOW; red under the flip (2/2), green
3/3 on head.

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

ingestion/cmd/server/jwt_validator.go

@@ -0,0 +1,25 @@
+package main
+
+import (
+	"context"
+	"log/slog"
+
+	chassisauth "git.d-ma.be/mathias/mcp-chassis/auth"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/startupretry"
+)
+
+// buildJWTValidator runs OIDC discovery under policy, so a 502 from an auth
+// upstream that is not serving yet on a cold boot is retried instead of
+// exiting (#83). It honours ctx between attempts.
+func buildJWTValidator(
+	ctx context.Context, logger *slog.Logger, issuer, audience string, policy startupretry.Policy,
+) (*chassisauth.JWTValidator, error) {
+	return startupretry.Do(ctx, policy, func(ctx context.Context) (*chassisauth.JWTValidator, error) {
+		v, err := chassisauth.NewJWTValidator(ctx, issuer, audience)
+		if err != nil {
+			logger.Warn("oidc discovery not ready, retrying", "err", err)
+		}
+		return v, err
+	})
+}

ingestion/cmd/server/jwt_validator_test.go

@@ -0,0 +1,86 @@
+package main
+
+import (
+	"context"
+	"io"
+	"log/slog"
+	"net/http"
+	"net/http/httptest"
+	"sync/atomic"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/startupretry"
+)
+
+// fakeIssuer answers OIDC discovery with 502 for the first fail requests, as
+// ingress does while dex is not yet serving on a cold boot (#83), then with a
+// real discovery document and an empty JWKS.
+func fakeIssuer(t *testing.T, fail int32) (*httptest.Server, *atomic.Int32) {
+	t.Helper()
+	var discoveries atomic.Int32
+	mux := http.NewServeMux()
+	var srv *httptest.Server
+	mux.HandleFunc("/.well-known/openid-configuration", func(w http.ResponseWriter, _ *http.Request) {
+		if discoveries.Add(1) <= fail {
+			w.WriteHeader(http.StatusBadGateway)
+			return
+		}
+		w.Header().Set("Content-Type", "application/json")
+		_, _ = io.WriteString(w, `{"issuer":"`+srv.URL+`","jwks_uri":"`+srv.URL+`/keys"}`)
+	})
+	mux.HandleFunc("/keys", func(w http.ResponseWriter, _ *http.Request) {
+		w.Header().Set("Content-Type", "application/json")
+		_, _ = io.WriteString(w, `{"keys":[]}`)
+	})
+	srv = httptest.NewServer(mux)
+	t.Cleanup(srv.Close)
+	return srv, &discoveries
+}
+
+var fastPolicy = startupretry.Policy{Attempts: 8, Base: time.Millisecond, Max: 5 * time.Millisecond}
+
+func TestBuildJWTValidatorRetriesDiscovery502sThenSucceeds(t *testing.T) {
+	srv, discoveries := fakeIssuer(t, 3)
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+
+	v, err := buildJWTValidator(ctx, slog.New(slog.DiscardHandler), srv.URL, "brain", fastPolicy)
+	require.NoError(t, err)
+	assert.NotNil(t, v)
+	assert.Equal(t, int32(4), discoveries.Load(), "three 502s, then the successful discovery")
+}
+
+func TestBuildJWTValidatorGivesUpAfterTheBudgetWithTheLastError(t *testing.T) {
+	srv, discoveries := fakeIssuer(t, 1000)
+	ctx, cancel := context.WithCancel(context.Background())
+	defer cancel()
+
+	_, err := buildJWTValidator(ctx, slog.New(slog.DiscardHandler), srv.URL, "brain", fastPolicy)
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "status 502")
+	assert.Equal(t, int32(8), discoveries.Load(), "bounded: exactly the attempt budget")
+}
+
+func TestBuildJWTValidatorStopsRetryingWhenTheContextIsCancelled(t *testing.T) {
+	srv, _ := fakeIssuer(t, 1000)
+	ctx, cancel := context.WithCancel(context.Background())
+	slow := startupretry.Policy{Attempts: 8, Base: time.Hour, Max: time.Hour}
+
+	done := make(chan error, 1)
+	go func() {
+		_, err := buildJWTValidator(ctx, slog.New(slog.DiscardHandler), srv.URL, "brain", slow)
+		done <- err
+	}()
+	time.Sleep(50 * time.Millisecond)
+	cancel()
+	select {
+	case err := <-done:
+		assert.ErrorIs(t, err, context.Canceled)
+	case <-time.After(3 * time.Second):
+		t.Fatal("did not return after the context was cancelled")
+	}
+}

ingestion/cmd/server/main.go

@@ -381,15 +381,9 @@ func main() {
 	//
 	// The budget stays bounded: retrying forever would turn a misconfiguration
 	// into a process that looks alive and never serves.
-	jwtValidator, err := startupretry.Do(ctx,
+	jwtValidator, err := buildJWTValidator(ctx, logger,
-		startupretry.Policy{Attempts: 8, Base: time.Second, Max: 30 * time.Second},
+		os.Getenv("DEX_ISSUER_URL"), os.Getenv("MCP_AUDIENCE"),
-		func(ctx context.Context) (*chassisauth.JWTValidator, error) {
+		startupretry.Policy{Attempts: 8, Base: time.Second, Max: 30 * time.Second})
-			v, err := chassisauth.NewJWTValidator(ctx, os.Getenv("DEX_ISSUER_URL"), os.Getenv("MCP_AUDIENCE"))
-			if err != nil {
-				logger.Warn("oidc discovery not ready, retrying", "err", err)
-			}
-			return v, err
-		})
 	if err != nil {
 		logger.Error("build jwt validator", "err", err)
 		os.Exit(1)

ingestion/go.mod

@@ -34,9 +34,9 @@ require (
 	github.com/rogpeppe/go-internal v1.15.0 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/x448/float16 v0.8.4 // indirect
-	golang.org/x/net v0.26.0 // indirect
+	golang.org/x/net v0.55.0 // indirect
 	golang.org/x/oauth2 v0.21.0 // indirect
-	golang.org/x/term v0.28.0 // indirect
+	golang.org/x/term v0.43.0 // indirect
 	golang.org/x/time v0.3.0 // indirect
 	google.golang.org/protobuf v1.34.2 // indirect
 	gopkg.in/evanphx/json-patch.v4 v4.12.0 // indirect
@@ -66,9 +66,9 @@ require (
 	github.com/lestrrat-go/option v1.0.1 // indirect
 	github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect
 	github.com/segmentio/asm v1.2.0 // indirect
-	golang.org/x/crypto v0.32.0 // indirect
+	golang.org/x/crypto v0.51.0 // indirect
-	golang.org/x/sync v0.17.0 // indirect
+	golang.org/x/sync v0.21.0 // indirect
-	golang.org/x/sys v0.31.0 // indirect
+	golang.org/x/sys v0.45.0 // indirect
-	golang.org/x/text v0.29.0 // indirect
+	golang.org/x/text v0.39.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1
 )

ingestion/go.sum

@@ -117,42 +117,42 @@ github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9dec
 golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w=
 golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI=
 golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto=
-golang.org/x/crypto v0.32.0 h1:euUpcYgM8WcP71gNpTqQCn6rC2t6ULUPiOzfWaXVVfc=
+golang.org/x/crypto v0.51.0 h1:IBPXwPfKxY7cWQZ38ZCIRPI50YLeevDLlLnyC5wRGTI=
-golang.org/x/crypto v0.32.0/go.mod h1:ZnnJkOaASj8g0AjIduWNlq2NRxL0PlBrbKVyZ6V/Ugc=
+golang.org/x/crypto v0.51.0/go.mod h1:8AdwkbraGNABw2kOX6YFPs3WM22XqI4EXEd8g+x7Oc8=
 golang.org/x/mod v0.2.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
 golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
 golang.org/x/net v0.0.0-20200226121028-0de0cce0169b/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s=
 golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU=
-golang.org/x/net v0.26.0 h1:soB7SVo0PWrY4vPW/+ay0jKDNScG2X9wFeYlXIvJsOQ=
+golang.org/x/net v0.55.0 h1:bcvxaJn3e1U6InsFWt1JUq1aSjnRxLzT2rtD2KfkDF8=
-golang.org/x/net v0.26.0/go.mod h1:5YKkiSynbBIh3p6iOc/vibscux0x38BZDkn8sCUPxHE=
+golang.org/x/net v0.55.0/go.mod h1:L5U2KuzuOe1lY7Z+aWVIKK6qEeJXnXV9yzGA+WCHJww=
 golang.org/x/oauth2 v0.21.0 h1:tsimM75w1tF/uws5rbeHzIWxEqElMehnc+iW793zsZs=
 golang.org/x/oauth2 v0.21.0/go.mod h1:XYTD2NtWslqkgxebSiOHnXEap4TF09sJSc7H1sXbhtI=
 golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20190911185100-cd5d95a43a6e/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
-golang.org/x/sync v0.17.0 h1:l60nONMj9l5drqw6jlhIELNv9I0A4OFgRsG9k2oT9Ug=
+golang.org/x/sync v0.21.0 h1:HLII4xRRTtCRkxYp4HNFF0Js/Og6q2i++KXbg0gHCwM=
-golang.org/x/sync v0.17.0/go.mod h1:9KTHXmSnoGruLpwFjVSX0lNNA75CykiMECbovNTZqGI=
+golang.org/x/sync v0.21.0/go.mod h1:9xrNwdLfx4jkKbNva9FpL6vEN7evnE43NNNJQ2LF3+0=
 golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
 golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.31.0 h1:ioabZlmFYtWhL+TRYpcnNlLwhyxaM9kWTDEmfnprqik=
+golang.org/x/sys v0.45.0 h1:dO4czNzziLiiXplLQgBCEpCvXQ3dnkn0SdaZSYdQ+FY=
-golang.org/x/sys v0.31.0/go.mod h1:BJP2sWEmIv4KK5OTEluFJCKSidICx8ciO85XgH3Ak8k=
+golang.org/x/sys v0.45.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
-golang.org/x/term v0.28.0 h1:/Ts8HFuMR2E6IP/jlo7QVLZHggjKQbhu/7H0LJFr3Gg=
+golang.org/x/term v0.43.0 h1:S4RLU2sB31O/NCl+zFN9Aru9A/Cq2aqKpTZJ6B+DwT4=
-golang.org/x/term v0.28.0/go.mod h1:Sw/lC2IAUZ92udQNf3WodGtn4k/XoLyZoh8v/8uiwek=
+golang.org/x/term v0.43.0/go.mod h1:lrhlHNdQJHO+1qVYiHfFKVuVioJIheAc3fBSMFYEIsk=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
-golang.org/x/text v0.29.0 h1:1neNs90w9YzJ9BocxfsQNHKuAT4pkghyXc4nhZ6sJvk=
+golang.org/x/text v0.39.0 h1:UbZz4pLOvn600D6Oh6GGEI6VAmndrEBLv8/6BEXzyus=
-golang.org/x/text v0.29.0/go.mod h1:7MhJOA9CD2qZyOKYazxdYMF85OwPdEr9jTtBpO7ydH4=
+golang.org/x/text v0.39.0/go.mod h1:3UwRclnC2g0TU9x8PZiyfOajCd1zaUNHF9cvqcQZ+ZM=
 golang.org/x/time v0.3.0 h1:rg5rLMjNzMS1RkNLzCG38eapWhnYLFYXDXj2gOlr8j4=
 golang.org/x/time v0.3.0/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
 golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
 golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
 golang.org/x/tools v0.0.0-20200619180055-7c47624df98f/go.mod h1:EkVYQZoAsY45+roYkvgYkIh4xh/qjgUK9TdY2XT94GE=
 golang.org/x/tools v0.0.0-20210106214847-113979e3529a/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA=
-golang.org/x/tools v0.36.0 h1:kWS0uv/zsvHEle1LbV5LE8QujrxB3wfQyxHfhOk0Qkg=
+golang.org/x/tools v0.47.0 h1:7Kn5x/d1svx/PzryTsqeoZN4TZwqeH5pGWjefhLi/1Q=
-golang.org/x/tools v0.36.0/go.mod h1:WBDiHKJK8YgLHlcQPYQzNCkUxUypCaa5ZegCVutKm+s=
+golang.org/x/tools v0.47.0/go.mod h1:dFHnyTvFWY212G+h7ZY4Vsp/K3U4/7W9TyVaAul8uCA=
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
 golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=

ingestion/internal/brainfs/brainfs.go

@@ -13,7 +13,9 @@ import (
 	"io"
 	"io/fs"
 	"os"
+	"path"
 	"path/filepath"
+	"strings"
 	"syscall"
 )
 
@@ -53,6 +55,55 @@ func (b *Brain) Rel(path string) (string, error) {
 	return filepath.ToSlash(rel), nil
 }
 
+// Lstat stats a brain-relative path through the root without following a
+// final symlink.
+func (b *Brain) Lstat(rel string) (fs.FileInfo, error) {
+	return b.root.Lstat(filepath.ToSlash(rel))
+}
+
+// realDir returns ErrNotRegular unless every component of rel is a real
+// directory. A swap after the check is not caught (accepted residual,
+// hyperguild#157).
+func (b *Brain) realDir(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 err != nil {
+			return err
+		}
+		if !fi.IsDir() {
+			return fmt.Errorf("%s: walk root component %s is not a directory: %w", rel, prefix, ErrNotRegular)
+		}
+	}
+	return nil
+}
+
+// ReadDirRegular lists the regular files directly in a brain-relative
+// directory, by name. Every component of relDir must be a real directory
+// (ErrNotRegular otherwise); symlinks, FIFOs, devices and subdirectories in
+// it are left out.
+func (b *Brain) ReadDirRegular(relDir string) ([]string, error) {
+	relDir = filepath.ToSlash(relDir)
+	if err := b.realDir(relDir); err != nil {
+		return nil, err
+	}
+	ents, err := fs.ReadDir(b.root.FS(), relDir)
+	if err != nil {
+		return nil, err
+	}
+	var names []string
+	for _, e := range ents {
+		if e.Type().IsRegular() {
+			names = append(names, e.Name())
+		}
+	}
+	return names, nil
+}
+
 // ReadRegular reads a brain-relative path, refusing anything that is not a
 // regular file, both before the open and on the opened handle.
 func (b *Brain) ReadRegular(rel string) ([]byte, error) {
@@ -63,7 +114,7 @@ func (b *Brain) ReadRegular(rel string) ([]byte, error) {
 	if !fi.Mode().IsRegular() {
 		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
 	}
-	return b.readOpened(rel)
+	return b.readOpenedMax(rel, -1, fi)
 }
 
 // readOpened opens rel non-blocking and reads it only if the OPENED handle is
@@ -77,7 +128,7 @@ func (b *Brain) ReadRegular(rel string) ([]byte, error) {
 // cannot create one; fs.protected_hardlinks=1 and the pod's secrets are on a
 // different filesystem from the brain volume, so a local caller cannot link
 // them in. Refusing Nlink > 1 is the next step if either changes.
-func (b *Brain) readOpened(rel string) ([]byte, error) { return b.readOpenedMax(rel, -1) }
+func (b *Brain) readOpened(rel string) ([]byte, error) { return b.readOpenedMax(rel, -1, nil) }
 
 // ReadRegularMax is ReadRegular with a size limit, checked on the opened
 // handle before reading (max < 0 means no limit).
@@ -89,10 +140,14 @@ func (b *Brain) ReadRegularMax(rel string, max int64) ([]byte, error) {
 	if !fi.Mode().IsRegular() {
 		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
 	}
-	return b.readOpenedMax(rel, max)
+	return b.readOpenedMax(rel, max, fi)
 }
 
-func (b *Brain) readOpenedMax(rel string, max int64) ([]byte, error) {
+// readOpenedMax opens rel and reads it if the opened handle is a regular file
+// and, when lfi is set, the same file the caller Lstat-ed: os.Root follows an
+// in-root final symlink even with O_NOFOLLOW, so a symlink to another brain
+// file swapped in between the Lstat and the open is refused only here.
+func (b *Brain) readOpenedMax(rel string, max int64, lfi fs.FileInfo) ([]byte, error) {
 	f, err := b.root.OpenFile(rel, os.O_RDONLY|syscall.O_NONBLOCK, 0)
 	if err != nil {
 		return nil, err
@@ -105,6 +160,9 @@ func (b *Brain) readOpenedMax(rel string, max int64) ([]byte, error) {
 	if !hfi.Mode().IsRegular() {
 		return nil, fmt.Errorf("%s: %w", rel, ErrNotRegular)
 	}
+	if lfi != nil && !os.SameFile(lfi, hfi) {
+		return nil, fmt.Errorf("%s: changed while opening: %w", rel, ErrNotRegular)
+	}
 	if max >= 0 && hfi.Size() > max {
 		return nil, fmt.Errorf("%s is %d bytes (limit %d): %w", rel, hfi.Size(), max, ErrTooLarge)
 	}
@@ -127,15 +185,34 @@ func (b *Brain) readOpenedMax(rel string, max int64) ([]byte, error) {
 }
 
 // wrapAfterStat is a test seam: it runs between the size check and the read,
-// and wraps the reader the read consumes.
+// and wraps the reader the read consumes. A package global: brainfs tests
+// must not use t.Parallel.
 var wrapAfterStat func(io.Reader) io.Reader
 
 // WalkRegular walks a brain-relative directory through the root and calls fn
-// for each regular file (directories are descended; symlinks, FIFOs and
+// for each regular file. Directories are descended; symlinks, FIFOs and
-// devices are skipped, never followed). An entry error is passed to onErr and
+// devices found by the walk are skipped. A walk root with any component that
-// the walk continues; a nil onErr ignores it.
+// is not a real directory goes to onErr as ErrNotRegular and nothing is
+// yielded. An entry error is passed to onErr and the walk continues; a nil
+// onErr ignores it.
+//
+// Accepted residual (hyperguild#157): a directory swapped for a symlink
+// between the listing and the read is followed. os.Root still keeps the read
+// inside the brain, but not inside relDir.
 func (b *Brain) WalkRegular(relDir string, fn func(rel string) error, onErr func(rel string, err error)) error {
-	return fs.WalkDir(b.root.FS(), filepath.ToSlash(relDir), func(p string, d fs.DirEntry, err error) error {
+	relDir = filepath.ToSlash(relDir)
+	// fs.WalkDir stats its root with a follow, and os.Root allows a symlink
+	// that stays inside the brain: knowledge -> . would alias the whole
+	// brain. Require every component of the root to be a real directory
+	// (Lstat checks only the last one).
+	err := b.realDir(relDir)
+	if err != nil {
+		if onErr != nil {
+			onErr(relDir, err)
+		}
+		return nil
+	}
+	return fs.WalkDir(b.root.FS(), relDir, func(p string, d fs.DirEntry, err error) error {
 		if err != nil {
 			if onErr != nil {
 				onErr(p, err)

ingestion/internal/brainfs/brainfs_test.go

@@ -3,8 +3,11 @@ package brainfs
 import (
 	"errors"
 	"io"
+	"io/fs"
 	"os"
 	"path/filepath"
+	"sync"
+	"sync/atomic"
 	"syscall"
 	"testing"
 	"time"
@@ -139,3 +142,123 @@ func (c *countingReader) Read(p []byte) (int, error) {
 	c.n += n
 	return n, err
 }
+
+func TestLstatDoesNotFollowSymlinksAndRefusesEscapes(t *testing.T) {
+	dir := t.TempDir()
+	outside := filepath.Join(t.TempDir(), "o.md")
+	require.NoError(t, os.WriteFile(outside, []byte("o"), 0o644))
+	require.NoError(t, os.Symlink(outside, filepath.Join(dir, "l.md")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	fi, err := b.Lstat("l.md")
+	require.NoError(t, err)
+	assert.Equal(t, fs.ModeSymlink, fi.Mode().Type())
+	_, err = b.Lstat("../" + filepath.Base(filepath.Dir(outside)) + "/o.md")
+	assert.Error(t, err)
+}
+
+func TestWalkRegularReportsASymlinkedWalkRootAndYieldsNothing(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "real"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "real", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.Symlink("real", filepath.Join(dir, "alias")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	var got []string
+	var errs []error
+	require.NoError(t, b.WalkRegular("alias", func(rel string) error { got = append(got, rel); return nil },
+		func(_ string, err error) { errs = append(errs, err) }))
+	assert.Empty(t, got)
+	require.Len(t, errs, 1)
+	assert.ErrorIs(t, errs[0], ErrNotRegular)
+}
+
+func TestWalkRegularReportsASymlinkedIntermediateComponentOfTheWalkRoot(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "real", "sub"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "real", "sub", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.Symlink("real", filepath.Join(dir, "alias")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+	var got []string
+	var errs []error
+	require.NoError(t, b.WalkRegular("alias/sub", func(rel string) error { got = append(got, rel); return nil },
+		func(_ string, err error) { errs = append(errs, err) }))
+	assert.Empty(t, got)
+	require.Len(t, errs, 1)
+	assert.ErrorIs(t, errs[0], ErrNotRegular)
+}
+
+func TestReadDirRegularListsOnlyRegularFilesAndRefusesSymlinkedComponents(t *testing.T) {
+	dir := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "a", "b", "sub"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "a", "b", "n.md"), []byte("n"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "other.md"), []byte("o"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "other.md"), filepath.Join(dir, "a", "b", "l.md")))
+	require.NoError(t, syscall.Mkfifo(filepath.Join(dir, "a", "b", "f.md"), 0o644))
+	require.NoError(t, os.Symlink("a", filepath.Join(dir, "alias")))
+	require.NoError(t, os.MkdirAll(filepath.Join(dir, "x"), 0o755))
+	require.NoError(t, os.Symlink(filepath.Join("..", "a"), filepath.Join(dir, "x", "mid")))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+
+	names, err := b.ReadDirRegular("a/b")
+	require.NoError(t, err)
+	assert.Equal(t, []string{"n.md"}, names)
+	for _, rel := range []string{"alias/b", "x/mid/b"} {
+		_, err := b.ReadDirRegular(rel)
+		assert.ErrorIs(t, err, ErrNotRegular, rel)
+	}
+}
+
+// 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) {
+	dir := t.TempDir()
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "s.md"), []byte("zqsamefilesentinel"), 0o644))
+	p := filepath.Join(dir, "r.md")
+	require.NoError(t, os.WriteFile(p, []byte("inside"), 0o644))
+	b, err := Open(dir)
+	require.NoError(t, err)
+	defer func() { _ = b.Close() }()
+
+	var stop atomic.Bool
+	var wg sync.WaitGroup
+	wg.Add(1)
+	go func() {
+		defer wg.Done()
+		tmp := p + ".swap"
+		for i := 0; !stop.Load(); i++ {
+			_ = os.Remove(tmp)
+			if i%2 == 0 {
+				_ = os.WriteFile(tmp, []byte("inside"), 0o644)
+			} else {
+				_ = os.Symlink("s.md", tmp)
+			}
+			_ = os.Rename(tmp, p)
+		}
+	}()
+	leaks, ok := 0, 0
+	for deadline := time.Now().Add(1500 * time.Millisecond); time.Now().Before(deadline); {
+		got, err := b.ReadRegular("r.md")
+		if err == nil {
+			ok++
+		}
+		if string(got) == "zqsamefilesentinel" {
+			leaks++
+		}
+		got, _ = b.ReadRegularMax("r.md", 1<<20)
+		if string(got) == "zqsamefilesentinel" {
+			leaks++
+		}
+	}
+	stop.Store(true)
+	wg.Wait()
+	assert.Zero(t, leaks)
+	assert.Positive(t, ok, "positive control: the regular file is read")
+}

ingestion/internal/brainfs/brainfstest/brainfstest.go

@@ -7,6 +7,7 @@
 package brainfstest
 
 import (
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -20,16 +21,23 @@ import (
 // Sentinel marks the outside file's contents.
 const Sentinel = "zqbrainfssentinelonefiftyseven"
 
+// outsideContent carries Sentinel in every field a reader might extract: the
+// frontmatter title and aliases, a heading, a wikilink and the body.
+const outsideContent = "---\ntitle: " + Sentinel + "\naliases:\n  - " + Sentinel + "\n---\n# " + Sentinel +
+	"\n\n" + Sentinel + " [[" + Sentinel + "]]\n"
+
 // Outside writes a file outside any brain dir containing Sentinel.
 func Outside(t *testing.T) string {
 	t.Helper()
 	p := filepath.Join(t.TempDir(), "secret.md")
-	if err := os.WriteFile(p, []byte("# secret\n\n"+Sentinel), 0o644); err != nil {
+	if err := os.WriteFile(p, []byte(outsideContent), 0o644); err != nil {
 		t.Fatal(err)
 	}
 	return p
 }
 
+var swapSeq atomic.Int64
+
 // StartSwap renames, in a loop, a regular note (content inside) and either
 // a symlink to outside or a FIFO into path, until the test ends. FIFOs get a
 // writer held open until the swapper exits, so a reader that skips the
@@ -42,7 +50,15 @@ func StartSwap(t *testing.T, path, inside, outside string, fifo bool) {
 	wg.Add(1)
 	go func() {
 		defer wg.Done()
-		tmp := path + ".swap"
+		// A name of its own: swappers on one path share a test, and one
+		// opening another's FIFO for write would block forever.
+		tmp := fmt.Sprintf("%s.swap%d", path, swapSeq.Add(1))
+		// A relative link: os.Root refuses every absolute link on its own, so
+		// an absolute in-brain target would test nothing.
+		link := outside
+		if rel, err := filepath.Rel(filepath.Dir(path), outside); err == nil {
+			link = rel
+		}
 		var writers []*os.File
 		defer func() {
 			for _, w := range writers {
@@ -61,7 +77,7 @@ func StartSwap(t *testing.T, path, inside, outside string, fifo bool) {
 					}
 				}
 			default:
-				_ = os.Symlink(outside, tmp)
+				_ = os.Symlink(link, tmp)
 			}
 			_ = os.Rename(tmp, path)
 		}
@@ -69,11 +85,33 @@ func StartSwap(t *testing.T, path, inside, outside string, fifo bool) {
 	t.Cleanup(func() { stop.Store(true); wg.Wait() })
 }
 
+// WriteSentinelAt writes a file carrying Sentinel at p (creating its
+// directory), for an in-brain symlink target.
+func WriteSentinelAt(t *testing.T, p string) string {
+	t.Helper()
+	if err := os.MkdirAll(filepath.Dir(p), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(p, []byte(outsideContent), 0o644); err != nil {
+		t.Fatal(err)
+	}
+	return p
+}
+
 // AssertNoLeak loops read for d while a symlink swapper runs on path, and
-// fails if any output contains Sentinel.
+// fails if any output contains Sentinel. The symlink points outside the
+// brain; os.Root refuses that on its own, so pair it with AssertNoLeakFrom
+// and an in-brain target.
 func AssertNoLeak(t *testing.T, path, inside string, d time.Duration, read func() string) {
 	t.Helper()
-	StartSwap(t, path, inside, Outside(t), false)
+	AssertNoLeakFrom(t, path, inside, Outside(t), d, read)
+}
+
+// AssertNoLeakFrom is AssertNoLeak with the symlink pointing at target, e.g.
+// a file elsewhere in the brain written with WriteSentinelAt.
+func AssertNoLeakFrom(t *testing.T, path, inside, target string, d time.Duration, read func() string) {
+	t.Helper()
+	StartSwap(t, path, inside, target, false)
 	leaks, iters := 0, 0
 	for deadline := time.Now().Add(d); time.Now().Before(deadline); iters++ {
 		leaks += strings.Count(read(), Sentinel)

ingestion/internal/classification/classification.go

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

ingestion/internal/classification/root_test.go

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

ingestion/internal/graphsync/graphsync.go

@@ -12,10 +12,14 @@ package graphsync
 
 import (
 	"context"
+	"errors"
 	"fmt"
-	"os"
+	"io/fs"
+	"path"
 	"path/filepath"
+	"strings"
 
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/graph"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/graphstore"
 )
@@ -46,8 +50,25 @@ func IndexDoc(ctx context.Context, store Store, brainDir, relPath string) error
 	if relPath == "" {
 		return nil
 	}
-	abs := filepath.Join(brainDir, filepath.FromSlash(relPath))
+	// Callers pass caller-supplied paths (brain_tunnel, brain_update): index
-	content, err := os.ReadFile(abs)
+	// only a clean path under wiki/ or knowledge/.
+	if path.Clean(relPath) != relPath || !filepath.IsLocal(relPath) ||
+		(!strings.HasPrefix(relPath, "wiki/") && !strings.HasPrefix(relPath, "knowledge/")) {
+		return fmt.Errorf("index %q: not a clean wiki/ or knowledge/ path", relPath)
+	}
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+	return indexDoc(ctx, store, bfs, relPath)
+}
+
+// indexDoc reads relPath through the brain root, regular files only
+// (hyperguild#157): the brain is a Syncthing folder, and os.ReadFile
+// followed a synced symlink into the graph and blocked on a FIFO.
+func indexDoc(ctx context.Context, store Store, bfs *brainfs.Brain, relPath string) error {
+	content, err := bfs.ReadRegular(relPath)
 	if err != nil {
 		return fmt.Errorf("read %q: %w", relPath, err)
 	}
@@ -77,33 +98,34 @@ func BackfillFromBrainDir(ctx context.Context, store Store, brainDir string) (in
 	if store == nil {
 		return 0, nil
 	}
-	roots := []string{"wiki", "knowledge"}
+	bfs, err := brainfs.Open(brainDir)
-	for _, root := range roots {
+	if err != nil {
-		base := filepath.Join(brainDir, root)
+		return 0, fmt.Errorf("open brain: %w", err)
-		if _, err := os.Stat(base); os.IsNotExist(err) {
+	}
+	defer func() { _ = bfs.Close() }()
+	for _, root := range []string{"wiki", "knowledge"} {
+		if _, err := bfs.Lstat(root); errors.Is(err, fs.ErrNotExist) {
 			continue
 		}
-		err := filepath.WalkDir(base, func(path string, d os.DirEntry, walkErr error) error {
+		// Any walk error, including a root that is a symlink, aborts.
-			if walkErr != nil {
+		var walkErr error
-				return walkErr
+		err := bfs.WalkRegular(root, func(rel string) error {
-			}
+			if path.Ext(rel) != ".md" {
-			if d.IsDir() {
 				return nil
 			}
-			if filepath.Ext(path) != ".md" {
+			if err := indexDoc(ctx, store, bfs, rel); err != nil {
-				return nil
-			}
-			rel, relErr := filepath.Rel(brainDir, path)
-			if relErr != nil {
-				return fmt.Errorf("rel %q: %w", path, relErr)
-			}
-			rel = filepath.ToSlash(rel)
-			if err := IndexDoc(ctx, store, brainDir, rel); err != nil {
 				return fmt.Errorf("index %q: %w", rel, err)
 			}
 			indexed++
 			return nil
+		}, func(rel string, err error) {
+			if walkErr == nil {
+				walkErr = fmt.Errorf("%s: %w", rel, err)
+			}
 		})
+		if err == nil {
+			err = walkErr
+		}
 		if err != nil {
 			return indexed, fmt.Errorf("walk %s: %w", root, err)
 		}

ingestion/internal/graphsync/graphsync_root_test.go

@@ -0,0 +1,92 @@
+package graphsync
+
+import (
+	"context"
+	"fmt"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+func (f *fakeStore) dump() string {
+	f.mu.Lock()
+	defer f.mu.Unlock()
+	return fmt.Sprintf("%+v %+v", f.upserts, f.replaces)
+}
+
+// hyperguild#157 slice 4: IndexDoc and BackfillFromBrainDir read notes with
+// os.ReadFile, so a symlinked note put the target's title and wikilinks into
+// the graph, and a FIFO hung the read.
+func TestIndexDocRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "ok.md"), []byte("---\ntitle: zqinside\n---\nbody [[other]]\n"), 0o644))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
+
+	store := newFakeStore()
+	require.NoError(t, IndexDoc(context.Background(), store, brain, "wiki/w/facts/ok.md"))
+	assert.Contains(t, store.dump(), "zqinside", "positive control: a regular note is indexed")
+	assert.Error(t, IndexDoc(context.Background(), store, brain, "wiki/w/facts/leak.md"))
+	// A link to a file elsewhere in the brain: os.Root allows it, only the
+	// regular-file check refuses it.
+	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.Error(t, IndexDoc(context.Background(), store, brain, "wiki/w/facts/inlink.md"))
+	assert.NotContains(t, store.dump(), brainfstest.Sentinel)
+
+	p := filepath.Join(facts, "r.md")
+	read := func() string {
+		s := newFakeStore()
+		_ = IndexDoc(context.Background(), s, brain, "wiki/w/facts/r.md")
+		return s.dump()
+	}
+	brainfstest.AssertNoLeak(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, read)
+	brainfstest.AssertNoLeakFrom(t, p, "---\ntitle: zqinside\n---\n", inBrain, 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}
+
+func TestBackfillSkipsSymlinkedNotesAndAbortsOnASymlinkedRoot(t *testing.T) {
+	brain := t.TempDir()
+	facts := filepath.Join(brain, "wiki", "w", "facts")
+	require.NoError(t, os.MkdirAll(facts, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(facts, "ok.md"), []byte("---\ntitle: zqinside\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(facts, "leak.md")))
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "r.md"), []byte("---\ntitle: zqrawonly\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "..", "raw", "r.md"), filepath.Join(facts, "inlink.md")))
+	require.NoError(t, os.Symlink(".", filepath.Join(brain, "knowledge")))
+
+	store := newFakeStore()
+	_, err := BackfillFromBrainDir(context.Background(), store, brain)
+	assert.Error(t, err, "a symlinked root aborts the backfill")
+	assert.NotContains(t, store.dump(), brainfstest.Sentinel)
+	assert.NotContains(t, store.dump(), "zqrawonly")
+
+	require.NoError(t, os.Remove(filepath.Join(brain, "knowledge")))
+	store = newFakeStore()
+	n, err := BackfillFromBrainDir(context.Background(), store, brain)
+	require.NoError(t, err)
+	assert.Equal(t, 1, n, "only the regular note is indexed")
+	assert.Contains(t, store.dump(), "zqinside")
+	assert.NotContains(t, store.dump(), brainfstest.Sentinel)
+}
+
+// IndexDoc gets caller-supplied paths (brain_tunnel, brain_update): only a
+// clean path under wiki/ or knowledge/ is indexed.
+func TestIndexDocRefusesPathsOutsideWikiAndKnowledgeAndUncleanPaths(t *testing.T) {
+	brain := t.TempDir()
+	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "secret.md"))
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki", "w"), 0o755))
+	for _, p := range []string{"raw/secret.md", "wiki/w/../../raw/secret.md", "./raw/secret.md", "/raw/secret.md"} {
+		store := newFakeStore()
+		assert.Error(t, IndexDoc(context.Background(), store, brain, p), p)
+		assert.NotContains(t, store.dump(), brainfstest.Sentinel, p)
+	}
+}

ingestion/internal/pipeline/backfill.go

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

ingestion/internal/pipeline/pipeline.go

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

ingestion/internal/pipeline/refs.go

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

ingestion/internal/pipeline/root_test.go

@@ -0,0 +1,167 @@
+package pipeline
+
+import (
+	"context"
+	"fmt"
+	"io"
+	"os"
+	"path/filepath"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/wiki"
+)
+
+// hyperguild#157 slice 6: the pipeline read the source page, schema.md, the
+// pages it revises and the pages it adds source refs to with os.ReadFile, so
+// a symlinked file's content reached the LLM prompt and the written pages,
+// and a FIFO hung the ingest.
+
+func mkdirs(t *testing.T, brain string, dirs ...string) {
+	t.Helper()
+	for _, d := range dirs {
+		require.NoError(t, os.MkdirAll(filepath.Join(brain, filepath.FromSlash(d)), 0o755))
+	}
+}
+
+func TestReadSourcePageAndSchemaRefuseSymlinksAndSurviveSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/sources")
+	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok.md"), []byte("zqinside source"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "schema.md"), []byte("zqinside schema"), 0o644))
+	assert.Equal(t, "zqinside source", readSourcePage(brain, "ok"), "positive control")
+	assert.Equal(t, "zqinside schema", loadSchema(brain), "positive control")
+
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(brain, "wiki", "sources", "out.md")))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "sources", "in.md")))
+	assert.NotContains(t, readSourcePage(brain, "out"), brainfstest.Sentinel)
+	assert.NotContains(t, readSourcePage(brain, "in"), brainfstest.Sentinel)
+	assert.NotContains(t, storedSourceHash(brain, "in"), brainfstest.Sentinel)
+
+	src := filepath.Join(brain, "wiki", "sources", "r.md")
+	read := func() string { return readSourcePage(brain, "r") }
+	brainfstest.AssertNoLeak(t, src, "zqinside", 1500*time.Millisecond, read)
+	brainfstest.AssertNoLeakFrom(t, src, "zqinside", inBrain, 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, src, "zqinside", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+
+	schema := filepath.Join(brain, "schema.md")
+	rs := func() string { return loadSchema(brain) }
+	brainfstest.AssertNoLeakFrom(t, schema, "zqinside schema", inBrain, 1500*time.Millisecond, rs)
+	brainfstest.AssertNoHang(t, schema, "zqinside schema", 1500*time.Millisecond, 6*time.Second, func() { _ = rs() })
+}
+
+func TestReviseOrCreateRefusesASymlinkedExistingPage(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/concepts")
+	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "concepts", "c.md")))
+	page := wiki.Page{Path: "wiki/concepts/c.md", Content: "---\ntitle: C\n---\nnew\n"}
+	out, _, err := reviseOrCreate(brain, page)
+	assert.Error(t, err)
+	assert.NotContains(t, out, brainfstest.Sentinel)
+
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "d.md"), []byte("---\ntitle: D\n---\nzqold\n"), 0o644))
+	out, _, err = reviseOrCreate(brain, wiki.Page{Path: "wiki/concepts/d.md", Content: "---\ntitle: D\n---\nnew\n"})
+	require.NoError(t, err)
+	assert.Contains(t, out, "zqold", "positive control: the existing page is read")
+	out, _, err = reviseOrCreate(brain, wiki.Page{Path: "wiki/concepts/new.md", Content: "fresh"})
+	require.NoError(t, err)
+	assert.Equal(t, "fresh", out, "positive control: a missing page is created")
+}
+
+func TestInjectSourceRefsDoesNotReadASymlinkedPage(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/concepts")
+	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(brain, "wiki", "concepts", "c.md")))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "d.md"), []byte("zqinside d"), 0o644))
+	inv := map[wiki.PageType][]wiki.Entry{wiki.PageTypeConcept: {
+		{Slug: "c", Type: wiki.PageTypeConcept}, {Slug: "d", Type: wiki.PageTypeConcept},
+	}}
+	src := wiki.Page{Path: "wiki/sources/src.md", Content: "---\ntitle: Src\n---\nsee [[c|C]] and [[d|D]]\n"}
+	out := injectSourceRefs([]wiki.Page{src}, inv, brain)
+	got := fmt.Sprintf("%+v", out)
+	assert.Contains(t, got, "zqinside d", "positive control")
+	assert.NotContains(t, got, brainfstest.Sentinel)
+}
+
+func TestBackfillRefsSkipsSymlinkedSourcesAndPages(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "concepts", "real.md"), []byte("---\ntitle: R\n---\nbody\n"), 0o644))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok.md"), []byte("---\ntitle: zqinside\n---\n[[real|R]]\n"), 0o644))
+	// A source elsewhere in the brain whose title is the sentinel and which
+	// links the real concept with the [[slug|title]] form the pipeline follows.
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "src.md"),
+		[]byte("---\ntitle: "+brainfstest.Sentinel+"\n---\n[[real|R]]\n"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "src.md"), filepath.Join(brain, "wiki", "sources", "in.md")))
+	// A concept page linked by the regular source that is itself a symlink.
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "ok2.md"), []byte("---\ntitle: Two\n---\n[[lnk|L]]\n"), 0o644))
+	brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "page.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "page.md"), filepath.Join(brain, "wiki", "concepts", "lnk.md")))
+
+	_, err := BackfillRefs(context.Background(), brain)
+	require.NoError(t, err)
+	b, _ := os.ReadFile(filepath.Join(brain, "wiki", "concepts", "real.md"))
+	assert.Contains(t, string(b), "zqinside", "positive control: the regular source's ref is added")
+	assert.NotContains(t, string(b), brainfstest.Sentinel, "a symlinked source's title was written as a ref")
+	raw, _ := os.ReadFile(filepath.Join(brain, "raw", "page.md"))
+	assert.NotContains(t, string(raw), "[[ok2", "the symlinked concept page's target was rewritten")
+}
+
+// A source swapped between a regular file and a symlink to an in-brain source
+// whose title is the sentinel: the read refuses the swapped-in link, so the
+// sentinel never lands in the concept page as a ref.
+func TestBackfillRefsDoesNotWriteARefFromASourceSwappedInBehindASymlink(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
+	realPage := filepath.Join(brain, "wiki", "concepts", "real.md")
+	target := filepath.Join(brain, "raw", "src.md")
+	require.NoError(t, os.WriteFile(target, []byte("---\ntitle: "+brainfstest.Sentinel+"\n---\n[[real|R]]\n"), 0o644))
+	src := filepath.Join(brain, "wiki", "sources", "r.md")
+	inside := "---\ntitle: zqinside\n---\n[[real|R]]\n"
+	read := func() string {
+		_ = os.WriteFile(realPage, []byte("---\ntitle: R\n---\nbody\n"), 0o644)
+		_, _ = BackfillRefs(context.Background(), brain)
+		b, _ := os.ReadFile(realPage)
+		return string(b)
+	}
+	require.NoError(t, os.WriteFile(src, []byte(inside), 0o644))
+	require.Contains(t, read(), "zqinside", "positive control")
+	brainfstest.AssertNoLeakFrom(t, src, inside, target, 1500*time.Millisecond, read)
+}
+
+// A concept page that is regular when the inventory lists it, then swapped
+// for a symlink to an in-brain file before BackfillRefs reads it: only the
+// page read's own check refuses it (a static symlink never gets this far,
+// because LoadInventory does not list it).
+func TestBackfillRefsDoesNotCopyAPageSwappedInBehindASymlink(t *testing.T) {
+	brain := t.TempDir()
+	mkdirs(t, brain, "wiki/sources", "wiki/concepts", "raw")
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "wiki", "sources", "s.md"), []byte("---\ntitle: S\n---\n[[c|C]]\n"), 0o644))
+	page := filepath.Join(brain, "wiki", "concepts", "c.md")
+	target := filepath.Join(brain, "raw", "secret.md")
+	inside := "---\ntitle: C\n---\nzqinside\n"
+	read := func() string {
+		// The write path still follows a swapped-in link (#158) and can
+		// overwrite the target, so restore it each round.
+		_ = os.WriteFile(target, []byte("---\ntitle: X\n---\n"+brainfstest.Sentinel+"\n"), 0o644)
+		_, _ = BackfillRefs(context.Background(), brain)
+		f, err := os.OpenFile(page, os.O_RDONLY|syscall.O_NOFOLLOW|syscall.O_NONBLOCK, 0)
+		if err != nil {
+			return ""
+		}
+		defer func() { _ = f.Close() }()
+		b, _ := io.ReadAll(f)
+		return string(b)
+	}
+	require.NoError(t, os.WriteFile(page, []byte(inside), 0o644))
+	require.Contains(t, read(), "zqinside", "positive control: the regular page gets the ref")
+	brainfstest.AssertNoLeakFrom(t, page, inside, target, 3*time.Second, read)
+}

ingestion/internal/search/brainroot_test.go

@@ -61,6 +61,31 @@ func TestQueryDoesNotFollowASymlinkedDirectory(t *testing.T) {
 	assert.Zero(t, leaked(rs))
 }
 
+// A search root that is a symlink staying inside the brain (wiki/<w> -> ..)
+// was followed by fs.WalkDir, aliasing raw/ and root files into results
+// (PR #166 review). The root is now Lstat-checked and skipped.
+func TestQueryDoesNotFollowASymlinkedWingRootInsideTheBrain(t *testing.T) {
+	brain, _, _ := searchBrain(t)
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "r.md"), []byte("# r\n\nzqrawonly"), 0o644))
+	require.NoError(t, os.Symlink("..", filepath.Join(brain, "wiki", "alias")))
+	rs, err := Query(brain, QueryOptions{Query: "zqrawonly", Wing: "alias", Limit: 10})
+	require.NoError(t, err)
+	assert.Empty(t, rs)
+}
+
+// With a hall the search root is wiki/<wing>/<hall>; a symlinked <wing> with
+// a real <hall> directory under its target was followed (PR #166 round 2).
+func TestQueryDoesNotFollowASymlinkedWingUnderAWingAndHallRoot(t *testing.T) {
+	brain, _, _ := searchBrain(t)
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "facts", "r.md"), []byte("# r\n\nzqrawhall"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(brain, "wiki", "alias")))
+	rs, err := Query(brain, QueryOptions{Query: "zqrawhall", Wing: "alias", Hall: "facts", Limit: 10})
+	require.NoError(t, err)
+	assert.Empty(t, rs)
+}
+
 // swapInto keeps renaming a regular note, and either a symlink to outside or
 // a FIFO, into path. Each FIFO has a writer held open (as any local process
 // can): a FIFO with no writer reads EOF at once, which would let a reader

ingestion/internal/vectorstore/sync.go

@@ -2,12 +2,15 @@ package vectorstore
 
 import (
 	"context"
+	"errors"
 	"fmt"
+	"io/fs"
 	"log/slog"
-	"os"
+	"path"
-	"path/filepath"
 	"strings"
 	"time"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 )
 
 // Embedder produces dense vectors. The embed package's Client satisfies
@@ -90,31 +93,38 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 	}
 	seenParents := make(map[string]struct{})
 
+	// Through the brain root, regular files only (hyperguild#157): the brain
+	// is a Syncthing folder, and os.ReadFile followed a synced symlink into
+	// the embeddings and blocked on a FIFO.
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return res, fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
+
 	for _, sub := range scanDirs {
-		root := filepath.Join(brainDir, sub)
+		if _, err := bfs.Lstat(sub); errors.Is(err, fs.ErrNotExist) {
-		if _, err := os.Stat(root); os.IsNotExist(err) {
 			continue
 		}
-
+		// Any other walk error, including a scan root that is a symlink,
-		err = filepath.WalkDir(root, func(path string, d os.DirEntry, err error) error {
+		// aborts the run below.
-			if err != nil {
+		var walkErr error
-				return err
+		onErr := func(rel string, err error) {
+			if walkErr == nil {
+				walkErr = fmt.Errorf("%s: %w", rel, err)
 			}
-			if d.IsDir() || !strings.HasSuffix(path, ".md") || d.Name() == "_index.md" {
+		}
+		err = bfs.WalkRegular(sub, func(relSlash string) error {
+			if !strings.HasSuffix(relSlash, ".md") || path.Base(relSlash) == "_index.md" {
 				return nil
 			}
-			rel, err := filepath.Rel(brainDir, path)
-			if err != nil {
-				return err
-			}
-			relSlash := filepath.ToSlash(rel)
 			seenParents[relSlash] = struct{}{}
 
 			if ps, ok := parents[relSlash]; ok {
 				// File already has chunks in the store. Re-embed only when
 				// the file has been edited since the oldest chunk was
 				// written. Tolerate clock skew with a sub-second grace.
-				info, statErr := d.Info()
+				info, statErr := bfs.Lstat(relSlash)
 				if statErr != nil {
 					res.Errors = append(res.Errors, fmt.Errorf("stat %s: %w", relSlash, statErr))
 					return nil
@@ -132,7 +142,7 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 				}
 			}
 
-			content, readErr := os.ReadFile(path)
+			content, readErr := bfs.ReadRegular(relSlash)
 			if readErr != nil {
 				res.Errors = append(res.Errors, fmt.Errorf("read %s: %w", relSlash, readErr))
 				return nil
@@ -151,7 +161,12 @@ func Sync(ctx context.Context, brainDir string, store Store, embedder Embedder)
 				res.Added++
 			}
 			return nil
-		})
+		}, onErr)
+		if err == nil {
+			err = walkErr
+		}
+		// Abort before the delete pass: an incomplete walk would leave
+		// seenParents short and delete chunks of files that still exist.
 		if err != nil {
 			return res, fmt.Errorf("walk %s: %w", sub, err)
 		}

ingestion/internal/vectorstore/sync_root_test.go

@@ -0,0 +1,126 @@
+package vectorstore_test
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"strings"
+	"sync"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/vectorstore"
+)
+
+// recordingEmbedder keeps every text it was asked to embed.
+type recordingEmbedder struct {
+	mu    sync.Mutex
+	texts []string
+}
+
+func (e *recordingEmbedder) Embed(_ context.Context, text string) ([]float32, error) {
+	e.mu.Lock()
+	defer e.mu.Unlock()
+	e.texts = append(e.texts, text)
+	return []float32{1}, nil
+}
+
+func (e *recordingEmbedder) all() string {
+	e.mu.Lock()
+	defer e.mu.Unlock()
+	return strings.Join(e.texts, "\n")
+}
+
+// hyperguild#157 slice 3: Sync walked wiki/ and knowledge/ and read each .md
+// with os.ReadFile, so a symlinked note had its target embedded and served by
+// semantic search, and a FIFO stalled the sync.
+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")))
+
+	emb := &recordingEmbedder{}
+	store := &stubStore{}
+	_, err := vectorstore.Sync(context.Background(), brain, store, emb)
+	require.NoError(t, err)
+	assert.Contains(t, emb.all(), "inside note", "positive control: the regular note is embedded")
+	assert.NotContains(t, emb.all(), brainfstest.Sentinel)
+	for p := range store.upserts {
+		assert.NotContains(t, p, "leak.md")
+	}
+
+	p := filepath.Join(brain, "knowledge", "r.md")
+	require.NoError(t, os.MkdirAll(filepath.Dir(p), 0o755))
+	sync := func() string {
+		e := &recordingEmbedder{}
+		_, _ = vectorstore.Sync(context.Background(), brain, &stubStore{}, e)
+		return e.all()
+	}
+	brainfstest.AssertNoLeak(t, p, "inside", 1500*time.Millisecond, sync)
+	brainfstest.AssertNoHang(t, p, "inside", 1500*time.Millisecond, 6*time.Second, func() { _ = sync() })
+}
+
+// Chunks embedded from a symlinked note before this fix are deleted: the
+// note is no longer seen, so the delete pass drops its rows.
+func TestSyncDeletesChunksOfASymlinkedNote(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")))
+	store := &stubStore{known: map[string]time.Time{
+		"wiki/w/facts/leak.md#0001": {},
+		"wiki/w/facts/ok.md#0001":   {},
+	}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, &recordingEmbedder{})
+	require.NoError(t, err)
+	assert.Equal(t, []string{"wiki/w/facts/leak.md#0001"}, store.deletes)
+}
+
+// A walk error aborts Sync before the delete pass, so chunks of files the
+// walk could not see are kept.
+func TestSyncAbortsBeforeDeletingWhenASubdirIsUnreadable(t *testing.T) {
+	if os.Geteuid() == 0 {
+		t.Skip("root ignores directory permissions")
+	}
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/facts/ok.md", "inside note")
+	locked := filepath.Join(brain, "wiki", "w")
+	require.NoError(t, os.Chmod(locked, 0o000))
+	t.Cleanup(func() { _ = os.Chmod(locked, 0o755) })
+	store := &stubStore{known: map[string]time.Time{"wiki/w/facts/ok.md#0001": {}}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, &recordingEmbedder{})
+	assert.Error(t, err)
+	assert.Empty(t, store.deletes)
+}
+
+// A scan root that is a symlink inside the brain (knowledge -> .) was
+// followed by fs.WalkDir, aliasing raw/, sessions/ and root files into the
+// index. Sync now aborts on it, before embedding or deleting anything.
+func TestSyncAbortsOnASymlinkedScanRoot(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/a.md", "wiki note")
+	writeNote(t, brain, "sessions/s1.md", "session note")
+	require.NoError(t, os.Symlink(".", filepath.Join(brain, "knowledge")))
+	emb := &recordingEmbedder{}
+	store := &stubStore{known: map[string]time.Time{"wiki/w/a.md#0001": {}}}
+	_, err := vectorstore.Sync(context.Background(), brain, store, emb)
+	assert.Error(t, err)
+	assert.NotContains(t, emb.all(), "session note")
+	for p := range store.upserts {
+		assert.False(t, strings.HasPrefix(p, "knowledge/"), "upserted %s", p)
+	}
+	assert.Empty(t, store.deletes)
+}
+
+// A missing scan root is skipped; the other root still syncs.
+func TestSyncSkipsAMissingScanRoot(t *testing.T) {
+	brain := t.TempDir()
+	writeNote(t, brain, "wiki/w/a.md", "wiki note")
+	emb := &recordingEmbedder{}
+	_, err := vectorstore.Sync(context.Background(), brain, &stubStore{}, emb)
+	require.NoError(t, err)
+	assert.Contains(t, emb.all(), "wiki note")
+}

ingestion/internal/wiki/index.go

@@ -7,6 +7,7 @@ import (
 	"path/filepath"
 	"strings"
 
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 	"github.com/mathiasbq/hyperguild/ingestion/internal/textutil"
 )
 
@@ -16,6 +17,11 @@ func RebuildIndex(brainDir, date string) error {
 	if err != nil {
 		return fmt.Errorf("load inventory: %w", err)
 	}
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
 
 	total := len(inv[PageTypeConcept]) + len(inv[PageTypeEntity]) + len(inv[PageTypeSource])
 	var sb strings.Builder
@@ -34,7 +40,7 @@ func RebuildIndex(brainDir, date string) error {
 		label := strings.ToUpper(string(pt)[:1]) + string(pt)[1:]
 		fmt.Fprintf(&sb, "## %s\n\n", label)
 		for _, e := range entries {
-			summary := pageFirstSentence(brainDir, e)
+			summary := pageFirstSentence(bfs, e)
 			if summary != "" {
 				fmt.Fprintf(&sb, "- [[%s|%s]] — %s\n", e.Slug, e.Title, summary)
 			} else {
@@ -48,9 +54,10 @@ func RebuildIndex(brainDir, date string) error {
 	return os.WriteFile(dest, []byte(sb.String()), 0o644)
 }
 
-func pageFirstSentence(brainDir string, e Entry) string {
+// pageFirstSentence reads the page through the brain root, regular files
-	path := filepath.Join(brainDir, "wiki", string(e.Type), e.Slug+".md")
+// only (hyperguild#157).
-	content, err := os.ReadFile(path)
+func pageFirstSentence(bfs *brainfs.Brain, e Entry) string {
+	content, err := bfs.ReadRegular("wiki/" + string(e.Type) + "/" + e.Slug + ".md")
 	if err != nil {
 		return ""
 	}

ingestion/internal/wiki/inventory.go

@@ -3,36 +3,45 @@ package wiki
 
 import (
 	"bufio"
+	"bytes"
+	"errors"
 	"fmt"
-	"os"
+	"io/fs"
-	"path/filepath"
 	"strings"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
 )
 
 // LoadInventory walks brain/wiki/ and returns all pages grouped by type.
-// Missing subdirectories are silently skipped.
+// Missing subdirectories are silently skipped. Pages are listed and read
+// through the brain root, regular files only (hyperguild#157); a type
+// directory that is a symlink is an error.
 func LoadInventory(brainDir string) (map[PageType][]Entry, error) {
 	result := map[PageType][]Entry{
 		PageTypeConcept: {},
 		PageTypeEntity:  {},
 		PageTypeSource:  {},
 	}
+	bfs, err := brainfs.Open(brainDir)
+	if err != nil {
+		return nil, fmt.Errorf("open brain: %w", err)
+	}
+	defer func() { _ = bfs.Close() }()
 	for pt := range result {
-		dir := filepath.Join(brainDir, "wiki", string(pt))
+		dir := "wiki/" + string(pt)
-		entries, err := os.ReadDir(dir)
+		names, err := bfs.ReadDirRegular(dir)
-		if os.IsNotExist(err) {
+		if errors.Is(err, fs.ErrNotExist) {
 			continue
 		}
 		if err != nil {
 			return nil, fmt.Errorf("read dir %s: %w", dir, err)
 		}
-		for _, e := range entries {
+		for _, name := range names {
-			if e.IsDir() || !strings.HasSuffix(e.Name(), ".md") {
+			if !strings.HasSuffix(name, ".md") {
 				continue
 			}
-			slug := strings.TrimSuffix(e.Name(), ".md")
+			slug := strings.TrimSuffix(name, ".md")
-			path := filepath.Join(dir, e.Name())
+			title, aliases := readFrontmatter(bfs, dir+"/"+name, slug)
-			title, aliases := readFrontmatter(path, slug)
 			result[pt] = append(result[pt], Entry{Slug: slug, Title: title, Aliases: aliases, Type: pt})
 		}
 	}
@@ -41,15 +50,14 @@ func LoadInventory(brainDir string) (map[PageType][]Entry, error) {
 
 // readFrontmatter extracts title and aliases from YAML frontmatter.
 // Falls back to slug for title and empty aliases on any error.
-func readFrontmatter(path, fallbackSlug string) (title string, aliases []string) {
+func readFrontmatter(bfs *brainfs.Brain, rel, fallbackSlug string) (title string, aliases []string) {
 	title = fallbackSlug
-	f, err := os.Open(path)
+	content, err := bfs.ReadRegular(rel)
 	if err != nil {
 		return
 	}
-	defer f.Close() //nolint:errcheck
 
-	scanner := bufio.NewScanner(f)
+	scanner := bufio.NewScanner(bytes.NewReader(content))
 	inFM := false
 	inAliases := false
 	for scanner.Scan() {

ingestion/internal/wiki/root_test.go

@@ -0,0 +1,79 @@
+package wiki
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs"
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brainfs/brainfstest"
+)
+
+// hyperguild#157 slice 4: LoadInventory listed wiki/<type>/ with os.ReadDir
+// and opened each .md by path, so a symlinked page put the target's title and
+// aliases into the inventory (and the LLM prompts built from it), and a FIFO
+// hung it. RebuildIndex read first sentences the same way.
+func TestLoadInventoryRefusesSymlinksAndSurvivesSwapRaces(t *testing.T) {
+	brain := t.TempDir()
+	dir := filepath.Join(brain, "wiki", "concepts")
+	require.NoError(t, os.MkdirAll(dir, 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(dir, "ok.md"), []byte("---\ntitle: zqinside\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(brainfstest.Outside(t), filepath.Join(dir, "leak.md")))
+	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
+	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "s.md"), filepath.Join(dir, "inlink.md")))
+
+	inv, err := LoadInventory(brain)
+	require.NoError(t, err)
+	got := fmt.Sprintf("%+v", inv)
+	assert.Contains(t, got, "zqinside", "positive control")
+	assert.NotContains(t, got, brainfstest.Sentinel)
+	assert.NotContains(t, got, "leak", "a symlinked page is not listed")
+	assert.NotContains(t, got, "inlink", "a page linked to another brain file is not listed")
+
+	p := filepath.Join(dir, "r.md")
+	read := func() string {
+		inv, _ := LoadInventory(brain)
+		return fmt.Sprintf("%+v", inv)
+	}
+	brainfstest.AssertNoLeak(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, read)
+	brainfstest.AssertNoLeakFrom(t, p, "---\ntitle: zqinside\n---\n", inBrain, 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}
+
+func TestLoadInventoryReturnsErrNotRegularForASymlinkedTypeDir(t *testing.T) {
+	brain := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "wiki"), 0o755))
+	require.NoError(t, os.MkdirAll(filepath.Join(brain, "raw"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(brain, "raw", "r.md"), []byte("---\ntitle: zqrawonly\n---\n"), 0o644))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(brain, "wiki", "concepts")))
+	inv, err := LoadInventory(brain)
+	require.ErrorIs(t, err, brainfs.ErrNotRegular)
+	assert.NotContains(t, fmt.Sprintf("%+v", inv), "zqrawonly")
+}
+
+func TestRebuildIndexDoesNotReadAPageSwappedForASymlink(t *testing.T) {
+	brain := t.TempDir()
+	dir := filepath.Join(brain, "wiki", "concepts")
+	require.NoError(t, os.MkdirAll(dir, 0o755))
+	p := filepath.Join(dir, "r.md")
+	require.NoError(t, os.WriteFile(p, []byte("---\ntitle: R\n---\nzqinside sentence.\n"), 0o644))
+	require.NoError(t, RebuildIndex(brain, "2026-10-04"))
+	idx, err := os.ReadFile(filepath.Join(brain, "wiki", "index.md"))
+	require.NoError(t, err)
+	require.Contains(t, string(idx), "zqinside", "positive control: the summary is read")
+
+	read := func() string {
+		_ = RebuildIndex(brain, "2026-10-04")
+		b, _ := os.ReadFile(filepath.Join(brain, "wiki", "index.md"))
+		return string(b)
+	}
+	brainfstest.AssertNoLeak(t, p, "---\ntitle: R\n---\nzqinside sentence.\n", 1500*time.Millisecond, read)
+	inBrain := brainfstest.WriteSentinelAt(t, filepath.Join(brain, "raw", "s.md"))
+	brainfstest.AssertNoLeakFrom(t, p, "---\ntitle: R\n---\nzqinside sentence.\n", inBrain, 1500*time.Millisecond, read)
+	brainfstest.AssertNoHang(t, p, "---\ntitle: R\n---\nzqinside sentence.\n", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
+}