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

Review round 1 on PR #175:

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

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

ingestion/internal/brain/index_root_test.go

@@ -21,7 +21,7 @@ func readIndex(t *testing.T, brainDir, wing string) string {
 
 // hyperguild#157 slice 5: BuildWingIndex listed wiki/<wing>/<hall>/ with
 // os.ReadDir and opened each note by path, so a symlinked note put the
-// target's title into _index.md, and a FIFO hung every brain_write.
+// target's title into _index.md, and a FIFO hung the index build.
 func TestBuildWingIndexRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
 	b := t.TempDir()
 	facts := filepath.Join(b, "wiki", "w", "facts")
@@ -48,24 +48,44 @@ func TestBuildWingIndexRefusesSymlinkedNotesAndSurvivesSwapRaces(t *testing.T) {
 	brainfstest.AssertNoHang(t, p, "---\ntitle: zqinside\n---\n", 1500*time.Millisecond, 6*time.Second, func() { _ = read() })
 }
 
-// A wing or hall directory that is a symlink is not listed, and nothing is
-// written into its target.
-func TestBuildWingIndexDoesNotFollowASymlinkedWingOrHall(t *testing.T) {
+// A symlinked hall is skipped while a real hall next to it is indexed; a
+// symlinked wing is refused and nothing is written into its target.
+func TestBuildWingIndexSkipsASymlinkedHallAndRefusesASymlinkedWing(t *testing.T) {
 	b := t.TempDir()
 	require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "facts"), 0o755))
 	require.NoError(t, os.WriteFile(filepath.Join(b, "raw", "facts", "r.md"), []byte("---\ntitle: zqrawonly\n---\n"), 0o644))
-	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w"), 0o755))
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w", "decisions"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "w", "decisions", "d.md"), []byte("---\ntitle: zqrealhall\n---\n"), 0o644))
 	require.NoError(t, os.Symlink(filepath.Join("..", "..", "raw", "facts"), filepath.Join(b, "wiki", "w", "facts")))
 	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(b, "wiki", "alias")))
 
-	_ = brain.BuildWingIndex(b, "w")
-	assert.NotContains(t, readIndex(t, b, "w"), "zqrawonly", "symlinked hall")
+	require.NoError(t, brain.BuildWingIndex(b, "w"))
+	idx, err := os.ReadFile(filepath.Join(b, "wiki", "w", "_index.md"))
+	require.NoError(t, err, "the wing index is written")
+	assert.Contains(t, string(idx), "zqrealhall", "the real hall is indexed")
+	assert.NotContains(t, string(idx), "zqrawonly", "the symlinked hall is not")
 
 	assert.Error(t, brain.BuildWingIndex(b, "alias"))
-	_, err := os.Stat(filepath.Join(b, "raw", "_index.md"))
+	_, err = os.Stat(filepath.Join(b, "raw", "_index.md"))
 	assert.True(t, os.IsNotExist(err), "an index was written into the symlinked wing's target")
 }
 
+// BuildAllWingIndexes indexes the real wings and skips a symlinked one.
+func TestBuildAllWingIndexesSkipsASymlinkedWing(t *testing.T) {
+	b := t.TempDir()
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w", "facts"), 0o755))
+	require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "w", "facts", "n.md"), []byte("---\ntitle: zqrealwing\n---\n"), 0o644))
+	require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "facts"), 0o755))
+	require.NoError(t, os.Symlink(filepath.Join("..", "raw"), filepath.Join(b, "wiki", "alias")))
+
+	require.NoError(t, brain.BuildAllWingIndexes(b))
+	idx, err := os.ReadFile(filepath.Join(b, "wiki", "w", "_index.md"))
+	require.NoError(t, err)
+	assert.Contains(t, string(idx), "zqrealwing")
+	_, err = os.Stat(filepath.Join(b, "raw", "_index.md"))
+	assert.True(t, os.IsNotExist(err))
+}
+
 // A link to a symlinked note does not resolve: only regular files count as
 // entries, so StripUnresolvedLinks unwraps it.
 func TestStripUnresolvedLinksDoesNotCountASymlinkedNoteAsAnEntry(t *testing.T) {
@@ -81,3 +101,32 @@ func TestStripUnresolvedLinksDoesNotCountASymlinkedNoteAsAnEntry(t *testing.T) {
 	assert.NotContains(t, out, "[[ghost]]")
 	assert.Contains(t, unlinked, "ghost")
 }
+
+// A linked tree (knowledge/ or wiki/) that is not a real directory is
+// skipped, not an error: StripUnresolvedLinks runs before every brain_write,
+// and an error there loses the learning.
+func TestStripUnresolvedLinksSkipsALinkedTreeThatIsNotARealDirectory(t *testing.T) {
+	for name, mk := range map[string]func(t *testing.T, b string){
+		"symlink to an in-brain dir": func(t *testing.T, b string) {
+			require.NoError(t, os.MkdirAll(filepath.Join(b, "raw", "k"), 0o755))
+			require.NoError(t, os.Symlink(filepath.Join("raw", "k"), filepath.Join(b, "knowledge")))
+		},
+		"dangling symlink": func(t *testing.T, b string) {
+			require.NoError(t, os.Symlink("nowhere", filepath.Join(b, "knowledge")))
+		},
+		"regular file": func(t *testing.T, b string) {
+			require.NoError(t, os.WriteFile(filepath.Join(b, "knowledge"), []byte("x"), 0o644))
+		},
+	} {
+		t.Run(name, func(t *testing.T) {
+			b := t.TempDir()
+			require.NoError(t, os.MkdirAll(filepath.Join(b, "wiki", "w", "facts"), 0o755))
+			require.NoError(t, os.WriteFile(filepath.Join(b, "wiki", "w", "facts", "real.md"), []byte("x"), 0o644))
+			mk(t, b)
+			out, _, err := brain.StripUnresolvedLinks(b, "learning [[real]] and [[gone]]")
+			require.NoError(t, err)
+			assert.Contains(t, out, "[[real]]", "links into wiki/ still resolve")
+			assert.NotContains(t, out, "[[gone]]")
+		})
+	}
+}

ingestion/internal/brain/linkcheck.go

@@ -4,6 +4,7 @@ import (
 	"errors"
 	"fmt"
 	"io/fs"
+	"log/slog"
 	"path"
 	"regexp"
 	"sort"
@@ -121,6 +122,13 @@ func entryIndex(brainDir string) (map[string]struct{}, error) {
 			index[strings.TrimPrefix(strings.TrimSuffix(rel, ".md"), "wiki/")] = struct{}{}
 			return nil
 		}, func(rel string, err error) {
+			// A linked tree that is not a real directory (a symlink, a
+			// file) is skipped, as filepath.WalkDir did: this runs before
+			// every brain_write, and an error here loses the learning.
+			if rel == dir && errors.Is(err, brainfs.ErrNotRegular) {
+				slog.Warn("link check: skipping a linked tree that is not a real directory", "dir", dir)
+				return
+			}
 			if walkErr == nil {
 				walkErr = fmt.Errorf("%s: %w", rel, err)
 			}