chore: update marketplace for v0.21.127

Automated dependency update. All tests passed.

.github/workflows/autoupdate.yaml

@@ -16,6 +16,7 @@ jobs:
     uses: lukaszraczylo/shared-actions/.github/workflows/renovate-autoupdate.yaml@main
     with:
       go-version: ">=1.24"
+      build-tags: "fts5"
       node-working-directory: ui
       require-node-tests: false
       release-workflow: release.yaml

go.mod

@@ -16,7 +16,7 @@ require (
 	github.com/stretchr/testify v1.12.1
 	github.com/sugarme/tokenizer v0.3.0
 	github.com/yalue/onnxruntime_go v1.36.0
-	golang.org/x/sync v0.23.0
+	golang.org/x/sync v0.24.0
 	gorm.io/driver/sqlite v1.6.0
 	gorm.io/gorm v1.31.2
 )
@@ -25,7 +25,7 @@ require (
 	github.com/emirpasic/gods v1.18.1 // indirect
 	github.com/jinzhu/inflection v1.0.0 // indirect
 	github.com/jinzhu/now v1.1.5 // indirect
-	github.com/mattn/go-colorable v0.1.15 // indirect
+	github.com/mattn/go-colorable v0.1.16 // indirect
 	github.com/mattn/go-isatty v0.0.24 // indirect
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db // indirect
 	github.com/patrickmn/go-cache v2.1.0+incompatible // indirect
@@ -33,6 +33,6 @@ require (
 	github.com/schollz/progressbar/v2 v2.15.0 // indirect
 	github.com/sugarme/regexpset v0.0.0-20200920021344-4d4ec8eaf93c // indirect
 	go.yaml.in/yaml/v3 v3.0.5 // indirect
-	golang.org/x/sys v0.48.0 // indirect
-	golang.org/x/text v0.42.0 // indirect
+	golang.org/x/sys v0.49.0 // indirect
+	golang.org/x/text v0.43.0 // indirect
 )

go.sum

@@ -20,8 +20,8 @@ github.com/jinzhu/now v1.1.5 h1:/o9tlHleP7gOFmsnYNz3RGnqzefHA47wQpKrrdTIwXQ=
 github.com/jinzhu/now v1.1.5/go.mod h1:d3SSVoowX0Lcu0IBviAWJpolVfI5UJVZZ7cO71lE/z8=
 github.com/lukaszraczylo/oss-telemetry v0.2.5 h1:W6Qgwp7IY4yBRO361MmnEAmM59motdQpbAFAx8v6fJM=
 github.com/lukaszraczylo/oss-telemetry v0.2.5/go.mod h1:+Cn78qZo8rc3T9eZt0v3oICYRdd75wORtSidc8lNjDQ=
-github.com/mattn/go-colorable v0.1.15 h1:+u9SLTRGnXv73cEsnsmoZBom+dMU88B2M0aDcWy0/jY=
-github.com/mattn/go-colorable v0.1.15/go.mod h1:6LmQG8QLFO4G5z1gPvYEzlUgJ2wF+stgPZH1UqBm1s8=
+github.com/mattn/go-colorable v0.1.16 h1:+2YjeAe7xP1OQbZW1jERPWWCDLlNqFNCvjiqGiAt84A=
+github.com/mattn/go-colorable v0.1.16/go.mod h1:6LmQG8QLFO4G5z1gPvYEzlUgJ2wF+stgPZH1UqBm1s8=
 github.com/mattn/go-isatty v0.0.24 h1:tGZZoVgT/KiqK1c8ocVLeDS8BSWMRd47J3Lbz7vsReI=
 github.com/mattn/go-isatty v0.0.24/go.mod h1:nMCL3Zebbrt45jsMDgnfIwz6ydEQApk5oEI3HqDio6A=
 github.com/mattn/go-sqlite3 v1.14.52 h1:wVbm2Qnf4OXkqhBTSPuCRZDRnxfbVrrmiCEroVdog8U=
@@ -47,12 +47,12 @@ github.com/yalue/onnxruntime_go v1.36.0 h1:iH1Q++DcsyT9sWtN26KYimESlI5hhXpKaChHD
 github.com/yalue/onnxruntime_go v1.36.0/go.mod h1:b4X26A8pekNb1ACJ58wAXgNKeUCGEAQ9dmACut9Sm/4=
 go.yaml.in/yaml/v3 v3.0.5 h1:N6y/pJk8buWs9NY5ERU2HSMfm+IuD/OtfdAnq6kESPw=
 go.yaml.in/yaml/v3 v3.0.5/go.mod h1:HVTZu1O7/Vkt2N+BFy8Zza+lnLsABggaTM2ZpNIGuKg=
-golang.org/x/sync v0.23.0 h1:KameEIfc1IkluZyXWLn39Wd4tURc6GbCiISGiZm2bQk=
-golang.org/x/sync v0.23.0/go.mod h1:sUUOizhqBxiL6pEWpqNLUiaJn1ShEbZ6BBqskPbjZm0=
-golang.org/x/sys v0.48.0 h1:bbX/i/6MgT9BVLM9RT1thmxL04yeTAhbEz4SyadbXoo=
-golang.org/x/sys v0.48.0/go.mod h1:hNLxWAXmnKAxqDtdwIYC4bM9oQPEecfsnNMuSxOs3og=
-golang.org/x/text v0.42.0 h1:JbOZXgfeCPU9gacVtYliJqOhD+zhrEqK4LfdpmlUZqI=
-golang.org/x/text v0.42.0/go.mod h1:ojzP1Z+2QtioaF8DTtO8K5q7JWVVYwZKenzujK0Zd0E=
+golang.org/x/sync v0.24.0 h1:iqiDrGoDgyuvAKrhLQthUEzU/R378N78gXbBjxed7oA=
+golang.org/x/sync v0.24.0/go.mod h1:sUUOizhqBxiL6pEWpqNLUiaJn1ShEbZ6BBqskPbjZm0=
+golang.org/x/sys v0.49.0 h1:XbzkgYJHdqh/8m2Uu0W/dQv8nktxx4BFHp1M0gROTXA=
+golang.org/x/sys v0.49.0/go.mod h1:hNLxWAXmnKAxqDtdwIYC4bM9oQPEecfsnNMuSxOs3og=
+golang.org/x/text v0.43.0 h1:1QivrlhwAsnMOcqgOdl9my7s9OyZl8O5/UGUTJVXoWc=
+golang.org/x/text v0.43.0/go.mod h1:hbSIYA/amXcRXTFSZqh8tWHEoqRvvbKPJ2uz/KU+a+s=
 gorm.io/driver/sqlite v1.6.0 h1:WHRRrIiulaPiPFmDcod6prc4l2VGVWHz80KspNsxSfQ=
 gorm.io/driver/sqlite v1.6.0/go.mod h1:AO9V1qIQddBESngQUKWL9yoH93HIeA1X6V633rBwyT8=
 gorm.io/gorm v1.31.2 h1:3o8FXNo9v9S858gil+3LlZA1LkCOzgb4g5BL64FgaCo=

internal/db/gorm/observation_store.go

@@ -252,9 +252,6 @@ func (s *ObservationStore) UpdateObservation(ctx context.Context, id int64, upda
 		updates["scope"] = sql.NullString{String: *update.Scope, Valid: true}
 	}
 
-	// Add updated_at timestamp
-	updates["updated_at_epoch"] = sql.NullInt64{Int64: time.Now().Unix(), Valid: true}
-
 	if len(updates) == 0 {
 		// Nothing to update, just return existing observation
 		return toModelObservation(&dbObs), nil

internal/db/gorm/observation_update_test.go

@@ -0,0 +1,96 @@
+//go:build fts5
+
+package gorm
+
+import (
+	"context"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
+)
+
+func storeForUpdate(t *testing.T) (*ObservationStore, int64, func()) {
+	t.Helper()
+	obsStore, store, cleanup := testObservationStore(t)
+	ctx := context.Background()
+	sessionID, err := NewSessionStore(store).CreateSDKSession(ctx, "claude-1", "test-project", "")
+	require.NoError(t, err)
+	id, _, err := obsStore.StoreObservation(ctx, "claude-1", "test-project", &models.ParsedObservation{
+		Type: models.ObsTypeDiscovery, Title: "Original title", Subtitle: "Original subtitle", Narrative: "Original narrative",
+		Facts: []string{"fact one"}, Concepts: []string{"cache"}, FilesRead: []string{"a.go"},
+	}, int(sessionID), 1)
+	require.NoError(t, err)
+	return obsStore, id, cleanup
+}
+
+func ptr[T any](v T) *T { return &v }
+
+func TestUpdateObservation_ChangesOnlyTheGivenFields(t *testing.T) {
+	obsStore, id, cleanup := storeForUpdate(t)
+	defer cleanup()
+	ctx := context.Background()
+
+	got, err := obsStore.UpdateObservation(ctx, id, &ObservationUpdate{Title: ptr("New title"), Narrative: ptr("New narrative")})
+	require.NoError(t, err)
+	assert.Equal(t, "New title", got.Title.String)
+	assert.Equal(t, "New narrative", got.Narrative.String)
+	assert.Equal(t, "Original subtitle", got.Subtitle.String, "a field that was not given stays")
+	assert.Equal(t, []string{"fact one"}, []string(got.Facts))
+
+	stored, err := obsStore.GetObservationByID(ctx, id)
+	require.NoError(t, err)
+	assert.Equal(t, "New title", stored.Title.String, "and it is stored, not only returned")
+}
+
+func TestUpdateObservation_ReplacesListsAndScope(t *testing.T) {
+	obsStore, id, cleanup := storeForUpdate(t)
+	defer cleanup()
+	ctx := context.Background()
+
+	got, err := obsStore.UpdateObservation(ctx, id, &ObservationUpdate{
+		Facts: &[]string{"a", "b"}, Concepts: &[]string{}, FilesRead: &[]string{"x.go"}, FilesModified: &[]string{"y.go"}, Scope: ptr("global"),
+	})
+	require.NoError(t, err)
+	assert.Equal(t, []string{"a", "b"}, []string(got.Facts))
+	assert.Empty(t, got.Concepts, "an empty list clears the field")
+	assert.Equal(t, []string{"x.go"}, []string(got.FilesRead))
+	assert.Equal(t, []string{"y.go"}, []string(got.FilesModified))
+	assert.Equal(t, models.ScopeGlobal, got.Scope)
+}
+
+func TestUpdateObservation_NothingToChangeReturnsTheObservation(t *testing.T) {
+	obsStore, id, cleanup := storeForUpdate(t)
+	defer cleanup()
+
+	got, err := obsStore.UpdateObservation(context.Background(), id, &ObservationUpdate{})
+	require.NoError(t, err)
+	assert.Equal(t, "Original title", got.Title.String)
+}
+
+func TestUpdateObservation_Refusals(t *testing.T) {
+	obsStore, id, cleanup := storeForUpdate(t)
+	defer cleanup()
+	ctx := context.Background()
+
+	_, err := obsStore.UpdateObservation(ctx, id, nil)
+	assert.Error(t, err, "a nil update")
+	_, err = obsStore.UpdateObservation(ctx, 999999, &ObservationUpdate{Title: ptr("x")})
+	require.Error(t, err)
+	assert.Contains(t, err.Error(), "not found")
+}
+
+func TestUpdateObservation_KeepsTheSearchIndexInStep(t *testing.T) {
+	obsStore, id, cleanup := storeForUpdate(t)
+	defer cleanup()
+	ctx := context.Background()
+
+	_, err := obsStore.UpdateObservation(ctx, id, &ObservationUpdate{Title: ptr("Zebrafish enclosure")})
+	require.NoError(t, err)
+	var n int64
+	require.NoError(t, obsStore.db.WithContext(ctx).Raw(
+		`SELECT COUNT(*) FROM observations_fts WHERE observations_fts MATCH 'zebrafish'`).Scan(&n).Error)
+	assert.EqualValues(t, 1, n, "the full-text index sees the new title")
+}

internal/mcp/idle_env_test.go

@@ -0,0 +1,38 @@
+package mcp
+
+import (
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestIdleTimeoutFromEnv(t *testing.T) {
+	// The idle shutdown is off unless asked for; anything that is not a positive duration leaves it off.
+	for value, want := range map[string]time.Duration{
+		"":     0,
+		"0":    0,
+		"abc":  0,
+		"-5m":  0,
+		"45":   0, // a bare number is not a duration
+		"90m":  90 * time.Minute,
+		"2h":   2 * time.Hour,
+		"30s":  30 * time.Second,
+		" 2h ": 0, // not trimmed: the operator wrote it, so it is wrong rather than guessed
+	} {
+		t.Run(value, func(t *testing.T) {
+			t.Setenv(IdleTimeoutEnv, value)
+			assert.Equal(t, want, idleTimeoutFromEnv())
+		})
+	}
+}
+
+func TestNewServer_HasNoIdleTimeoutByDefault(t *testing.T) {
+	t.Setenv(IdleTimeoutEnv, "")
+	assert.Zero(t, NewServer(nil, "http://localhost:1", "p", "v").idleTimeout)
+}
+
+func TestNewServer_TakesTheIdleTimeoutFromTheEnvironment(t *testing.T) {
+	t.Setenv(IdleTimeoutEnv, "3h")
+	assert.Equal(t, 3*time.Hour, NewServer(nil, "http://localhost:1", "p", "v").idleTimeout)
+}

internal/mcp/idle_test.go

@@ -0,0 +1,97 @@
+//go:build unix
+
+package mcp
+
+import (
+	"bytes"
+	"context"
+	"os"
+	"sync"
+	"syscall"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+// blockingPipe returns the two ends of a pipe in blocking mode, the way an inherited stdin is: a Read on it cannot be
+// woken by closing the file (the standard pipe from os.Pipe is pollable and can, which hid this).
+func blockingPipe(t *testing.T) (r, w *os.File) {
+	t.Helper()
+	var fds [2]int
+	require.NoError(t, syscall.Pipe(fds[:]))
+	r = os.NewFile(uintptr(fds[0]), "stdin-like")
+	w = os.NewFile(uintptr(fds[1]), "stdin-writer")
+	t.Cleanup(func() { _ = w.Close(); _ = r.Close() })
+	return r, w
+}
+
+type lockedBuffer struct {
+	buf bytes.Buffer
+	mu  sync.Mutex
+}
+
+func (b *lockedBuffer) Write(p []byte) (int, error) {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+	return b.buf.Write(p)
+}
+
+func (b *lockedBuffer) String() string {
+	b.mu.Lock()
+	defer b.mu.Unlock()
+	return b.buf.String()
+}
+
+// The idle timeout used to close stdin and hope the read loop ended. On a real (blocking) stdin the read stays blocked,
+// so the server logged "shutting down" and then lived on with a closed stdin; the next message from the client woke the
+// read, which failed with "file already closed" and killed the connection mid-call (seen in Claude Desktop after the
+// connector sat unused for more than 30 minutes). An idle timeout that is on must end Run for real.
+func TestRun_IdleTimeoutEndsTheServerCleanly(t *testing.T) {
+	t.Parallel()
+
+	stdin, _ := blockingPipe(t)
+	server := &Server{stdin: stdin, stdout: &lockedBuffer{}, idleTimeout: 50 * time.Millisecond, monitorInterval: 10 * time.Millisecond}
+
+	done := make(chan error, 1)
+	go func() { done <- server.Run(context.Background()) }()
+
+	select {
+	case err := <-done:
+		require.NoError(t, err, "an idle shutdown is a clean exit, not an error")
+	case <-time.After(3 * time.Second):
+		t.Fatal("Run did not return after the idle timeout: stdin was closed but the blocked read never ended")
+	}
+}
+
+// By default there is no idle timeout: a stdio server lives as long as its client, and a client that talks to it after a
+// long pause must get an answer.
+func TestRun_WithoutAnIdleTimeoutTheServerKeepsAnsweringAfterALongPause(t *testing.T) {
+	t.Parallel()
+
+	stdin, stdinWriter := blockingPipe(t)
+	stdout := &lockedBuffer{}
+	server := &Server{stdin: stdin, stdout: stdout, monitorInterval: 5 * time.Millisecond}
+
+	done := make(chan error, 1)
+	go func() { done <- server.Run(context.Background()) }()
+
+	time.Sleep(300 * time.Millisecond) // many monitor ticks with no traffic
+	select {
+	case err := <-done:
+		t.Fatalf("Run ended during a pause with no traffic: %v", err)
+	default:
+	}
+
+	_, err := stdinWriter.WriteString(`{"jsonrpc":"2.0","id":7,"method":"tools/list"}` + "\n")
+	require.NoError(t, err)
+
+	assert.Eventually(t, func() bool { return bytes.Contains([]byte(stdout.String()), []byte(`"id":7`)) }, 3*time.Second, 10*time.Millisecond,
+		"the request after the pause is answered")
+	select {
+	case err := <-done:
+		t.Fatalf("Run ended after answering: %v", err)
+	default:
+	}
+}

internal/mcp/server.go

@@ -30,6 +30,11 @@ type Server struct {
 	version      string
 	writeMu      sync.Mutex
 	lastActivity atomic.Int64
+	// idleTimeout ends the server after this long without a message; 0 (the default) never does. A stdio server lives
+	// as long as its client: ending it while the client is still connected makes the client's next call fail.
+	idleTimeout time.Duration
+	// monitorInterval is how often the parent and idle checks run (30s when 0).
+	monitorInterval time.Duration
 }
 
 // NewServer creates a new MCP server that proxies to the worker HTTP API.
@@ -41,9 +46,24 @@ func NewServer(client *http.Client, workerURL, project, version string) *Server
 		version:   version,
 		stdin:     os.Stdin,
 		stdout:    os.Stdout,
+
+		idleTimeout: idleTimeoutFromEnv(),
 	}
 }
 
+// IdleTimeoutEnv names the environment variable that turns the idle shutdown on, as a Go duration such as "2h".
+// It is off by default.
+const IdleTimeoutEnv = "CLAUDE_MNEMONIC_MCP_IDLE_TIMEOUT"
+
+// idleTimeoutFromEnv reads IdleTimeoutEnv; an unset, invalid or non-positive value means no idle shutdown.
+func idleTimeoutFromEnv() time.Duration {
+	d, err := time.ParseDuration(os.Getenv(IdleTimeoutEnv))
+	if err != nil || d <= 0 {
+		return 0
+	}
+	return d
+}
+
 // Request represents a JSON-RPC request.
 type Request struct {
 	JSONRPC string          `json:"jsonrpc"`
@@ -82,6 +102,13 @@ type Tool struct {
 
 // Run starts the MCP server loop.
 func (s *Server) Run(ctx context.Context) error {
+	// An idle shutdown cancels this context. Closing stdin does not do it: on a real (blocking) stdin the read stays
+	// blocked, the server lived on with a closed stdin, and the client's next message woke the read with "file already
+	// closed", which killed the connection mid-call.
+	ctx, cancel := context.WithCancel(ctx)
+	defer cancel()
+	var idleStopped atomic.Bool
+
 	scanner := bufio.NewScanner(s.stdin)
 	buf := make([]byte, 0, 64*1024)
 	scanner.Buffer(buf, 1024*1024) // 1MB max message size
@@ -100,11 +127,15 @@ func (s *Server) Run(ctx context.Context) error {
 		scanErr <- scanner.Err()
 	}()
 
-	// Monitor parent process liveness and idle timeout.
-	// If the parent dies (ppid changes) or no messages arrive for 30 minutes, shut down.
+	// Monitor parent process liveness and, when one is set, the idle timeout.
+	// If the parent dies (ppid changes) or no messages arrive for idleTimeout, shut down.
 	parentPID := os.Getppid()
 	go func() {
-		ticker := time.NewTicker(30 * time.Second)
+		interval := s.monitorInterval
+		if interval <= 0 {
+			interval = 30 * time.Second
+		}
+		ticker := time.NewTicker(interval)
 		defer ticker.Stop()
 		for {
 			select {
@@ -118,11 +149,10 @@ func (s *Server) Run(ctx context.Context) error {
 					}
 					return
 				}
-				if time.Since(time.Unix(s.lastActivity.Load(), 0)) > 30*time.Minute {
-					log.Info().Msg("MCP server idle timeout (30m), shutting down")
-					if closer, ok := s.stdin.(io.Closer); ok {
-						_ = closer.Close()
-					}
+				if s.idleTimeout > 0 && time.Since(time.Unix(s.lastActivity.Load(), 0)) > s.idleTimeout {
+					log.Info().Dur("idle", s.idleTimeout).Msg("MCP server idle timeout, shutting down")
+					idleStopped.Store(true)
+					cancel()
 					return
 				}
 			}
@@ -140,6 +170,9 @@ func (s *Server) Run(ctx context.Context) error {
 		case <-ctx.Done():
 			// Drain in-flight requests before returning.
 			wg.Wait()
+			if idleStopped.Load() {
+				return nil // an idle shutdown the operator asked for is a clean exit
+			}
 			return ctx.Err()
 		case line, ok := <-lines:
 			if !ok {

internal/vector/sqlitevec/client.go

@@ -5,6 +5,7 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"sort"
 	"strconv"
 	"strings"
 	"sync"
@@ -314,67 +315,13 @@ func (c *Client) Query(ctx context.Context, query string, limit int, where map[s
 	}
 	defer c.readMu.RUnlock()
 
-	// Build query with filters
-	// vec0 supports WHERE clauses on metadata columns
-	args := []any{queryBlob}
-
-	sqlQuery := `
-		SELECT
-			doc_id,
-			distance,
-			sqlite_id,
-			doc_type,
-			field_type,
-			project,
-			scope
-		FROM vectors
-		WHERE embedding MATCH ?
-	`
-
-	// Add filters - these work with vec0 metadata columns
-	if docType, ok := where["doc_type"].(string); ok && docType != "" {
-		sqlQuery += " AND doc_type = ?"
-		args = append(args, docType)
-	}
-	if project, ok := where["project"].(string); ok && project != "" {
-		// Include project-specific OR global scope
-		sqlQuery += " AND (project = ? OR scope = 'global')"
-		args = append(args, project)
-	}
-
-	sqlQuery += " ORDER BY distance LIMIT ?"
-	args = append(args, limit)
-
-	rows, err := c.db.QueryContext(ctx, sqlQuery, args...)
+	// vec0 answers equality filters on metadata columns, but not an OR between them, so a project filter
+	// (the project's own documents, plus global ones) is asked as two searches and merged.
+	docType, _ := where["doc_type"].(string)
+	project, _ := where["project"].(string)
+	results, err := c.nearest(ctx, queryBlob, docType, project, limit)
 	if err != nil {
-		return nil, fmt.Errorf("query vectors: %w", err)
-	}
-	defer rows.Close()
-
-	var results []QueryResult
-	for rows.Next() {
-		var r QueryResult
-		var sqliteID int64
-		var docType, fieldType, project, scope sql.NullString
-
-		if err := rows.Scan(&r.ID, &r.Distance, &sqliteID, &docType, &fieldType, &project, &scope); err != nil {
-			return nil, fmt.Errorf("scan row: %w", err)
-		}
-
-		r.Similarity = DistanceToSimilarity(r.Distance)
-		r.Metadata = map[string]any{
-			"sqlite_id":  float64(sqliteID), // Keep as float64 for compatibility
-			"doc_type":   docType.String,
-			"field_type": fieldType.String,
-			"project":    project.String,
-			"scope":      scope.String,
-		}
-
-		results = append(results, r)
-	}
-
-	if err = rows.Err(); err != nil {
-		return nil, fmt.Errorf("iterate rows: %w", err)
+		return nil, err
 	}
 
 	// Cache the results
@@ -529,60 +476,109 @@ func (c *Client) QueryMultiField(ctx context.Context, query string, limit int, d
 	}
 	defer c.readMu.RUnlock()
 
-	// Query with field type aggregation - get best match per document
-	sqlQuery := `
-		WITH ranked_results AS (
-			SELECT
-				doc_id,
-				distance,
-				sqlite_id,
-				doc_type,
-				field_type,
-				project,
-				scope,
-				ROW_NUMBER() OVER (PARTITION BY sqlite_id ORDER BY distance ASC) as rn
-			FROM vectors
-			WHERE embedding MATCH ?
-				AND doc_type = ?
-				AND (project = ? OR scope = 'global')
-		)
-		SELECT doc_id, distance, sqlite_id, doc_type, field_type, project, scope
-		FROM ranked_results
-		WHERE rn = 1
-		ORDER BY distance
-		LIMIT ?
-	`
+	// Each observation has several vector documents (one per field). Ask for enough of them that `limit`
+	// distinct observations are likely to be among them, then keep the best match per observation.
+	found, err := c.nearest(ctx, queryBlob, docType, project, limit*multiFieldFetchFactor)
+	if err != nil {
+		return nil, err
+	}
+	results := make([]QueryResult, 0, limit)
+	seen := make(map[float64]bool, limit)
+	for _, r := range found { // best first
+		id, _ := r.Metadata["sqlite_id"].(float64)
+		if seen[id] {
+			continue
+		}
+		seen[id] = true
+		results = append(results, r)
+		if len(results) == limit {
+			break
+		}
+	}
+	return results, nil
+}
 
-	rows, err := c.db.QueryContext(ctx, sqlQuery, queryBlob, docType, project, limit)
+// multiFieldFetchFactor is how many vector documents QueryMultiField asks for per wanted observation.
+const multiFieldFetchFactor = 6
+
+// nearest runs the nearest-neighbour search for a document type and, when project is not empty, for that
+// project's documents and the global ones. The caller holds the read lock. Results are best first, at most limit.
+func (c *Client) nearest(ctx context.Context, queryBlob []byte, docType, project string, limit int) ([]QueryResult, error) {
+	base := " WHERE embedding MATCH ?"
+	baseArgs := []any{queryBlob}
+	if docType != "" {
+		base += " AND doc_type = ?"
+		baseArgs = append(baseArgs, docType)
+	}
+	if project == "" {
+		return c.knn(ctx, base, baseArgs, limit)
+	}
+	own, err := c.knn(ctx, base+" AND project = ?", append(append([]any{}, baseArgs...), project), limit)
+	if err != nil {
+		return nil, err
+	}
+	global, err := c.knn(ctx, base+" AND scope = 'global'", baseArgs, limit)
+	if err != nil {
+		return nil, err
+	}
+	return mergeNearest(limit, own, global), nil
+}
+
+// knn runs one vec0 nearest-neighbour query. where holds the MATCH and filters vec0 can answer on their own.
+func (c *Client) knn(ctx context.Context, where string, args []any, limit int) ([]QueryResult, error) {
+	// #nosec G202 -- where is built from constant clauses with "?" placeholders only (see nearest); every value goes via args
+	rows, err := c.db.QueryContext(ctx,
+		"SELECT doc_id, distance, sqlite_id, doc_type, field_type, project, scope FROM vectors"+where+" ORDER BY distance LIMIT ?",
+		append(append([]any{}, args...), limit)...)
 	if err != nil {
 		return nil, fmt.Errorf("query vectors: %w", err)
 	}
 	defer rows.Close()
 
-	// Pre-allocate with limit to avoid repeated slice growth
-	results := make([]QueryResult, 0, limit)
+	var results []QueryResult
 	for rows.Next() {
 		var r QueryResult
 		var sqliteID int64
-		var docTypeVal, fieldType, projectVal, scope sql.NullString
+		var docType, fieldType, project, scope sql.NullString
 
-		if err := rows.Scan(&r.ID, &r.Distance, &sqliteID, &docTypeVal, &fieldType, &projectVal, &scope); err != nil {
+		if err := rows.Scan(&r.ID, &r.Distance, &sqliteID, &docType, &fieldType, &project, &scope); err != nil {
 			return nil, fmt.Errorf("scan row: %w", err)
 		}
 
 		r.Similarity = DistanceToSimilarity(r.Distance)
 		r.Metadata = map[string]any{
-			"sqlite_id":  float64(sqliteID),
-			"doc_type":   docTypeVal.String,
+			"sqlite_id":  float64(sqliteID), // Keep as float64 for compatibility
+			"doc_type":   docType.String,
 			"field_type": fieldType.String,
-			"project":    projectVal.String,
+			"project":    project.String,
 			"scope":      scope.String,
 		}
 
 		results = append(results, r)
 	}
+	if err = rows.Err(); err != nil {
+		return nil, fmt.Errorf("iterate rows: %w", err)
+	}
+	return results, nil
+}
 
-	return results, rows.Err()
+// mergeNearest combines result lists into one, best first, without repeating a document, at most limit long.
+func mergeNearest(limit int, lists ...[]QueryResult) []QueryResult {
+	var all []QueryResult
+	seen := map[string]bool{}
+	for _, list := range lists {
+		for _, r := range list {
+			if !seen[r.ID] {
+				seen[r.ID] = true
+				all = append(all, r)
+			}
+		}
+	}
+	sort.SliceStable(all, func(i, j int) bool { return all[i].Distance < all[j].Distance })
+	if len(all) > limit {
+		all = all[:limit]
+	}
+	return all
 }
 
 // acquireRLockWithContext acquires a read lock on mu, respecting ctx cancellation.

internal/vector/sqlitevec/client_test.go

@@ -405,6 +405,50 @@ func TestClient_Query_WithProjectFilter(t *testing.T) {
 	results, err := client.Query(context.Background(), "authentication security", 10, nil)
 	require.NoError(t, err)
 	assert.NotEmpty(t, results, "Should find some results")
+	assert.Len(t, results, 3)
+
+	ids := func(rs []QueryResult) []string {
+		var out []string
+		for _, r := range rs {
+			out = append(out, r.ID)
+		}
+		return out
+	}
+
+	// With a project filter: the project's own documents and the global ones, not another project's.
+	results, err = client.Query(context.Background(), "authentication security", 10, BuildWhereFilter(DocTypeObservation, "project-a"))
+	require.NoError(t, err, "a project filter must be answerable (vec0 rejects an OR between metadata filters)")
+	assert.ElementsMatch(t, []string{"obs-1", "obs-3"}, ids(results), "project-a's note and the global one, not project-b's own")
+
+	results, err = client.Query(context.Background(), "authentication security", 10, BuildWhereFilter(DocTypeObservation, "project-b"))
+	require.NoError(t, err)
+	assert.ElementsMatch(t, []string{"obs-2", "obs-3"}, ids(results))
+
+	// Best first, and the limit applies to the merged list.
+	results, err = client.Query(context.Background(), "authentication security", 1, BuildWhereFilter(DocTypeObservation, "project-a"))
+	require.NoError(t, err)
+	require.Len(t, results, 1)
+	all, err := client.Query(context.Background(), "authentication security", 10, BuildWhereFilter(DocTypeObservation, "project-a"))
+	require.NoError(t, err)
+	assert.Equal(t, all[0].ID, results[0].ID, "the one result is the best of the merged list")
+	assert.LessOrEqual(t, all[0].Distance, all[1].Distance)
+
+	// A project nobody wrote to still sees the global documents.
+	results, err = client.Query(context.Background(), "authentication security", 10, BuildWhereFilter(DocTypeObservation, "project-z"))
+	require.NoError(t, err)
+	assert.Equal(t, []string{"obs-3"}, ids(results))
+}
+
+func TestMergeNearest(t *testing.T) {
+	r := func(id string, d float64) QueryResult { return QueryResult{ID: id, Distance: d} }
+	got := mergeNearest(3, []QueryResult{r("a", 0.5), r("b", 0.9)}, []QueryResult{r("b", 0.9), r("c", 0.1), r("d", 0.7)})
+	var ids []string
+	for _, x := range got {
+		ids = append(ids, x.ID)
+	}
+	assert.Equal(t, []string{"c", "a", "d"}, ids, "best first, a document found twice counts once, cut to the limit")
+	assert.Empty(t, mergeNearest(5))
+	assert.Len(t, mergeNearest(5, []QueryResult{r("a", 1)}, nil), 1)
 }
 
 func TestClient_IsConnected(t *testing.T) {
@@ -1105,8 +1149,6 @@ func TestClient_QueryBatch_WithContextCancellation(t *testing.T) {
 // =============================================================================
 
 func TestClient_QueryMultiField_Basic(t *testing.T) {
-	t.Skip("QueryMultiField SQL query needs 'k' parameter fix for sqlite-vec")
-
 	db, dbCleanup := testDB(t)
 	defer dbCleanup()
 
@@ -1173,8 +1215,6 @@ func TestClient_QueryMultiField_Basic(t *testing.T) {
 }
 
 func TestClient_QueryMultiField_WithGlobalScope(t *testing.T) {
-	t.Skip("QueryMultiField SQL query needs 'k' parameter fix for sqlite-vec")
-
 	db, dbCleanup := testDB(t)
 	defer dbCleanup()
 
@@ -1217,7 +1257,37 @@ func TestClient_QueryMultiField_WithGlobalScope(t *testing.T) {
 	require.NoError(t, err)
 
 	// Should include both project-scoped (matching project) and global
-	assert.NotEmpty(t, results)
+	require.Len(t, results, 2)
+	assert.ElementsMatch(t, []float64{1, 2}, []float64{
+		results[0].Metadata["sqlite_id"].(float64), results[1].Metadata["sqlite_id"].(float64),
+	})
+}
+
+// The query the de-duplication of new observations makes: the same project, a few results, and a note that
+// says nearly the same thing must come back with a high similarity.
+func TestClient_Query_ProjectFilterFindsANearDuplicate(t *testing.T) {
+	db, dbCleanup := testDB(t)
+	defer dbCleanup()
+	embedSvc, embedCleanup := testEmbeddingService(t)
+	defer embedCleanup()
+	client, err := NewClient(Config{DB: db}, embedSvc)
+	require.NoError(t, err)
+
+	text := "The shipping rate cache lives for sixty minutes and is stored in Redis."
+	require.NoError(t, client.AddDocuments(context.Background(), []Document{
+		{ID: "obs-1", Content: text, Metadata: map[string]any{"sqlite_id": int64(1), "doc_type": "observation", "project": "shop", "scope": "project"}},
+		{ID: "obs-2", Content: text, Metadata: map[string]any{"sqlite_id": int64(2), "doc_type": "observation", "project": "elsewhere", "scope": "project"}},
+		{ID: "obs-3", Content: "Parcel labels are printed as PDF.", Metadata: map[string]any{"sqlite_id": int64(3), "doc_type": "observation", "project": "shop", "scope": "project"}},
+	}))
+
+	results, err := client.Query(context.Background(), text, 3, BuildWhereFilter(DocTypeObservation, "shop"))
+	require.NoError(t, err)
+	require.NotEmpty(t, results)
+	assert.Equal(t, "obs-1", results[0].ID, "the same text in the same project is the best match")
+	assert.GreaterOrEqual(t, results[0].Similarity, 0.99)
+	for _, r := range results {
+		assert.NotEqual(t, "obs-2", r.ID, "another project's note is not a duplicate")
+	}
 }
 
 // =============================================================================

internal/worker/handlers_update_test.go

@@ -0,0 +1,59 @@
+package worker
+
+import (
+	"bytes"
+	"encoding/json"
+	"fmt"
+	"net/http"
+	"net/http/httptest"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func doUpdateRequest(t *testing.T, svc *Service, method, target string, body any) *httptest.ResponseRecorder {
+	t.Helper()
+	var buf bytes.Buffer
+	if body != nil {
+		require.NoError(t, json.NewEncoder(&buf).Encode(body))
+	}
+	rec := httptest.NewRecorder()
+	svc.router.ServeHTTP(rec, httptest.NewRequest(method, target, &buf))
+	return rec
+}
+
+func TestHandleUpdateObservation_EditsAndReturnsTheObservation(t *testing.T) {
+	svc, cleanup := testService(t)
+	defer cleanup()
+	id := createTestObservation(t, svc.observationStore, "proj_aaaaaa", "Old title", "Old narrative", []string{"cache"})
+
+	rec := doUpdateRequest(t, svc, http.MethodPut, fmt.Sprintf("/api/observations/%d", id),
+		map[string]any{"title": "New title", "facts": []string{"one", "two"}})
+	require.Equal(t, http.StatusOK, rec.Code, rec.Body.String())
+	var resp struct {
+		Observation struct {
+			Title     string   `json:"title"`
+			Narrative string   `json:"narrative"`
+			Facts     []string `json:"facts"`
+		} `json:"observation"`
+	}
+	require.NoError(t, json.Unmarshal(rec.Body.Bytes(), &resp))
+	assert.Equal(t, "New title", resp.Observation.Title)
+	assert.Equal(t, "Old narrative", resp.Observation.Narrative)
+	assert.Equal(t, []string{"one", "two"}, resp.Observation.Facts)
+
+	rec = doUpdateRequest(t, svc, http.MethodGet, fmt.Sprintf("/api/observations/%d", id), nil)
+	require.Equal(t, http.StatusOK, rec.Code)
+	assert.Contains(t, rec.Body.String(), "New title", "the edit is stored")
+}
+
+func TestHandleUpdateObservation_Refusals(t *testing.T) {
+	svc, cleanup := testService(t)
+	defer cleanup()
+	id := createTestObservation(t, svc.observationStore, "proj_aaaaaa", "A title", "A narrative", nil)
+
+	assert.Equal(t, http.StatusNotFound, doUpdateRequest(t, svc, http.MethodPut, "/api/observations/999999", map[string]any{"title": "x"}).Code)
+	assert.Equal(t, http.StatusBadRequest, doUpdateRequest(t, svc, http.MethodPut, fmt.Sprintf("/api/observations/%d", id), map[string]any{"scope": "galaxy"}).Code)
+	assert.Equal(t, http.StatusBadRequest, doUpdateRequest(t, svc, http.MethodPut, "/api/observations/abc", map[string]any{"title": "x"}).Code)
+}

internal/worker/sdk/dedup.go

@@ -51,7 +51,7 @@ func (p *Processor) checkVectorDeduplication(ctx context.Context, obs *models.Pa
 	for _, r := range results {
 		if r.Similarity >= cfg.DeduplicationThreshold {
 			obsID := extractObservationIDFromVectorDoc(r)
-			if obsID > 0 {
+			if obsID > 0 && p.canMergeInto(ctx, obsID) {
 				return &DeduplicationResult{
 					ExistingID: obsID,
 					Similarity: r.Similarity,
@@ -64,6 +64,20 @@ func (p *Processor) checkVectorDeduplication(ctx context.Context, obs *models.Pa
 	return &DeduplicationResult{Action: "insert"}
 }
 
+// canMergeInto says whether a new observation may be merged into the existing one. A note a person superseded
+// is hidden from sessions, so what was merged into it would be hidden as well: such a note is not a target,
+// and neither is one that is gone.
+func (p *Processor) canMergeInto(ctx context.Context, id int64) bool {
+	if p.observationStore == nil {
+		return true
+	}
+	existing, err := p.observationStore.GetObservationByID(ctx, id)
+	if err != nil {
+		return false
+	}
+	return existing != nil && !existing.IsSuperseded
+}
+
 // buildObservationSearchText creates searchable text from a parsed observation.
 func buildObservationSearchText(obs *models.ParsedObservation) string {
 	var parts []string

internal/worker/sdk/dedup_test.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"testing"
 
+	"github.com/lukaszraczylo/claude-mnemonic/internal/db/gorm"
 	"github.com/lukaszraczylo/claude-mnemonic/internal/vector/sqlitevec"
 	"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
 )
@@ -142,3 +143,35 @@ func TestCheckVectorDeduplication_EmptySearchText(t *testing.T) {
 		t.Errorf("expected Action='insert' for empty observation, got %q", result.Action)
 	}
 }
+
+func TestCanMergeInto(t *testing.T) {
+	ctx := context.Background()
+	dir := t.TempDir()
+	store, err := gorm.NewStore(gorm.Config{Path: dir + "/test.db", MaxConns: 1})
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer store.Close()
+	obsStore := gorm.NewObservationStore(store, nil, nil, nil)
+	id, _, err := obsStore.StoreObservation(ctx, "s1", "proj", &models.ParsedObservation{Type: models.ObsTypeDiscovery, Title: "A note"}, 1, 1)
+	if err != nil {
+		t.Fatal(err)
+	}
+	p := &Processor{observationStore: obsStore}
+
+	if !p.canMergeInto(ctx, id) {
+		t.Error("a live observation is a merge target")
+	}
+	if p.canMergeInto(ctx, id+1000) {
+		t.Error("an observation that does not exist is not")
+	}
+	if err := store.DB.Exec(`UPDATE observations SET is_superseded = 1 WHERE id = ?`, id).Error; err != nil {
+		t.Fatal(err)
+	}
+	if p.canMergeInto(ctx, id) {
+		t.Error("a superseded observation is hidden from sessions, so nothing is merged into it")
+	}
+	if !(&Processor{}).canMergeInto(ctx, id) {
+		t.Error("without an observation store there is nothing to check against")
+	}
+}

marketplace.json

@@ -13,7 +13,7 @@
     {
       "name": "claude-mnemonic",
       "description": "Persistent memory system for Claude Code - Go implementation with SQLite and ChromaDB vector search",
-      "version": "0.21.95",
+      "version": "0.21.127",
       "author": {
         "name": "lukaszraczylo",
         "url": "https://github.com/lukaszraczylo"
@@ -23,25 +23,25 @@
       "license": "MIT",
       "homepage": "https://github.com/lukaszraczylo/claude-mnemonic",
       "releases": {
-        "latest": "0.21.95",
+        "latest": "0.21.127",
         "versions": {
-          "0.21.95": {
-            "releaseDate": "2026-10-04",
+          "0.21.127": {
+            "releaseDate": "2026-10-12",
             "downloads": {
               "darwin-arm64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.95/claude-mnemonic_0.21.95_darwin_arm64.tar.gz",
+                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.127/claude-mnemonic_0.21.127_darwin_arm64.tar.gz",
                 "format": "tar.gz",
-                "sha256": "3224be650ead03a23078f7033909ecaedf89c88d665b3aa83c70b2eb952722b9"
+                "sha256": "4191ab626fb31a046f6eaeb0f3e5febdbb50285bd0d6d4e21a69e626fe5bbda0"
               },
               "linux-amd64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.95/claude-mnemonic_0.21.95_linux_amd64.tar.gz",
+                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.127/claude-mnemonic_0.21.127_linux_amd64.tar.gz",
                 "format": "tar.gz",
-                "sha256": "4af6927b7857b03143e6eb817da7f44c39dd2b5674a7d1b7f505db7c3dd25b2f"
+                "sha256": "9245e63dc10ee88bae33d1519d8c31951ab0abeef045cfd940903bfcf5db3272"
               },
               "windows-amd64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.95/claude-mnemonic_0.21.95_windows_amd64.zip",
+                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.127/claude-mnemonic_0.21.127_windows_amd64.zip",
                 "format": "zip",
-                "sha256": "d779920957eea6b21a344556b5a36ec2a1a6c596e095575e73110c5cb997fc1a"
+                "sha256": "ced294d3791c4ebd0bfe37375589d1eff091a75f488eadf0b3b019bc87e3ea1d"
               }
             }
           }

ui/package-lock.json

@@ -802,9 +802,9 @@
       "peer": true
     },
     "node_modules/@types/node": {
-      "version": "26.6.4",
-      "resolved": "https://registry.npmjs.org/@types/node/-/node-26.6.4.tgz",
-      "integrity": "sha512-ldVPDCzj7fsaGZrLB0NuHuTvJcsNasysBAqMolr/cgxrLd1xbqxIr3XJiPnHHJUCxj5sNF1vnRj9aWnrVh5Jcg==",
+      "version": "26.6.5",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-26.6.5.tgz",
+      "integrity": "sha512-uMzsv9stDdofIZBx4UGh4Z9ZgXnGC9seRDscilBcTHAeOFk67MZg/k9bWVfO+bk4qZmG+l52hRnLwUiH2LnJTg==",
       "dev": true,
       "license": "MIT",
       "dependencies": {
@@ -1430,9 +1430,9 @@
       }
     },
     "node_modules/postcss": {
-      "version": "8.5.28",
-      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.5.28.tgz",
-      "integrity": "sha512-RRuzqDtt5Y9h3quz5hWhK+TPnsmVs6WwSU6LkJMeY4HstUEDuYTG8UJSdawMRzmzAtV+KEoG8N3Qg2qLy5vM/A==",
+      "version": "8.5.29",
+      "resolved": "https://registry.npmjs.org/postcss/-/postcss-8.5.29.tgz",
+      "integrity": "sha512-49cGhUbXj8Qenv0iTMxA1cFBzxXoctpC9Ujd77t1WcbJIr6nF/eI7g/8MgxrYldFRuAXvja7xQRwavoW7kgrxQ==",
       "funding": [
         {
           "type": "opencollective",
@@ -1449,9 +1449,9 @@
       ],
       "license": "MIT",
       "dependencies": {
-        "nanoid": "^3.3.18",
+        "nanoid": "^3.3.19",
         "picocolors": "^1.1.1",
-        "source-map-js": "^1.2.1"
+        "source-map-js": "^1.2.2"
       },
       "engines": {
         "node": "^10 || ^12 || >=14"
@@ -1492,9 +1492,9 @@
       }
     },
     "node_modules/source-map-js": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.1.tgz",
-      "integrity": "sha512-UXWMKhLOwVKb728IUtQPXxfYU+usdybtUrK/8uGE8CQMvrhOpwvzDBwj0QhSL7MQc7vIsISBG8VQ8+IDQxpfQA==",
+      "version": "1.2.2",
+      "resolved": "https://registry.npmjs.org/source-map-js/-/source-map-js-1.2.2.tgz",
+      "integrity": "sha512-KGj/8Y43x35aZVDtt+J4mK1hoLGHULMYfSkODJNQjNDC3oW1PqPoxMwo0pLUsWM/UEGzON/NxeHywEfNXNP3Vw==",
       "license": "BSD-3-Clause",
       "engines": {
         "node": ">=0.10.0"
@@ -1624,16 +1624,16 @@
       }
     },
     "node_modules/vite": {
-      "version": "8.3.2",
-      "resolved": "https://registry.npmjs.org/vite/-/vite-8.3.2.tgz",
-      "integrity": "sha512-SQr1x6W5vVSbROg7vsyXIaxK9b0G7zsT68acdWWRmnBUsgDieLCRG+Rep9WdZgcposvv/GSnr4GUUBqB3vXq6w==",
+      "version": "8.3.4",
+      "resolved": "https://registry.npmjs.org/vite/-/vite-8.3.4.tgz",
+      "integrity": "sha512-IftLE8phJhdNRIGNEV4JCCvfNScoZQVfcXaN8TQropWGJtOHcu+iAB9pHcuGvmEb/kddw0LBe/jS8ztdC6xdiQ==",
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