fix(brain): move the wikilink strip into WriteNote/UpdateNote

The BrainStore is not the only door. POST /write — the HTTP path CLAUDE.md
hands to curl and scripts — calls api.WriteNote directly, so the strip
shipped one commit ago covered brain_write and capture while leaving the raw
door ungated. A gate one door wide is not a gate.

The BrainStore keeps its own call so it can still report Ref.Unlinked to the
MCP caller; running the strip twice is a no-op on content the primitive has
already cleaned.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

ingestion/internal/api/handler.go

@@ -133,6 +133,16 @@ func WriteNote(brainDir string, opts WriteNoteOptions) (string, error) {
 		return "", fmt.Errorf("content is required")
 	}
 
+	// In the primitive, not in a caller: POST /write reaches here directly,
+	// without the BrainStore, and a gate one door wide is not a gate.
+	// BrainStore still calls the strip itself to report Ref.Unlinked; the
+	// second pass is a no-op on already-clean content.
+	clean, _, err := brain.StripUnresolvedLinks(brainDir, opts.Content)
+	if err != nil {
+		return "", err
+	}
+	opts.Content = clean
+
 	if opts.Wing != "" && opts.Hall != "" {
 		return writeHallNote(brainDir, opts)
 	}

ingestion/internal/api/handler_test.go

@@ -497,3 +497,45 @@ func TestWriteNote_RejectsClaimFieldWithoutProvenance(t *testing.T) {
 	_, statErr := os.Stat(filepath.Join(dir, "wiki/homelab/facts/no-provenance.md"))
 	assert.True(t, os.IsNotExist(statErr))
 }
+
+// The HTTP POST /write door reaches WriteNote directly, without the
+// BrainStore, so the unresolved-wikilink strip has to live in the primitive
+// or that door stays ungated.
+func TestWriteNote_UnwrapsUnresolvedWikilinks(t *testing.T) {
+	dir := t.TempDir()
+	_, err := api.WriteNote(dir, api.WriteNoteOptions{
+		Content: "# Target\n\nbody\n", Filename: "target", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+
+	rel, err := api.WriteNote(dir, api.WriteNoteOptions{
+		Content:  "See [[target]] and [[gitea-ci]].\n",
+		Filename: "src", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+
+	got, err := os.ReadFile(filepath.Join(dir, filepath.FromSlash(rel)))
+	require.NoError(t, err)
+	assert.Contains(t, string(got), "[[target]]")
+	assert.Contains(t, string(got), "and gitea-ci.")
+	assert.NotContains(t, string(got), "[[gitea-ci]]")
+}
+
+func TestUpdateNote_UnwrapsUnresolvedWikilinks(t *testing.T) {
+	dir := t.TempDir()
+	_, err := api.WriteNote(dir, api.WriteNoteOptions{
+		Content: "old\n", Filename: "n", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+
+	rel, _, _, err := api.UpdateNote(dir, api.UpdateNoteOptions{
+		Wing: "a", Hall: "facts", Slug: "n",
+		Content: "Related: [[secret-hygiene]].\n", Reason: "r",
+	})
+	require.NoError(t, err)
+
+	got, err := os.ReadFile(filepath.Join(dir, filepath.FromSlash(rel)))
+	require.NoError(t, err)
+	assert.Contains(t, string(got), "Related: secret-hygiene.")
+	assert.NotContains(t, string(got), "[[secret-hygiene]]")
+}

ingestion/internal/api/update.go

@@ -64,6 +64,14 @@ func UpdateNote(brainDir string, opts UpdateNoteOptions) (relPath, contentHash,
 		return "", "", "", fmt.Errorf("content is required")
 	}
 
+	// Same reason as WriteNote: the strip belongs in the primitive so every
+	// door inherits it.
+	clean, _, err := brain.StripUnresolvedLinks(brainDir, opts.Content)
+	if err != nil {
+		return "", "", "", err
+	}
+	opts.Content = clean
+
 	var rel string
 	if opts.Path != "" {
 		rel = opts.Path

ingestion/internal/brain/linkcheck.go

@@ -0,0 +1,157 @@
+package brain
+
+import (
+	"fmt"
+	"os"
+	"path/filepath"
+	"regexp"
+	"sort"
+	"strings"
+)
+
+// wikilinkRE matches [[target]] and [[target|Display Text]].
+var wikilinkRE = regexp.MustCompile(`\[\[([^\]|]+)(?:\|([^\]]*))?\]\]`)
+
+// fencedCodeRE and inlineCodeRE mark the regions where a [[...]] is a
+// syntax example rather than a link. Same exclusion brain-gardener's audit
+// applies on the read side, so the write gate and the audit agree on what
+// counts as a link at all.
+var (
+	fencedCodeRE = regexp.MustCompile("(?s)```.*?```")
+	inlineCodeRE = regexp.MustCompile("`[^`\n]*`")
+)
+
+// StripUnresolvedLinks unwraps every [[wikilink]] in content whose target
+// resolves to no entry under knowledge/ or wiki/, leaving the link's display
+// text (or its target) as plain prose. It returns the rewritten content and
+// the sorted, de-duplicated targets it unwrapped.
+//
+// WHY UNWRAP RATHER THAN REJECT THE WRITE
+// Agents write [[...]] around anything that feels related — a skill name, a
+// repo, an agent-local memory file — and none of those are brain entries.
+// Every one of those becomes a permanent [high] broken-link finding that no
+// deterministic Fixer can repair, because there is no target to repoint to:
+// the brain-audit digest grew from 19 to 63 high findings between 2026-08-26
+// and 2026-09-16, and 53 of the 63 were exactly this. Rejecting the write
+// instead would push the failure onto claudewatcher's unattended ingest path,
+// where a refused write is a lost learning. Unwrapping keeps the author's
+// words, keeps the write, and keeps the graph honest.
+//
+// An empty corpus (no knowledge/ or wiki/ yet, or a misconfigured brainDir)
+// returns content unchanged: nothing resolving is a bootstrap state, not
+// evidence that every target was invented.
+func StripUnresolvedLinks(brainDir, content string) (string, []string, error) {
+	index, err := entryIndex(brainDir)
+	if err != nil {
+		return "", nil, err
+	}
+	if len(index) == 0 {
+		return content, nil, nil
+	}
+
+	code := codeSpans(content)
+	stripped := map[string]struct{}{}
+
+	var b strings.Builder
+	last := 0
+	for _, m := range wikilinkRE.FindAllStringSubmatchIndex(content, -1) {
+		start, end := m[0], m[1]
+		if overlaps(start, end, code) {
+			continue
+		}
+		target := strings.TrimSpace(content[m[2]:m[3]])
+		if _, ok := index[linkKey(target)]; ok {
+			continue
+		}
+		display := target
+		if m[4] >= 0 {
+			if d := strings.TrimSpace(content[m[4]:m[5]]); d != "" {
+				display = d
+			}
+		}
+		b.WriteString(content[last:start])
+		b.WriteString(display)
+		last = end
+		stripped[target] = struct{}{}
+	}
+	if last == 0 {
+		return content, nil, nil
+	}
+	b.WriteString(content[last:])
+
+	targets := make([]string, 0, len(stripped))
+	for t := range stripped {
+		targets = append(targets, t)
+	}
+	sort.Strings(targets)
+	return b.String(), targets, nil
+}
+
+// linkedTrees are the two trees that hold linkable entries — the same pair
+// package notes admits under ScopeNotes. Duplicated rather than imported
+// because that list is unexported there and this is a read-only mirror.
+var linkedTrees = []string{"knowledge", "wiki"}
+
+// entryIndex maps every form a wikilink may name an entry by — its bare slug
+// and its path form (wiki/<wing>/<hall>/<slug>.md -> wing/hall/slug) — to a
+// present marker. Mirrors brain-gardener's resolver so an accepted link is
+// one the audit will also resolve.
+func entryIndex(brainDir string) (map[string]struct{}, error) {
+	index := map[string]struct{}{}
+	for _, dir := range linkedTrees {
+		root := filepath.Join(brainDir, dir)
+		if _, err := os.Stat(root); os.IsNotExist(err) {
+			continue
+		} else if err != nil {
+			return nil, fmt.Errorf("stat %s: %w", dir, err)
+		}
+		err := filepath.WalkDir(root, func(path string, d os.DirEntry, err error) error {
+			if err != nil {
+				return err
+			}
+			if d.IsDir() || !strings.HasSuffix(path, ".md") {
+				return nil
+			}
+			rel, err := filepath.Rel(brainDir, path)
+			if err != nil {
+				return err
+			}
+			rel = filepath.ToSlash(rel)
+			index[strings.TrimSuffix(filepath.Base(rel), ".md")] = struct{}{}
+			index[strings.TrimPrefix(strings.TrimSuffix(rel, ".md"), "wiki/")] = struct{}{}
+			return nil
+		})
+		if err != nil {
+			return nil, fmt.Errorf("walk %s: %w", dir, err)
+		}
+	}
+	return index, nil
+}
+
+// linkKey normalises a link target for index lookup: an exact path form is
+// tried as written, and anything else falls back to its final segment.
+func linkKey(target string) string {
+	return strings.TrimSuffix(target, ".md")
+}
+
+// codeSpans returns the byte ranges of fenced blocks and inline code spans.
+func codeSpans(content string) [][2]int {
+	var spans [][2]int
+	for _, m := range fencedCodeRE.FindAllStringIndex(content, -1) {
+		spans = append(spans, [2]int{m[0], m[1]})
+	}
+	for _, m := range inlineCodeRE.FindAllStringIndex(content, -1) {
+		spans = append(spans, [2]int{m[0], m[1]})
+	}
+	return spans
+}
+
+// overlaps reports whether [start,end) intersects any span.
+func overlaps(start, end int, spans [][2]int) bool {
+	for _, s := range spans {
+		if start < s[1] && end > s[0] {
+			return true
+		}
+	}
+	return false
+}

ingestion/internal/brain/linkcheck_test.go

@@ -0,0 +1,93 @@
+package brain_test
+
+import (
+	"testing"
+
+	"github.com/mathiasbq/hyperguild/ingestion/internal/brain"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// seedCorpus writes the two entries every linkcheck case resolves against.
+func seedCorpus(t *testing.T, dir string) {
+	t.Helper()
+	seedNote(t, dir, "wiki/homelab/facts/real-entry.md",
+		"---\nwing: homelab\nhall: facts\ntitle: 'Real entry'\n---\n\nbody.\n")
+	seedNote(t, dir, "knowledge/legacy-entry.md",
+		"---\ntitle: 'Legacy entry'\n---\n\nbody.\n")
+}
+
+func TestStripUnresolvedLinks(t *testing.T) {
+	tests := []struct {
+		name     string
+		body     string
+		want     string
+		stripped []string
+	}{
+		{
+			name: "bare slug that resolves is kept",
+			body: "See [[real-entry]] for the rule.",
+			want: "See [[real-entry]] for the rule.",
+		},
+		{
+			name: "path-style target that resolves is kept",
+			body: "See [[homelab/facts/real-entry]].",
+			want: "See [[homelab/facts/real-entry]].",
+		},
+		{
+			name: "knowledge/ entry resolves by bare slug",
+			body: "See [[legacy-entry]].",
+			want: "See [[legacy-entry]].",
+		},
+		{
+			name:     "unresolvable target is unwrapped to plain text",
+			body:     "Related: [[secret-hygiene]].",
+			want:     "Related: secret-hygiene.",
+			stripped: []string{"secret-hygiene"},
+		},
+		{
+			name:     "unresolvable aliased target keeps its display text",
+			body:     "Related: [[feedback_check_host_not_assume|check the host]].",
+			want:     "Related: check the host.",
+			stripped: []string{"feedback_check_host_not_assume"},
+		},
+		{
+			name: "link inside a fenced code block is left alone",
+			body: "Syntax:\n\n```\n[[wing/hall/slug]]\n```\n",
+			want: "Syntax:\n\n```\n[[wing/hall/slug]]\n```\n",
+		},
+		{
+			name: "link inside an inline code span is left alone",
+			body: "Write `[[wing/hall/slug]]` to link.",
+			want: "Write `[[wing/hall/slug]]` to link.",
+		},
+		{
+			name:     "every unresolvable target is reported once, sorted",
+			body:     "[[zeta-gap]] and [[alpha-gap]] and [[zeta-gap]] again.",
+			want:     "zeta-gap and alpha-gap and zeta-gap again.",
+			stripped: []string{"alpha-gap", "zeta-gap"},
+		},
+	}
+
+	for _, tc := range tests {
+		t.Run(tc.name, func(t *testing.T) {
+			dir := t.TempDir()
+			seedCorpus(t, dir)
+
+			got, stripped, err := brain.StripUnresolvedLinks(dir, tc.body)
+			require.NoError(t, err)
+			assert.Equal(t, tc.want, got)
+			assert.Equal(t, tc.stripped, stripped)
+		})
+	}
+}
+
+func TestStripUnresolvedLinks_MissingBrainDirIsNotAGate(t *testing.T) {
+	// A brain dir with no knowledge//wiki/ tree yet must not turn every link
+	// into an unresolved one — an empty corpus is a bootstrap state, not
+	// evidence that the author invented the target.
+	got, stripped, err := brain.StripUnresolvedLinks(t.TempDir(), "See [[real-entry]].")
+	require.NoError(t, err)
+	assert.Equal(t, "See [[real-entry]].", got)
+	assert.Nil(t, stripped)
+}

ingestion/internal/brainstore/store.go

@@ -42,6 +42,12 @@ func (s *Store) WithGraph(g graphsync.Store) *Store {
 
 // Write creates a brain note and returns its read-after-write handle.
 func (s *Store) Write(ctx context.Context, n capture.Note) (capture.Ref, error) {
+	content, unlinked, err := brain.StripUnresolvedLinks(s.brainDir, n.Content)
+	if err != nil {
+		return capture.Ref{}, err
+	}
+	n.Content = content
+
 	relPath, err := api.WriteNote(s.brainDir, api.WriteNoteOptions{
 		Content:  n.Content,
 		Filename: n.Filename,
@@ -57,13 +63,19 @@ func (s *Store) Write(ctx context.Context, n capture.Note) (capture.Ref, error)
 	s.indexInGraph(ctx, "brain_write", relPath)
 
 	_, _, hash, _ := api.ReadNote(s.brainDir, relPath)
-	return capture.Ref{ID: relPath, Path: relPath, ContentHash: hash}, nil
+	return capture.Ref{ID: relPath, Path: relPath, ContentHash: hash, Unlinked: unlinked}, nil
 }
 
 // Update supersedes an existing note in place. slug may be a bare slug
 // (resolved against n.Wing/n.Hall) or a full brain-relative path (when it
 // contains a slash). It never creates — a missing target is an error.
 func (s *Store) Update(ctx context.Context, slug string, n capture.Note) (capture.Ref, error) {
+	content, unlinked, err := brain.StripUnresolvedLinks(s.brainDir, n.Content)
+	if err != nil {
+		return capture.Ref{}, err
+	}
+	n.Content = content
+
 	opts := api.UpdateNoteOptions{Content: n.Content, Reason: n.Reason}
 	if strings.Contains(slug, "/") {
 		opts.Path = slug
@@ -80,7 +92,7 @@ func (s *Store) Update(ctx context.Context, slug string, n capture.Note) (captur
 	}
 	s.indexInGraph(ctx, "brain_update", relPath)
 
-	return capture.Ref{ID: relPath, Path: relPath, ContentHash: hash, Superseded: true}, nil
+	return capture.Ref{ID: relPath, Path: relPath, ContentHash: hash, Superseded: true, Unlinked: unlinked}, nil
 }
 
 // Get fetches a note by id/path — the read-after-write confirmation

ingestion/internal/brainstore/store_test.go

@@ -83,3 +83,45 @@ func TestStoreGetRoundTripsHash(t *testing.T) {
 	assert.Equal(t, "a", note.Frontmatter["wing"])
 	assert.Contains(t, note.Body, "# Body")
 }
+
+func TestStoreWriteUnwrapsUnresolvedWikilinks(t *testing.T) {
+	dir := t.TempDir()
+	s := brainstore.New(dir)
+	_, err := s.Write(context.Background(), capture.Note{
+		Content: "# Target\n\nbody\n", Filename: "target", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+
+	ref, err := s.Write(context.Background(), capture.Note{
+		Content:  "See [[target]] and [[secret-hygiene]].\n",
+		Filename: "src", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+	assert.Equal(t, []string{"secret-hygiene"}, ref.Unlinked)
+
+	got, err := os.ReadFile(filepath.Join(dir, "wiki/a/facts/src.md"))
+	require.NoError(t, err)
+	assert.Contains(t, string(got), "[[target]]")
+	assert.Contains(t, string(got), "and secret-hygiene.")
+	assert.NotContains(t, string(got), "[[secret-hygiene]]")
+}
+
+func TestStoreUpdateUnwrapsUnresolvedWikilinks(t *testing.T) {
+	dir := t.TempDir()
+	s := brainstore.New(dir)
+	_, err := s.Write(context.Background(), capture.Note{
+		Content: "old\n", Filename: "n", Wing: "a", Hall: "facts",
+	})
+	require.NoError(t, err)
+
+	ref, err := s.Update(context.Background(), "n", capture.Note{
+		Content: "Related: [[cad-babysit]].\n", Wing: "a", Hall: "facts", Reason: "r",
+	})
+	require.NoError(t, err)
+	assert.Equal(t, []string{"cad-babysit"}, ref.Unlinked)
+
+	got, err := os.ReadFile(filepath.Join(dir, "wiki/a/facts/n.md"))
+	require.NoError(t, err)
+	assert.Contains(t, string(got), "Related: cad-babysit.")
+	assert.NotContains(t, string(got), "[[cad-babysit]]")
+}

ingestion/internal/capture/ports.go

@@ -15,6 +15,10 @@ type Ref struct {
 	Path        string
 	ContentHash string
 	Superseded  bool
+	// Unlinked names the [[wikilink]] targets the store unwrapped to plain
+	// text because they resolve to no entry. Reported rather than rejected:
+	// see brain.StripUnresolvedLinks for why the write still lands.
+	Unlinked []string
 }
 
 // StoredNote is a brain note fetched by Get: the read-after-write

ingestion/internal/mcp/handlers.go

@@ -233,6 +233,15 @@ type brainWriteArgs struct {
 	Hall     string `json:"hall,omitempty"`
 }
 
+// unlinkedNote explains the `unlinked` field to the caller that caused it.
+// The write landed; what is gone is the [[...]] around a target that names no
+// brain entry. Said here rather than only in a doc comment because the caller
+// is a model that will otherwise repeat it on the next write.
+const unlinkedNote = "these [[wikilink]] targets resolve to no brain entry, " +
+	"so they were unwrapped to plain text. Link only entries that exist " +
+	"(a filename under knowledge/ or wiki/); write the target entry first if " +
+	"you want the link, and keep skills, repos and agent-local memory files as prose."
+
 func (s *Server) brainWrite(ctx context.Context, args json.RawMessage) (json.RawMessage, error) {
 	var a brainWriteArgs
 	if err := json.Unmarshal(args, &a); err != nil {
@@ -253,7 +262,12 @@ func (s *Server) brainWrite(ctx context.Context, args json.RawMessage) (json.Raw
 	if err != nil {
 		return nil, err
 	}
-	return json.Marshal(map[string]string{"id": ref.ID, "path": ref.Path, "content_hash": ref.ContentHash})
+	out := map[string]any{"id": ref.ID, "path": ref.Path, "content_hash": ref.ContentHash}
+	if len(ref.Unlinked) > 0 {
+		out["unlinked"] = ref.Unlinked
+		out["unlinked_note"] = unlinkedNote
+	}
+	return json.Marshal(out)
 }
 
 type brainUpdateArgs struct {
@@ -297,9 +311,14 @@ func (s *Server) brainUpdate(ctx context.Context, args json.RawMessage) (json.Ra
 	if err != nil {
 		return nil, err
 	}
-	return json.Marshal(map[string]any{
+	out := map[string]any{
 		"id": ref.ID, "path": ref.Path, "content_hash": ref.ContentHash, "superseded": ref.Superseded,
-	})
+	}
+	if len(ref.Unlinked) > 0 {
+		out["unlinked"] = ref.Unlinked
+		out["unlinked_note"] = unlinkedNote
+	}
+	return json.Marshal(out)
 }
 
 type brainGetArgs struct {