chore: update marketplace for v0.21.127

Automated dependency update. All tests passed.

.claude-plugin/plugin.json

@@ -14,7 +14,6 @@
   "mcpServers": {
     "claude-mnemonic": {
       "command": "${CLAUDE_PLUGIN_ROOT}/mcp-server",
-      "args": ["--project", "${CLAUDE_PROJECT}"],
       "env": {}
     }
   },

.github/workflows/autoupdate.yaml

@@ -1,4 +1,4 @@
-name: Autoupdate go.mod and go.sum
+name: Update dependencies
 
 on:
   workflow_dispatch:
@@ -6,16 +6,17 @@ on:
     - cron: "0 3 * * *"
 
 permissions:
-  contents: write
   actions: write
+  contents: write
+  issues: write
   pull-requests: write
-  security-events: write
 
 jobs:
-  autoupdate:
-    uses: lukaszraczylo/shared-actions/.github/workflows/go-autoupdate.yaml@main
+  update:
+    uses: lukaszraczylo/shared-actions/.github/workflows/renovate-autoupdate.yaml@main
     with:
       go-version: ">=1.24"
-      release-workflow: "release.yaml"
-      lfs: false
-    secrets: inherit
+      build-tags: "fts5"
+      node-working-directory: ui
+      require-node-tests: false
+      release-workflow: release.yaml

.gitignore

@@ -95,3 +95,6 @@ docs/dist
 plugin/.claude-plugin/plugin.json
 plugin/.claude-plugin/marketplace.json
 user-prompt
+
+# Compressed ONNX runtime libs are produced by scripts/download-onnx-libs.sh
+internal/embedding/assets/lib/**/*.gz

cmd/hooks/statusline/main.go

@@ -3,9 +3,9 @@
 package main
 
 import (
+	"context"
 	"encoding/json"
 	"fmt"
-	"net/http"
 	"net/url"
 	"os"
 	"time"
@@ -13,6 +13,9 @@ import (
 	"github.com/lukaszraczylo/claude-mnemonic/pkg/hooks"
 )
 
+// statsTimeout bounds the worker stats request.
+const statsTimeout = 100 * time.Millisecond
+
 // StatusInput is the JSON input from Claude Code's statusline feature.
 type StatusInput struct {
 	HookEventName string `json:"hook_event_name"`
@@ -105,26 +108,19 @@ func handleStatusline(input *StatusInput, port int) string {
 // getWorkerStats fetches stats from the worker service.
 func getWorkerStats(port int, project string) *WorkerStats {
 	// Build URL with optional project parameter
-	endpoint := fmt.Sprintf("http://127.0.0.1:%d/api/stats", port)
+	endpoint := "/api/stats"
 	if project != "" {
 		endpoint += "?project=" + url.QueryEscape(project)
 	}
 
-	// Create HTTP client with short timeout (statusline must be fast)
-	client := &http.Client{Timeout: 100 * time.Millisecond}
-
-	resp, err := client.Get(endpoint)
+	// Short timeout: statusline must be fast
+	body, err := hooks.GETBody(context.Background(), statsTimeout, port, endpoint)
 	if err != nil {
 		return nil
 	}
-	defer func() { _ = resp.Body.Close() }()
-
-	if resp.StatusCode != http.StatusOK {
-		return nil
-	}
 
 	var stats WorkerStats
-	if err := json.NewDecoder(resp.Body).Decode(&stats); err != nil {
+	if err := json.Unmarshal(body, &stats); err != nil {
 		return nil
 	}
 

cmd/mcp/main.go

@@ -8,12 +8,14 @@ import (
 	"net/http"
 	"os"
 	"os/signal"
+	"strings"
 	"syscall"
 	"time"
 
 	"github.com/lukaszraczylo/claude-mnemonic/internal/config"
 	"github.com/lukaszraczylo/claude-mnemonic/internal/mcp"
 	"github.com/lukaszraczylo/claude-mnemonic/internal/watcher"
+	"github.com/lukaszraczylo/claude-mnemonic/pkg/hooks"
 	"github.com/lukaszraczylo/oss-telemetry"
 	"github.com/rs/zerolog"
 	"github.com/rs/zerolog/log"
@@ -22,9 +24,18 @@ import (
 // Version is set at build time via ldflags.
 var Version = "dev"
 
+// defaultProject derives the project ID the same way the hooks do.
+func defaultProject() string {
+	dir := os.Getenv("CLAUDE_PROJECT_DIR")
+	if dir == "" {
+		dir, _ = os.Getwd()
+	}
+	return hooks.ProjectIDWithName(dir)
+}
+
 func main() {
 	// Parse flags
-	project := flag.String("project", "", "Project name (required)")
+	project := flag.String("project", "", "Project ID (default: derived from CLAUDE_PROJECT_DIR or cwd)")
 	debug := flag.Bool("debug", false, "Enable debug logging")
 	flag.Parse()
 
@@ -35,8 +46,8 @@ func main() {
 	}
 	log.Logger = log.Output(zerolog.ConsoleWriter{Out: os.Stderr, NoColor: true})
 
-	if *project == "" {
-		log.Fatal().Msg("--project is required")
+	if *project == "" || strings.Contains(*project, "${") {
+		*project = defaultProject()
 	}
 
 	// Get worker port from config

commands/restart.md

@@ -1,3 +1,8 @@
+---
+description: Restart the Claude Mnemonic worker process
+allowed-tools: Bash(curl:*)
+---
+
 # Restart Claude Mnemonic Worker
 
 Restart the claude-mnemonic worker process. Use this command when experiencing issues with the memory system.

experiments.md

@@ -0,0 +1,60 @@
+# Experiment journal
+
+## Campaign B: binary size
+
+Metric: sum of bytes of worker, mcp and 6 hook binaries (release flags, `-s -w -trimpath`, `-tags fts5`). Lower is better.
+Threshold: at least 3% drop, tests green. Stop: 5 consecutive no-improve trials or 15 trials.
+Mutate: Go code and build flags. Frozen: public API, DB schema, plugin manifest.
+
+| id | mutation | total bytes | delta vs base | kept? |
+|----|----------|-------------|---------------|-------|
+| 01 | baseline | 102698416 | - | base |
+| 02 | pkg/hooks: raw HTTP/1.0 client replaces net/http | 87603952 | -14.7% | KEEP |
+| 03 | statusline: shared client, drop net/http | 84531056 | -3.5% vs 02 | KEEP |
+| 04 | embed gzipped ONNX runtime libs, gunzip at first use | 57216880 | -32.3% vs 03 | KEEP |
+| 05 | hooks built with CGO_ENABLED=0 | 57216880 | 0% | revert (not applied) |
+| - | statically dedupe or compress tokenizer.json | - | projected ~1.2-1.6% | not run, under 3% threshold |
+| - | drop net/http from mcp | - | none possible | not run, oss-telemetry links net/http |
+
+Campaign B stopped on diminishing returns: 102698416 -> 57216880 bytes (-44.3%).
+
+## Campaign A: hook latency (stub worker, 200 runs, p50)
+
+Harness: hook binary against a local stub worker (100-observation context), same machine, alternating runs. Lower is better.
+
+| hook | before (ee28544) | after trial 02 | delta |
+|------|------------------|----------------|-------|
+| session-start | 4.6-5.6 ms | 3.3 ms | -30% or better |
+| user-prompt | 4.3-4.7 ms | 3.5-3.7 ms | -15% to -22% |
+
+Hooks now sit near the process-start floor. No further trials run.
+
+## Campaign D: reliability
+
+Metric: failing cases in the extraction fault test (`TestWriteGunzipped`). Lower is better.
+
+| id | mutation | failing cases | kept? |
+|----|----------|---------------|-------|
+| 01 | baseline (truncated archive leaves partial lib.so) | 1 | base |
+| 02 | extract via temp file and rename | 0 | KEEP |
+
+## Campaign C: search accuracy
+
+Harness: `scripts/eval-search` seeds 30 labelled observations, starts a real worker (fresh HOME, model cache copied), waits for the vector rebuild, then runs 30 paraphrased queries against `/api/context/search`. Metric: MRR@10 (higher is better). Threshold: at least +0.02. Runs are deterministic (repeat runs identical).
+
+| id | mutation | MRR@10 | recall@5 | kept? |
+|----|----------|--------|----------|-------|
+| 01 | baseline | 0.7944 | 0.8667 | base |
+| 02 | L2-normalise embeddings (similarity was negative for every vector hit, so search fell back to FTS) | 0.8944 | 0.9667 | KEEP |
+| 03 | reranking alpha 0.7 -> 0.5 | 0.9111 | 0.9667 | revert (+0.017 < 0.02) |
+| 04 | reranking alpha 0.7 -> 0.9 | 0.9111 | 0.9667 | revert (+0.017 < 0.02) |
+| 05 | reranker off | 0.8889 | 0.9667 | revert |
+| 06 | reranker pure mode | 0.8714 | 0.9667 | revert |
+| 07 | CLS pooling instead of mean | 0.8944 | 0.9667 | revert |
+
+Trial 02 changes stored vectors. `BGEStorageVersion` is bumped to `bge-v1.5-l2`, so existing installs rebuild vectors on next start.
+Caveat: 30 queries is a small set, so borderline gains such as alpha 0.5 are not distinguishable from noise.
+
+Notes:
+- Trial 04 needs `scripts/download-onnx-libs.sh` to produce `.gz` files; existing raw libs trigger a re-download.
+- Extracted library verified byte-identical to the raw dylib (`cmp`).

go.mod

@@ -1,40 +1,38 @@
 module github.com/lukaszraczylo/claude-mnemonic
 
-go 1.25.1
+go 1.26.0
 
 replace github.com/sugarme/tokenizer => github.com/clems4ever/tokenizer v0.0.0-20250926133620-9ddc80533c43
 
 require (
 	github.com/asg017/sqlite-vec-go-bindings v0.1.6
 	github.com/fsnotify/fsnotify v1.10.1
-	github.com/go-chi/chi/v5 v5.3.0
-	github.com/go-gormigrate/gormigrate/v2 v2.1.6
-	github.com/goccy/go-json v0.10.6
-	github.com/lukaszraczylo/oss-telemetry v0.2.3
-	github.com/mattn/go-sqlite3 v1.14.46
+	github.com/go-chi/chi/v5 v5.3.2
+	github.com/go-gormigrate/gormigrate/v2 v2.1.7
+	github.com/goccy/go-json v0.11.2
+	github.com/lukaszraczylo/oss-telemetry v0.2.5
+	github.com/mattn/go-sqlite3 v1.14.52
 	github.com/rs/zerolog v1.35.1
-	github.com/stretchr/testify v1.11.1
+	github.com/stretchr/testify v1.12.1
 	github.com/sugarme/tokenizer v0.3.0
-	github.com/yalue/onnxruntime_go v1.31.0
-	golang.org/x/sync v0.21.0
+	github.com/yalue/onnxruntime_go v1.36.0
+	golang.org/x/sync v0.24.0
 	gorm.io/driver/sqlite v1.6.0
-	gorm.io/gorm v1.31.1
+	gorm.io/gorm v1.31.2
 )
 
 require (
-	github.com/davecgh/go-spew v1.1.1 // indirect
 	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-isatty v0.0.22 // 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
-	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/rivo/uniseg v0.4.7 // indirect
 	github.com/schollz/progressbar/v2 v2.15.0 // indirect
 	github.com/sugarme/regexpset v0.0.0-20200920021344-4d4ec8eaf93c // indirect
-	golang.org/x/sys v0.46.0 // indirect
-	golang.org/x/text v0.38.0 // indirect
-	gopkg.in/yaml.v3 v3.0.1 // indirect
+	go.yaml.in/yaml/v3 v3.0.5 // indirect
+	golang.org/x/sys v0.49.0 // indirect
+	golang.org/x/text v0.43.0 // indirect
 )

go.sum

@@ -3,35 +3,33 @@ github.com/asg017/sqlite-vec-go-bindings v0.1.6/go.mod h1:A8+cTt/nKFsYCQF6OgzSNp
 github.com/clems4ever/tokenizer v0.0.0-20250926133620-9ddc80533c43 h1:j8YQypEqa5OjqbGciCNb9hOcYbo1oTVuEjd/iu9U2SY=
 github.com/clems4ever/tokenizer v0.0.0-20250926133620-9ddc80533c43/go.mod h1:VJ+DLK5ZEZwzvODOWwY0cw+B1dabTd3nCB5HuFCItCc=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/emirpasic/gods v1.18.1 h1:FXtiHYKDGKCW2KzwZKx0iC0PQmdlorYgdFG9jPXJ1Bc=
 github.com/emirpasic/gods v1.18.1/go.mod h1:8tpGGwCnJ5H4r6BWwaV6OrWmMoPhUl5jm/FMNAnJvWQ=
 github.com/fsnotify/fsnotify v1.10.1 h1:b0/UzAf9yR5rhf3RPm9gf3ehBPpf0oZKIjtpKrx59Ho=
 github.com/fsnotify/fsnotify v1.10.1/go.mod h1:TLheqan6HD6GBK6PrDWyDPBaEV8LspOxvPSjC+bVfgo=
-github.com/go-chi/chi/v5 v5.3.0 h1:halUjDxhshgXHMrao5bB8eNBXo/rnzwr8m5m36glehM=
-github.com/go-chi/chi/v5 v5.3.0/go.mod h1:R+tYY2hNuVUUjxoPtqUdgBqevM9s9njzkTLutVsOCto=
-github.com/go-gormigrate/gormigrate/v2 v2.1.6 h1:VtX+l1Stj2v5RGubVQk0LS/8EPGXR+ldcOyCmlmKoyg=
-github.com/go-gormigrate/gormigrate/v2 v2.1.6/go.mod h1:PZpedQc4tWaxn6kvXicwhinh3L0seLpMc5ReKRX5id4=
-github.com/goccy/go-json v0.10.6 h1:p8HrPJzOakx/mn/bQtjgNjdTcN+/S6FcG2CTtQOrHVU=
-github.com/goccy/go-json v0.10.6/go.mod h1:oq7eo15ShAhp70Anwd5lgX2pLfOS3QCiwU/PULtXL6M=
+github.com/go-chi/chi/v5 v5.3.2 h1:5YQkICvTCSZ25hoRsyJazN0scjzKGiu4VAUc7H1o1nY=
+github.com/go-chi/chi/v5 v5.3.2/go.mod h1:R+tYY2hNuVUUjxoPtqUdgBqevM9s9njzkTLutVsOCto=
+github.com/go-gormigrate/gormigrate/v2 v2.1.7 h1:PdT4jVPbRb4R+0Ey2R0yJOdctVf4Whiq1Qi4necaZdg=
+github.com/go-gormigrate/gormigrate/v2 v2.1.7/go.mod h1:3ouXglTuPrKF5+7cQyVGfvAXTU4vLMaYh9+EPl03uog=
+github.com/goccy/go-json v0.11.2 h1:jdZv93Tt4ioR8yW1CoNsvSxrcZlCXAUU1aZXN7gpXUA=
+github.com/goccy/go-json v0.11.2/go.mod h1:3NdmfEkZlB7YI5UFw/qdFKq8XN1aiWR0YyRPWZNQltY=
 github.com/jinzhu/inflection v1.0.0 h1:K317FqzuhWc8YvSVlFMCCUb36O/S9MCKRDI7QkRKD/E=
 github.com/jinzhu/inflection v1.0.0/go.mod h1:h+uFLlag+Qp1Va5pdKtLDYj+kHp5pxUVkryuEj+Srlc=
 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 v0.2.3 h1:xoDtBqeZGmXj7IteiE1M5WMuzeoqag58qEleI0Cf2Ms=
-github.com/lukaszraczylo/oss-telemetry v0.2.3/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-isatty v0.0.22 h1:j8l17JJ9i6VGPUFUYoTUKPSgKe/83EYU2zBC7YNKMw4=
-github.com/mattn/go-isatty v0.0.22/go.mod h1:ZXfXG4SQHsB/w3ZeOYbR0PrPwLy+n6xiMrJlRFqopa4=
-github.com/mattn/go-sqlite3 v1.14.46 h1:ZfaNcYO/CGNMRxkN1vvG9qf+Y+uvXfgT9a6MlEw+HmU=
-github.com/mattn/go-sqlite3 v1.14.46/go.mod h1:6JTjA44L93a0QCyJef5YvlPoKXntQPjzWv5gtm9sB6w=
+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 v0.1.16 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=
+github.com/mattn/go-sqlite3 v1.14.52/go.mod h1:6JTjA44L93a0QCyJef5YvlPoKXntQPjzWv5gtm9sB6w=
 github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
 github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
 github.com/patrickmn/go-cache v2.1.0+incompatible h1:HRMgzkcYKYpi3C8ajMPV8OFXaaRUnok+kx1WdO15EQc=
 github.com/patrickmn/go-cache v2.1.0+incompatible/go.mod h1:3Qf8kWWT7OJRJbdiICTKqZju1ZixQ/KpMGzzAfe6+WQ=
-github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/rivo/uniseg v0.4.7 h1:WUdvkW8uEhrYfLC4ZzdpI2ztxP1I582+49Oc5Mq64VQ=
 github.com/rivo/uniseg v0.4.7/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
@@ -41,23 +39,21 @@ github.com/schollz/progressbar/v2 v2.15.0 h1:dVzHQ8fHRmtPjD3K10jT3Qgn/+H+92jhPrh
 github.com/schollz/progressbar/v2 v2.15.0/go.mod h1:UdPq3prGkfQ7MOzZKlDRpYKcFqEMczbD7YmbPgpzKMI=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
-github.com/stretchr/testify v1.11.1 h1:7s2iGBzp5EwR7/aIZr8ao5+dra3wiQyKjjFuvgVKu7U=
-github.com/stretchr/testify v1.11.1/go.mod h1:wZwfW3scLgRK+23gO65QZefKpKQRnfz6sD981Nm4B6U=
+github.com/stretchr/testify v1.12.1 h1:EuwCh5fleGS7H32xRwO3wRGT7DxrDhLAT6FF8MpWDWE=
+github.com/stretchr/testify v1.12.1/go.mod h1:MDEgiDPPsNp5cuIrHPPCyornHKgEVbtFUmoNlxoYthg=
 github.com/sugarme/regexpset v0.0.0-20200920021344-4d4ec8eaf93c h1:pwb4kNSHb4K89ymCaN+5lPH/MwnfSVg4rzGDh4d+iy4=
 github.com/sugarme/regexpset v0.0.0-20200920021344-4d4ec8eaf93c/go.mod h1:2gwkXLWbDGUQWeL3RtpCmcY4mzCtU13kb9UsAg9xMaw=
-github.com/yalue/onnxruntime_go v1.31.0 h1:1ln4YW1SFOFfGJZXe3jNOb2JUSt+l2pEneZfV8HdtFA=
-github.com/yalue/onnxruntime_go v1.31.0/go.mod h1:b4X26A8pekNb1ACJ58wAXgNKeUCGEAQ9dmACut9Sm/4=
-golang.org/x/sync v0.21.0 h1:HLII4xRRTtCRkxYp4HNFF0Js/Og6q2i++KXbg0gHCwM=
-golang.org/x/sync v0.21.0/go.mod h1:9xrNwdLfx4jkKbNva9FpL6vEN7evnE43NNNJQ2LF3+0=
-golang.org/x/sys v0.46.0 h1:noSf2Fq6F8DBgS+LysIkx7rIExoNHJsxOAtPp4rthXw=
-golang.org/x/sys v0.46.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
-golang.org/x/text v0.38.0 h1:sXmwo9DwP3OK9EZ7PqAdaooSGozfl/3a6/xJcbzPRhE=
-golang.org/x/text v0.38.0/go.mod h1:YXZt3QhHUKYT53r2lLKFIVi6Ao1jdzrTR/KQ09qyxF4=
-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
-gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
-gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+github.com/yalue/onnxruntime_go v1.36.0 h1:iH1Q++DcsyT9sWtN26KYimESlI5hhXpKaChHDS44oV4=
+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 v0.24.0 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 v1.31.1 h1:7CA8FTFz/gRfgqgpeKIBcervUn3xSyPUmr6B2WXJ7kg=
-gorm.io/gorm v1.31.1/go.mod h1:XyQVbO2k6YkOis7C2437jSit3SsDK72s7n7rsSHd+Gs=
+gorm.io/gorm v1.31.2 h1:3o8FXNo9v9S858gil+3LlZA1LkCOzgb4g5BL64FgaCo=
+gorm.io/gorm v1.31.2/go.mod h1:XyQVbO2k6YkOis7C2437jSit3SsDK72s7n7rsSHd+Gs=

hooks/hooks.json

@@ -6,7 +6,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/session-start",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/session-start\"",
             "timeout": 30
           }
         ]
@@ -17,7 +17,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/user-prompt",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/user-prompt\"",
             "timeout": 10
           }
         ]
@@ -29,7 +29,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/post-tool-use",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/post-tool-use\"",
             "timeout": 10
           }
         ]
@@ -40,7 +40,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/subagent-stop",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/subagent-stop\"",
             "timeout": 10
           }
         ]
@@ -51,7 +51,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/stop",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/stop\"",
             "timeout": 30
           }
         ]

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_store_test.go

@@ -500,15 +500,13 @@ func TestObservationStore_CleanupOldObservations(t *testing.T) {
 
 	// Store observations beyond the limit WITHOUT async cleanup
 	// We disable async cleanup by not setting cleanupFunc
-	var allIDs []int64
 	for i := 0; i < 105; i++ {
 		observation := &models.ParsedObservation{
 			Type:  models.ObsTypeDiscovery,
 			Title: "Observation",
 		}
-		id, _, err := observationStore.StoreObservation(ctx, "claude-1", "test-project", observation, i, 10)
+		_, _, err := observationStore.StoreObservation(ctx, "claude-1", "test-project", observation, i, 10)
 		require.NoError(t, err)
-		allIDs = append(allIDs, id)
 		time.Sleep(2 * time.Millisecond) // Ensure different timestamps
 	}
 

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/embedding/assets/lib/darwin-arm64/.version

@@ -1 +1 @@
-1.26.0
+1.30.0

internal/embedding/assets/lib/linux-amd64/.version

@@ -1 +1 @@
-1.26.0
+1.30.0

internal/embedding/assets/lib/linux-arm64/.version

@@ -1 +1 @@
-1.26.0
+1.30.0

internal/embedding/assets/lib/windows-amd64/.version

@@ -1 +1 @@
-1.26.0
+1.30.0

internal/embedding/lib_darwin_arm64.go

@@ -6,7 +6,7 @@ import (
 	_ "embed"
 )
 
-//go:embed assets/lib/darwin-arm64/libonnxruntime.dylib
+//go:embed assets/lib/darwin-arm64/libonnxruntime.dylib.gz
 var onnxRuntimeLib []byte
 
 const onnxRuntimeLibName = "libonnxruntime.dylib"

internal/embedding/lib_linux_amd64.go

@@ -6,10 +6,10 @@ import (
 	_ "embed"
 )
 
-//go:embed assets/lib/linux-amd64/libonnxruntime.so
+//go:embed assets/lib/linux-amd64/libonnxruntime.so.gz
 var onnxRuntimeLib []byte
 
-//go:embed assets/lib/linux-amd64/libonnxruntime_providers_shared.so
+//go:embed assets/lib/linux-amd64/libonnxruntime_providers_shared.so.gz
 var onnxRuntimeProvidersLib []byte
 
 const onnxRuntimeLibName = "libonnxruntime.so"

internal/embedding/lib_linux_arm64.go

@@ -6,10 +6,10 @@ import (
 	_ "embed"
 )
 
-//go:embed assets/lib/linux-arm64/libonnxruntime.so
+//go:embed assets/lib/linux-arm64/libonnxruntime.so.gz
 var onnxRuntimeLib []byte
 
-//go:embed assets/lib/linux-arm64/libonnxruntime_providers_shared.so
+//go:embed assets/lib/linux-arm64/libonnxruntime_providers_shared.so.gz
 var onnxRuntimeProvidersLib []byte
 
 const onnxRuntimeLibName = "libonnxruntime.so"

internal/embedding/lib_windows_amd64.go

@@ -6,7 +6,7 @@ import (
 	_ "embed"
 )
 
-//go:embed assets/lib/windows-amd64/onnxruntime.dll
+//go:embed assets/lib/windows-amd64/onnxruntime.dll.gz
 var onnxRuntimeLib []byte
 
 const onnxRuntimeLibName = "onnxruntime.dll"

internal/embedding/service.go

@@ -3,10 +3,13 @@ package embedding
 
 import (
 	"bytes"
+	"compress/gzip"
 	"context"
 	"crypto/sha256"
 	"encoding/hex"
 	"fmt"
+	"io"
+	"math"
 	"os"
 	"path/filepath"
 	"strings"
@@ -24,6 +27,9 @@ const EmbeddingDim = 384
 
 // Model version constants
 const (
+	// BGEStorageVersion tags stored vectors; bump it to force a rebuild when vectors change.
+	BGEStorageVersion = "bge-v1.5-l2"
+
 	// BGEModelVersion is the version string for bge-small-en-v1.5
 	BGEModelVersion = "bge-v1.5"
 	// BGEModelName is the human-readable name for bge-small-en-v1.5
@@ -126,7 +132,7 @@ func (m *bgeModel) Name() string {
 
 // Version returns the short version string for storage.
 func (m *bgeModel) Version() string {
-	return BGEModelVersion
+	return BGEStorageVersion
 }
 
 // Dimensions returns the embedding vector size.
@@ -134,7 +140,7 @@ func (m *bgeModel) Dimensions() int {
 	return EmbeddingDim
 }
 
-// extractONNXLibrary extracts the embedded ONNX runtime library to a temp directory.
+// extractONNXLibrary gunzips the embedded ONNX runtime library to a temp directory.
 // Uses content hash to avoid re-extracting if already present.
 func extractONNXLibrary() (string, error) {
 	// Create a hash of the library content for cache key
@@ -157,16 +163,14 @@ func extractONNXLibrary() (string, error) {
 	}
 
 	// Write main library
-	// #nosec G306 -- Shared library needs executable permission (0755) for dynamic linker
-	if err := os.WriteFile(libPath, onnxRuntimeLib, 0755); err != nil {
+	if err := writeGunzipped(libPath, onnxRuntimeLib); err != nil {
 		return "", fmt.Errorf("write library: %w", err)
 	}
 
 	// Write providers library if present (Linux only)
 	if len(onnxRuntimeProvidersLib) > 0 && onnxRuntimeProvidersLibName != "" {
 		providersPath := filepath.Join(cacheDir, onnxRuntimeProvidersLibName)
-		// #nosec G306 -- Shared library needs executable permission (0755) for dynamic linker
-		if err := os.WriteFile(providersPath, onnxRuntimeProvidersLib, 0755); err != nil {
+		if err := writeGunzipped(providersPath, onnxRuntimeProvidersLib); err != nil {
 			return "", fmt.Errorf("write providers library: %w", err)
 		}
 	}
@@ -512,12 +516,28 @@ func meanPooling(embeddings []float32, attentionMask []int64, batchSize, seqLen,
 			}
 		}
 
-		results[b] = result
+		results[b] = l2Normalize(result)
 	}
 
 	return results
 }
 
+// l2Normalize scales v to unit length in place; sqlite-vec distances assume unit vectors.
+func l2Normalize(v []float32) []float32 {
+	var sum float64
+	for _, x := range v {
+		sum += float64(x) * float64(x)
+	}
+	if sum == 0 {
+		return v
+	}
+	inv := float32(1 / math.Sqrt(sum))
+	for i := range v {
+		v[i] *= inv
+	}
+	return v
+}
+
 // clsPooling extracts the [CLS] token embedding (first token).
 // Input shape: [batch, seq_len, hidden]
 // Output shape: [batch, hidden]
@@ -529,7 +549,7 @@ func clsPooling(embeddings []float32, batchSize, seqLen, hiddenSize int) [][]flo
 		// CLS token is at position 0
 		embOffset := b * seqLen * hiddenSize
 		copy(result, embeddings[embOffset:embOffset+hiddenSize])
-		results[b] = result
+		results[b] = l2Normalize(result)
 	}
 
 	return results
@@ -626,3 +646,38 @@ func (s *Service) EmbedBatchWithContext(ctx context.Context, texts []string) ([]
 func (s *Service) Close() error {
 	return s.model.Close()
 }
+
+// writeGunzipped decompresses gz into path with the executable bit the dynamic linker needs.
+// It writes a temp file and renames it, so a crash never leaves a truncated library at path.
+func writeGunzipped(path string, gz []byte) (err error) {
+	zr, err := gzip.NewReader(bytes.NewReader(gz))
+	if err != nil {
+		return err
+	}
+	defer func() { _ = zr.Close() }()
+
+	f, err := os.CreateTemp(filepath.Dir(path), filepath.Base(path)+".tmp*")
+	if err != nil {
+		return err
+	}
+	tmp := f.Name()
+	defer func() {
+		if err != nil {
+			_ = os.Remove(tmp)
+		}
+	}()
+
+	// #nosec G110 -- archive is embedded at build time, not external input
+	if _, err = io.Copy(f, zr); err != nil {
+		_ = f.Close()
+		return err
+	}
+	if err = f.Close(); err != nil {
+		return err
+	}
+	// #nosec G302 -- shared library needs the executable bit for the dynamic linker
+	if err = os.Chmod(tmp, 0o755); err != nil {
+		return err
+	}
+	return os.Rename(tmp, path)
+}

internal/embedding/service_test.go

@@ -1,9 +1,13 @@
 package embedding
 
 import (
+	"bytes"
+	"compress/gzip"
 	"context"
 	"errors"
 	"math"
+	"os"
+	"path/filepath"
 	"sync"
 	"testing"
 	"time"
@@ -475,3 +479,57 @@ func cosineSimilarity(a, b []float32) float64 {
 
 	return dotProduct / (math.Sqrt(normA) * math.Sqrt(normB))
 }
+
+func gzipBytes(t *testing.T, data []byte) []byte {
+	t.Helper()
+	var buf bytes.Buffer
+	zw := gzip.NewWriter(&buf)
+	_, err := zw.Write(data)
+	require.NoError(t, err)
+	require.NoError(t, zw.Close())
+	return buf.Bytes()
+}
+
+func TestWriteGunzipped(t *testing.T) {
+	payload := bytes.Repeat([]byte("onnx"), 50_000)
+	good := gzipBytes(t, payload)
+
+	tests := []struct {
+		name     string
+		gz       []byte
+		wantErr  bool
+		wantFile bool
+	}{
+		{"valid archive", good, false, true},
+		{"truncated archive leaves no file", good[:len(good)/2], true, false},
+		{"not gzip leaves no file", []byte("plain text"), true, false},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			path := filepath.Join(dir, "lib.so")
+
+			err := writeGunzipped(path, tt.gz)
+
+			if tt.wantErr {
+				require.Error(t, err)
+			} else {
+				require.NoError(t, err)
+			}
+			_, statErr := os.Stat(path)
+			assert.Equal(t, tt.wantFile, statErr == nil)
+			entries, _ := os.ReadDir(dir)
+			if !tt.wantFile {
+				assert.Empty(t, entries, "no partial or temp files may remain")
+			}
+			if tt.wantFile {
+				got, err := os.ReadFile(path)
+				require.NoError(t, err)
+				assert.Equal(t, payload, got)
+				info, err := os.Stat(path)
+				require.NoError(t, err)
+				assert.Equal(t, os.FileMode(0o755), info.Mode().Perm())
+			}
+		})
+	}
+}

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"
@@ -139,9 +140,22 @@ func NewClient(cfg Config, embedSvc *embedding.Service) (*Client, error) {
 	return c, nil
 }
 
-// AddDocuments adds documents with their embeddings to the vector store.
+// AddDocuments embeds the documents and inserts them. A document whose ID already exists is an error (the vec0
+// table does not replace on insert); use ReplaceDocuments to write the documents of a note that may have some.
 func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
-	if len(docs) == 0 {
+	return c.writeDocuments(ctx, docs, "", 0)
+}
+
+// ReplaceDocuments writes the documents of one note (observation, summary, ...) in place of the ones it had: the old
+// documents are deleted and the new ones inserted in one transaction, so an edit that removes a fact leaves no stale
+// document behind and a failure leaves the old ones untouched. docs may be empty, which only deletes.
+func (c *Client) ReplaceDocuments(ctx context.Context, docType string, sqliteID int64, docs []Document) error {
+	return c.writeDocuments(ctx, docs, docType, sqliteID)
+}
+
+// writeDocuments inserts docs; when docType is not empty it first deletes every document of that note.
+func (c *Client) writeDocuments(ctx context.Context, docs []Document, docType string, sqliteID int64) (err error) {
+	if len(docs) == 0 && docType == "" {
 		return nil
 	}
 
@@ -154,9 +168,11 @@ func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
 	// Compute embeddings OUTSIDE the write lock for better concurrency.
 	// Embedding is ONNX inference (slow, mutex-protected internally) — holding
 	// writeMu during inference blocks all concurrent writes and reads.
-	embeddings, err := c.embedSvc.EmbedBatchWithContext(ctx, texts)
-	if err != nil {
-		return fmt.Errorf("generate embeddings: %w", err)
+	var embeddings [][]float32
+	if len(texts) > 0 {
+		if embeddings, err = c.embedSvc.EmbedBatchWithContext(ctx, texts); err != nil {
+			return fmt.Errorf("generate embeddings: %w", err)
+		}
 	}
 
 	// Acquire write lock for DB operations only
@@ -165,7 +181,7 @@ func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
 
 	// Insert into vectors table with model version tracking
 	const insertQuery = `
-		INSERT OR REPLACE INTO vectors (doc_id, embedding, sqlite_id, doc_type, field_type, project, scope, model_version)
+		INSERT INTO vectors (doc_id, embedding, sqlite_id, doc_type, field_type, project, scope, model_version)
 		VALUES (?, ?, ?, ?, ?, ?, ?, ?)
 	`
 
@@ -176,6 +192,8 @@ func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
 	if err != nil {
 		return fmt.Errorf("begin transaction: %w", err)
 	}
+	// err is the named result, so every failed return below reaches this and the write lock is released. (A shadowed
+	// err in the loop once left the transaction open, and the database locked, after a failed insert.)
 	defer func() {
 		if err != nil {
 			if rbErr := tx.Rollback(); rbErr != nil {
@@ -185,6 +203,12 @@ func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
 		}
 	}()
 
+	if docType != "" {
+		if _, err = tx.ExecContext(ctx, `DELETE FROM vectors WHERE doc_type = ? AND sqlite_id = ?`, docType, sqliteID); err != nil {
+			return fmt.Errorf("delete old documents: %w", err)
+		}
+	}
+
 	stmt, err := tx.PrepareContext(ctx, insertQuery)
 	if err != nil {
 		return fmt.Errorf("prepare statement: %w", err)
@@ -193,29 +217,28 @@ func (c *Client) AddDocuments(ctx context.Context, docs []Document) error {
 
 	for i, doc := range docs {
 		// Serialize embedding to blob format
-		embBlob, err := sqlite_vec.SerializeFloat32(embeddings[i])
-		if err != nil {
+		var embBlob []byte
+		if embBlob, err = sqlite_vec.SerializeFloat32(embeddings[i]); err != nil {
 			return fmt.Errorf("serialize embedding for %s: %w", doc.ID, err)
 		}
 
 		// Extract metadata
-		sqliteID, _ := doc.Metadata["sqlite_id"].(int64)
-		docType, _ := doc.Metadata["doc_type"].(string)
+		docSQLiteID, _ := doc.Metadata["sqlite_id"].(int64)
+		docDocType, _ := doc.Metadata["doc_type"].(string)
 		fieldType, _ := doc.Metadata["field_type"].(string)
 		project, _ := doc.Metadata["project"].(string)
 		scope, _ := doc.Metadata["scope"].(string)
 
-		_, err = stmt.ExecContext(ctx,
+		if _, err = stmt.ExecContext(ctx,
 			doc.ID,
 			embBlob,
-			sqliteID,
-			docType,
+			docSQLiteID,
+			docDocType,
 			fieldType,
 			project,
 			scope,
 			modelVersion,
-		)
-		if err != nil {
+		); err != nil {
 			return fmt.Errorf("insert document %s: %w", doc.ID, err)
 		}
 	}
@@ -292,67 +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
@@ -507,60 +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")
+	}
 }
 
 // =============================================================================
@@ -2152,3 +2222,67 @@ func TestGetOrComputeEmbedding_ContextCancelDuringSingleflight(t *testing.T) {
 	// Wait for first call to finish
 	<-firstDone
 }
+
+func TestClient_AddDocuments_FailedBatchIsRolledBackAndDoesNotLockTheDatabase(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)
+
+	doc := func(id string, sqliteID int64) Document {
+		return Document{ID: id, Content: "text of " + id, Metadata: map[string]any{
+			"sqlite_id": sqliteID, "doc_type": "observation", "field_type": "narrative", "project": "alpha", "scope": "project",
+		}}
+	}
+	require.NoError(t, client.AddDocuments(context.Background(), []Document{doc("obs_1_narrative", 1)}))
+
+	// The second document of the batch exists already, so the batch fails after the first was inserted.
+	err = client.AddDocuments(context.Background(), []Document{doc("obs_2_narrative", 2), doc("obs_1_narrative", 1)})
+	require.Error(t, err)
+
+	var n int
+	require.NoError(t, db.QueryRow("SELECT COUNT(*) FROM vectors WHERE doc_id = 'obs_2_narrative'").Scan(&n))
+	assert.Zero(t, n, "nothing of the failed batch is kept")
+
+	// With the transaction left open, this would wait for the lock until the context ends.
+	ctx, cancel := context.WithTimeout(context.Background(), 5*time.Second)
+	defer cancel()
+	require.NoError(t, client.AddDocuments(ctx, []Document{doc("obs_3_narrative", 3)}), "a write after a failed one goes through")
+}
+
+func TestClient_ReplaceDocuments_ReplacesOnlyTheDocumentsOfThatNote(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)
+	ctx := context.Background()
+
+	doc := func(id string, sqliteID int64, docType, scope string) Document {
+		return Document{ID: id, Content: "text of " + id, Metadata: map[string]any{
+			"sqlite_id": sqliteID, "doc_type": docType, "field_type": "narrative", "project": "alpha", "scope": scope,
+		}}
+	}
+	require.NoError(t, client.AddDocuments(ctx, []Document{
+		doc("obs_1_narrative", 1, "observation", "global"), doc("obs_1_fact_0", 1, "observation", "global"),
+		doc("obs_2_narrative", 2, "observation", "global"),
+		doc("summary_1_request", 1, "session_summary", ""), // the same sqlite id, another kind of document
+	}))
+
+	require.NoError(t, client.ReplaceDocuments(ctx, "observation", 1, []Document{doc("obs_1_narrative", 1, "observation", "project")}))
+
+	count := func(where string, args ...any) (n int) {
+		require.NoError(t, db.QueryRow("SELECT COUNT(*) FROM vectors WHERE "+where, args...).Scan(&n))
+		return n
+	}
+	assert.Equal(t, 1, count("doc_type = 'observation' AND sqlite_id = 1"), "the fact document is gone")
+	assert.Equal(t, 1, count("doc_id = 'obs_1_narrative' AND scope = 'project'"), "and the narrative carries the new scope")
+	assert.Equal(t, 1, count("doc_id = 'obs_2_narrative' AND scope = 'global'"), "another note is untouched")
+	assert.Equal(t, 1, count("doc_id = 'summary_1_request'"), "so is a summary with the same id")
+
+	require.NoError(t, client.ReplaceDocuments(ctx, "observation", 1, nil), "no documents left: only the old ones are deleted")
+	assert.Zero(t, count("doc_type = 'observation' AND sqlite_id = 1"))
+}

internal/vector/sqlitevec/sync.go

@@ -22,11 +22,8 @@ func NewSync(client *Client) *Sync {
 // SyncObservation syncs a single observation to the vector store.
 func (s *Sync) SyncObservation(ctx context.Context, obs *models.Observation) error {
 	docs := s.formatObservationDocs(obs)
-	if len(docs) == 0 {
-		return nil
-	}
-
-	if err := s.client.AddDocuments(ctx, docs); err != nil {
+	// Replace, not add: a note that is synced again (after an edit, a re-scope or a re-import) already has documents.
+	if err := s.client.ReplaceDocuments(ctx, "observation", obs.ID, docs); err != nil {
 		return fmt.Errorf("add observation docs: %w", err)
 	}
 
@@ -102,11 +99,7 @@ func (s *Sync) formatObservationDocs(obs *models.Observation) []Document {
 // SyncSummary syncs a single session summary to the vector store.
 func (s *Sync) SyncSummary(ctx context.Context, summary *models.SessionSummary) error {
 	docs := s.formatSummaryDocs(summary)
-	if len(docs) == 0 {
-		return nil
-	}
-
-	if err := s.client.AddDocuments(ctx, docs); err != nil {
+	if err := s.client.ReplaceDocuments(ctx, "session_summary", summary.ID, docs); err != nil {
 		return fmt.Errorf("add summary docs: %w", err)
 	}
 

internal/vector/sqlitevec/sync_test.go

@@ -346,3 +346,57 @@ func TestSync_FormatObservationDocs_EmptyScope(t *testing.T) {
 	assert.Len(t, docs, 1)
 	assert.Equal(t, "project", docs[0].Metadata["scope"])
 }
+
+func vectorCount(t *testing.T, c *Client, where string, args ...any) int {
+	t.Helper()
+	var n int
+	require.NoError(t, c.db.QueryRow("SELECT COUNT(*) FROM vectors WHERE "+where, args...).Scan(&n))
+	return n
+}
+
+func TestSync_SyncObservation_AgainReplacesTheDocumentsOfTheNote(t *testing.T) {
+	client, cleanup := testClient(t)
+	defer cleanup()
+	sync := NewSync(client)
+	ctx := context.Background()
+
+	obs := &models.Observation{
+		ID: 7, SDKSessionID: "s", Project: "alpha", Type: models.ObsTypeDiscovery, Scope: models.ScopeGlobal,
+		Narrative: sql.NullString{String: "The queue keeps one consumer per tenant.", Valid: true},
+		Facts:     []string{"one consumer per tenant", "retries are capped", "dead letters go to a second queue"},
+	}
+	other := &models.Observation{
+		ID: 8, SDKSessionID: "s", Project: "alpha", Type: models.ObsTypeDiscovery, Scope: models.ScopeProject,
+		Narrative: sql.NullString{String: "Releases are cut on Thursdays.", Valid: true},
+	}
+	require.NoError(t, sync.SyncObservation(ctx, obs))
+	require.NoError(t, sync.SyncObservation(ctx, other))
+	require.Equal(t, 4, vectorCount(t, client, "doc_type = 'observation' AND sqlite_id = ?", 7))
+
+	// The note was edited: one fact fewer, and it is a project note now.
+	obs.Facts = obs.Facts[:2]
+	obs.Scope = models.ScopeProject
+	require.NoError(t, sync.SyncObservation(ctx, obs), "syncing a note that already has documents is not an error")
+
+	assert.Equal(t, 3, vectorCount(t, client, "doc_type = 'observation' AND sqlite_id = ?", 7), "narrative and two facts; the dropped fact's document is gone")
+	assert.Equal(t, 0, vectorCount(t, client, "doc_id = ?", "obs_7_fact_2"))
+	assert.Equal(t, 3, vectorCount(t, client, "sqlite_id = ? AND scope = 'project'", 7), "the new scope is what the vectors carry")
+	assert.Equal(t, 1, vectorCount(t, client, "sqlite_id = ?", 8), "other notes are not touched")
+}
+
+func TestSync_SyncSummary_AgainReplacesTheDocumentsOfTheSummary(t *testing.T) {
+	client, cleanup := testClient(t)
+	defer cleanup()
+	sync := NewSync(client)
+	ctx := context.Background()
+
+	summary := &models.SessionSummary{
+		ID: 3, SDKSessionID: "s", Project: "alpha",
+		Request: sql.NullString{String: "Add the queue", Valid: true}, Learned: sql.NullString{String: "One consumer per tenant", Valid: true},
+	}
+	require.NoError(t, sync.SyncSummary(ctx, summary))
+	summary.Learned = sql.NullString{}
+	require.NoError(t, sync.SyncSummary(ctx, summary))
+
+	assert.Equal(t, 1, vectorCount(t, client, "doc_type = 'session_summary' AND sqlite_id = ?", 3), "the field that was emptied has no document any more")
+}

internal/worker/handlers_update.go

@@ -218,9 +218,8 @@ func (s *Service) handleUpdateRestart(w http.ResponseWriter, r *http.Request) {
 
 	// Restart in background after response is sent
 	go func() {
-		if err := s.updater.Restart(); err != nil {
-			log.Error().Err(err).Msg("Failed to restart worker")
-		}
+		// Restart only returns when the new worker failed to start.
+		log.Error().Err(s.updater.Restart()).Msg("Failed to restart worker")
 	}()
 }
 
@@ -244,8 +243,7 @@ func (s *Service) handleRestart(w http.ResponseWriter, r *http.Request) {
 	go func() {
 		// Small delay to ensure response is sent
 		time.Sleep(100 * time.Millisecond)
-		if err := s.updater.Restart(); err != nil {
-			log.Error().Err(err).Msg("Failed to restart worker")
-		}
+		// Restart only returns when the new worker failed to start.
+		log.Error().Err(s.updater.Restart()).Msg("Failed to restart worker")
 	}()
 }

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/ratelimit.go

@@ -2,6 +2,7 @@
 package worker
 
 import (
+	"net"
 	"net/http"
 	"sync"
 	"time"
@@ -206,14 +207,13 @@ func (pcrl *PerClientRateLimiter) Stats() map[string]any {
 }
 
 // PerClientRateLimitMiddleware creates middleware that applies per-client rate limiting.
-// Uses X-Forwarded-For or RemoteAddr to identify clients.
+// Identifies clients by the peer IP of the connection; forwarding headers are spoofable and ignored.
 func PerClientRateLimitMiddleware(limiter *PerClientRateLimiter) func(http.Handler) http.Handler {
 	return func(next http.Handler) http.Handler {
 		return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
-			// Get client identifier (prefer X-Real-IP from RealIP middleware)
 			clientKey := r.RemoteAddr
-			if xff := r.Header.Get("X-Real-IP"); xff != "" {
-				clientKey = xff
+			if host, _, err := net.SplitHostPort(clientKey); err == nil {
+				clientKey = host
 			}
 
 			if !limiter.Allow(clientKey) {

internal/worker/ratelimit_test.go

@@ -0,0 +1,35 @@
+package worker
+
+import (
+	"net/http"
+	"net/http/httptest"
+	"testing"
+)
+
+func TestPerClientRateLimitMiddleware_KeysOnPeerIP(t *testing.T) {
+	h := PerClientRateLimitMiddleware(NewPerClientRateLimiter(0.001, 1))(
+		http.HandlerFunc(func(w http.ResponseWriter, _ *http.Request) { w.WriteHeader(http.StatusOK) }))
+
+	do := func(remote, realIP string) int {
+		req := httptest.NewRequest(http.MethodGet, "/", nil)
+		req.RemoteAddr = remote
+		if realIP != "" {
+			req.Header.Set("X-Real-IP", realIP)
+		}
+		rec := httptest.NewRecorder()
+		h.ServeHTTP(rec, req)
+		return rec.Code
+	}
+
+	if got := do("10.0.0.1:1111", "1.1.1.1"); got != http.StatusOK {
+		t.Fatalf("first request: got %d", got)
+	}
+	// Same peer, new port and forged header: must share the exhausted bucket.
+	if got := do("10.0.0.1:2222", "2.2.2.2"); got != http.StatusTooManyRequests {
+		t.Fatalf("spoofed header/new port bypassed limit: got %d", got)
+	}
+	// Different peer is unaffected.
+	if got := do("10.0.0.2:1111", ""); got != http.StatusOK {
+		t.Fatalf("other peer: got %d", got)
+	}
+}

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

@@ -1,8 +1,10 @@
 package sdk
 
 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"
 )
@@ -121,7 +123,7 @@ func TestCheckVectorDeduplication_NilClient(t *testing.T) {
 		Narrative: "Some narrative text",
 	}
 
-	result := p.checkVectorDeduplication(nil, obs, "test-project")
+	result := p.checkVectorDeduplication(context.Background(), obs, "test-project")
 	if result.Action != "insert" {
 		t.Errorf("expected Action='insert' when vectorClient is nil, got %q", result.Action)
 	}
@@ -136,8 +138,40 @@ func TestCheckVectorDeduplication_EmptySearchText(t *testing.T) {
 		// All empty fields
 	}
 
-	result := p.checkVectorDeduplication(nil, obs, "test-project")
+	result := p.checkVectorDeduplication(context.Background(), obs, "test-project")
 	if result.Action != "insert" {
 		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")
+	}
+}

internal/worker/service.go

@@ -1213,7 +1213,6 @@ func (s *Service) setupMiddleware() {
 
 	s.router.Use(middleware.Logger)
 	s.router.Use(middleware.Recoverer)
-	s.router.Use(middleware.RealIP)
 
 	// Add security headers (X-Frame-Options, X-Content-Type-Options, CSP, etc.)
 	s.router.Use(SecurityHeaders)
@@ -1227,7 +1226,7 @@ func (s *Service) setupMiddleware() {
 	// Add gzip compression for responses >1KB (reduces bandwidth ~70% for JSON)
 	s.router.Use(middleware.Compress(5)) // Level 5 = good balance of speed vs compression
 
-	// Apply per-client rate limiting (after RealIP so we get the real client IP)
+	// Apply per-client rate limiting (keyed on the socket peer address; forwarding headers are untrusted)
 	if s.rateLimiter != nil {
 		s.router.Use(PerClientRateLimitMiddleware(s.rateLimiter))
 	}

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": "0.21.4",
+      "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": "0.21.4",
+        "latest": "0.21.127",
         "versions": {
-          "0.21.4": {
-            "releaseDate": "2026-06-19",
+          "0.21.127": {
+            "releaseDate": "2026-10-12",
             "downloads": {
               "darwin-arm64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.4/claude-mnemonic_0.21.4_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": "caf7738e7956de8e41401750d652ea35a788b8cb1d40dfc650f1d34993bde163"
+                "sha256": "4191ab626fb31a046f6eaeb0f3e5febdbb50285bd0d6d4e21a69e626fe5bbda0"
               },
               "linux-amd64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.4/claude-mnemonic_0.21.4_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": "2d66980787db911786848680b267c72ef8f77a4c34b5f83c7e4c56375f620632"
+                "sha256": "9245e63dc10ee88bae33d1519d8c31951ab0abeef045cfd940903bfcf5db3272"
               },
               "windows-amd64": {
-                "url": "https://github.com/lukaszraczylo/claude-mnemonic/releases/download/v0.21.4/claude-mnemonic_0.21.4_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": "c2e77ef85755cab568e644d8ba4248bf3ab3c88ac4001a68bb96d7f1149c9530"
+                "sha256": "ced294d3791c4ebd0bfe37375589d1eff091a75f488eadf0b3b019bc87e3ea1d"
               }
             }
           }

pkg/hooks/httpclient.go

@@ -0,0 +1,94 @@
+package hooks
+
+import (
+	"bufio"
+	"bytes"
+	"context"
+	"errors"
+	"fmt"
+	"io"
+	"net"
+	"strconv"
+	"strings"
+	"time"
+)
+
+// maxResponseBytes caps a worker response so a misbehaving peer cannot exhaust memory.
+const maxResponseBytes = 32 << 20
+
+// Minimal HTTP/1.0 client over a raw TCP socket. Linking net/http adds ~3 MB to
+// every hook binary; hooks only speak plain JSON to the local worker. HTTP/1.0
+// makes the server skip chunked encoding and close the connection, so the body
+// is simply everything after the header block.
+type httpResponse struct {
+	StatusText string
+	Body       []byte
+	Status     int
+}
+
+func httpDo(ctx context.Context, timeout time.Duration, method string, port int, path string, body []byte) (*httpResponse, error) {
+	ctx, cancel := context.WithTimeout(ctx, timeout)
+	defer cancel()
+
+	addr := net.JoinHostPort("127.0.0.1", strconv.Itoa(port))
+	var d net.Dialer
+	conn, err := d.DialContext(ctx, "tcp", addr)
+	if err != nil {
+		return nil, err
+	}
+	defer func() { _ = conn.Close() }()
+
+	if dl, ok := ctx.Deadline(); ok {
+		_ = conn.SetDeadline(dl)
+	}
+	stop := context.AfterFunc(ctx, func() { _ = conn.Close() })
+	defer stop()
+
+	var req bytes.Buffer
+	fmt.Fprintf(&req, "%s %s HTTP/1.0\r\nHost: %s\r\n", method, path, addr)
+	if body != nil {
+		fmt.Fprintf(&req, "Content-Type: application/json\r\nContent-Length: %d\r\n", len(body))
+	}
+	req.WriteString("\r\n")
+	req.Write(body)
+	if _, err := conn.Write(req.Bytes()); err != nil {
+		return nil, err
+	}
+
+	raw, err := io.ReadAll(io.LimitReader(bufio.NewReader(conn), maxResponseBytes))
+	if err != nil {
+		return nil, err
+	}
+	return parseHTTPResponse(raw)
+}
+
+func parseHTTPResponse(raw []byte) (*httpResponse, error) {
+	head, body, found := bytes.Cut(raw, []byte("\r\n\r\n"))
+	if !found {
+		return nil, errors.New("malformed http response")
+	}
+	statusLine, _, _ := strings.Cut(string(head), "\r\n")
+	_, rest, ok := strings.Cut(statusLine, " ")
+	if !ok {
+		return nil, fmt.Errorf("malformed status line %q", statusLine)
+	}
+	codeStr, _, _ := strings.Cut(rest, " ")
+	code, err := strconv.Atoi(codeStr)
+	if err != nil {
+		return nil, fmt.Errorf("malformed status line %q", statusLine)
+	}
+	return &httpResponse{Status: code, StatusText: rest, Body: body}, nil
+}
+
+// GETBody fetches path from the worker within timeout and returns the raw body.
+// Statuses of 400 and above are returned as errors.
+func GETBody(ctx context.Context, timeout time.Duration, port int, path string) ([]byte, error) {
+	resp, err := httpDo(ctx, timeout, "GET", port, path, nil)
+	if err != nil {
+		return nil, err
+	}
+	if resp.Status >= 400 {
+		return nil, fmt.Errorf("request failed: %s", resp.StatusText)
+	}
+	return resp.Body, nil
+}

pkg/hooks/worker.go

@@ -2,12 +2,10 @@
 package hooks
 
 import (
-	"bytes"
 	"context"
 	"encoding/json"
 	"fmt"
 	"net"
-	"net/http"
 	"os"
 	"os/exec"
 	"path/filepath"
@@ -28,6 +26,9 @@ const (
 	// HealthCheckTimeout is the timeout for health checks.
 	HealthCheckTimeout = 2 * time.Second
 
+	// hookTimeout bounds a single hook->worker request.
+	hookTimeout = 10 * time.Second
+
 	// StartupTimeout is the timeout for worker startup.
 	StartupTimeout = 10 * time.Second
 
@@ -52,26 +53,6 @@ var (
 	// circuitBreakerMu protects lastStartupFailure.
 	circuitBreakerMu   sync.Mutex
 	lastStartupFailure time.Time
-
-	// hookClient is a shared HTTP client for hook->worker requests.
-	// DisableKeepAlives prevents TIME_WAIT connection leaks since each hook
-	// is a separate OS process that exits quickly.
-	hookClient = &http.Client{
-		Timeout: 10 * time.Second,
-		Transport: &http.Transport{
-			DisableKeepAlives: true,
-			MaxIdleConns:      1,
-		},
-	}
-
-	// healthClient is a shared HTTP client for health/version checks.
-	healthClient = &http.Client{
-		Timeout: HealthCheckTimeout,
-		Transport: &http.Transport{
-			DisableKeepAlives: true,
-			MaxIdleConns:      1,
-		},
-	}
 )
 
 // IsWorkerAvailable performs a fast check without network calls.
@@ -110,22 +91,21 @@ func GetWorkerPort() int {
 // Parses the JSON health response to check the "ready" field when available.
 // Falls back to HTTP status code check for backwards compatibility.
 func IsWorkerRunning(port int) bool {
-	resp, err := healthClient.Get(fmt.Sprintf("http://127.0.0.1:%d/api/health", port))
+	resp, err := httpDo(context.Background(), HealthCheckTimeout, "GET", port, "/api/health", nil)
 	if err != nil {
 		return false
 	}
-	defer func() { _ = resp.Body.Close() }()
 
 	// Try to parse JSON response for structured health check
 	var health struct {
 		Ready bool `json:"ready"`
 	}
-	if err := json.NewDecoder(resp.Body).Decode(&health); err == nil {
+	if err := json.Unmarshal(resp.Body, &health); err == nil {
 		return health.Ready
 	}
 
 	// Fallback: treat HTTP 200 as healthy (backwards compatibility)
-	return resp.StatusCode == http.StatusOK
+	return resp.Status == 200
 }
 
 // workerCachePath returns the path to the worker cache file.
@@ -396,18 +376,17 @@ func updateCacheFromPort(port int) {
 
 // GetWorkerVersion gets the version of the running worker.
 func GetWorkerVersion(port int) string {
-	resp, err := healthClient.Get(fmt.Sprintf("http://127.0.0.1:%d/api/version", port))
+	resp, err := httpDo(context.Background(), HealthCheckTimeout, "GET", port, "/api/version", nil)
 	if err != nil {
 		return ""
 	}
-	defer func() { _ = resp.Body.Close() }()
 
-	if resp.StatusCode != http.StatusOK {
+	if resp.Status != 200 {
 		return ""
 	}
 
 	var result map[string]string
-	if err := json.NewDecoder(resp.Body).Decode(&result); err != nil {
+	if err := json.Unmarshal(resp.Body, &result); err != nil {
 		return ""
 	}
 
@@ -510,58 +489,46 @@ func findWorkerBinary() string {
 	return ""
 }
 
-// POST sends a POST request to the worker.
-func POST(port int, path string, body interface{}) (map[string]interface{}, error) {
-	jsonBody, err := json.Marshal(body)
+// request performs one worker call and returns the decoded JSON object.
+// A non-JSON body yields (nil, nil) when lenient, else the decode error.
+func request(ctx context.Context, method string, port int, path string, body interface{}, lenient bool) (map[string]interface{}, error) {
+	var payload []byte
+	if body != nil {
+		var err error
+		if payload, err = json.Marshal(body); err != nil {
+			return nil, err
+		}
+	}
+
+	resp, err := httpDo(ctx, hookTimeout, method, port, path, payload)
 	if err != nil {
 		return nil, err
 	}
-
-	resp, err := hookClient.Post(
-		fmt.Sprintf("http://127.0.0.1:%d%s", port, path),
-		"application/json",
-		bytes.NewReader(jsonBody),
-	)
-	if err != nil {
-		return nil, err
-	}
-	defer func() { _ = resp.Body.Close() }()
-
-	if resp.StatusCode >= 400 {
-		return nil, fmt.Errorf("request failed: %s", resp.Status)
+	if resp.Status >= 400 {
+		return nil, fmt.Errorf("request failed: %s", resp.StatusText)
 	}
 
 	var result map[string]interface{}
-	if err := json.NewDecoder(resp.Body).Decode(&result); err != nil {
-		// Not all endpoints return JSON
-		return nil, nil
+	if err := json.Unmarshal(resp.Body, &result); err != nil {
+		if lenient {
+			// Not all endpoints return JSON
+			return nil, nil
+		}
+		return nil, err
 	}
-
 	return result, nil
 }
 
+// POST sends a POST request to the worker.
+func POST(port int, path string, body interface{}) (map[string]interface{}, error) {
+	return request(context.Background(), "POST", port, path, body, true)
+}
+
 // POSTWithContext sends a POST request using the provided context.
 // Used for fire-and-forget calls where we want to control the timeout externally.
 func POSTWithContext(ctx context.Context, port int, path string, body interface{}) error {
-	jsonBody, err := json.Marshal(body)
-	if err != nil {
-		return err
-	}
-
-	req, err := http.NewRequestWithContext(ctx, http.MethodPost,
-		fmt.Sprintf("http://127.0.0.1:%d%s", port, path),
-		bytes.NewReader(jsonBody))
-	if err != nil {
-		return err
-	}
-	req.Header.Set("Content-Type", "application/json")
-
-	resp, err := hookClient.Do(req)
-	if err != nil {
-		return err
-	}
-	defer func() { _ = resp.Body.Close() }()
-	return nil
+	_, err := request(ctx, "POST", port, path, body, true)
+	return err
 }
 
 // POSTWithContextResult sends a POST request using the provided context and
@@ -570,56 +537,12 @@ func POSTWithContext(ctx context.Context, port int, path string, body interface{
 // aborts at the hook deadline instead of blocking for the full client timeout.
 // A non-JSON body is returned as (nil, nil), matching POST's behavior.
 func POSTWithContextResult(ctx context.Context, port int, path string, body interface{}) (map[string]interface{}, error) {
-	jsonBody, err := json.Marshal(body)
-	if err != nil {
-		return nil, err
-	}
-
-	req, err := http.NewRequestWithContext(ctx, http.MethodPost,
-		fmt.Sprintf("http://127.0.0.1:%d%s", port, path),
-		bytes.NewReader(jsonBody))
-	if err != nil {
-		return nil, err
-	}
-	req.Header.Set("Content-Type", "application/json")
-
-	resp, err := hookClient.Do(req)
-	if err != nil {
-		return nil, err
-	}
-	defer func() { _ = resp.Body.Close() }()
-
-	if resp.StatusCode >= 400 {
-		return nil, fmt.Errorf("request failed: %s", resp.Status)
-	}
-
-	var result map[string]interface{}
-	if err := json.NewDecoder(resp.Body).Decode(&result); err != nil {
-		// Not all endpoints return JSON
-		return nil, nil
-	}
-
-	return result, nil
+	return request(ctx, "POST", port, path, body, true)
 }
 
 // GET sends a GET request to the worker.
 func GET(port int, path string) (map[string]interface{}, error) {
-	resp, err := hookClient.Get(fmt.Sprintf("http://127.0.0.1:%d%s", port, path))
-	if err != nil {
-		return nil, err
-	}
-	defer func() { _ = resp.Body.Close() }()
-
-	if resp.StatusCode >= 400 {
-		return nil, fmt.Errorf("request failed: %s", resp.Status)
-	}
-
-	var result map[string]interface{}
-	if err := json.NewDecoder(resp.Body).Decode(&result); err != nil {
-		return nil, err
-	}
-
-	return result, nil
+	return request(context.Background(), "GET", port, path, nil, false)
 }
 
 // GETWithContext sends a GET request using the provided context and decodes the
@@ -627,28 +550,7 @@ func GET(port int, path string) (map[string]interface{}, error) {
 // Used on the prompt critical path so a wedged worker aborts at the hook
 // deadline instead of blocking for the full client timeout.
 func GETWithContext(ctx context.Context, port int, path string) (map[string]interface{}, error) {
-	req, err := http.NewRequestWithContext(ctx, http.MethodGet,
-		fmt.Sprintf("http://127.0.0.1:%d%s", port, path), nil)
-	if err != nil {
-		return nil, err
-	}
-
-	resp, err := hookClient.Do(req)
-	if err != nil {
-		return nil, err
-	}
-	defer func() { _ = resp.Body.Close() }()
-
-	if resp.StatusCode >= 400 {
-		return nil, fmt.Errorf("request failed: %s", resp.Status)
-	}
-
-	var result map[string]interface{}
-	if err := json.NewDecoder(resp.Body).Decode(&result); err != nil {
-		return nil, err
-	}
-
-	return result, nil
+	return request(ctx, "GET", port, path, nil, false)
 }
 
 // versionsCompatible checks if two versions are compatible for dev builds.

pkg/hooks/worker_test.go

@@ -5,8 +5,12 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"io"
+	"net"
 	"net/http"
 	"net/http/httptest"
+	"strconv"
+	"strings"
 	"testing"
 	"time"
 
@@ -1481,22 +1485,101 @@ func TestSleepCtx_Cancelled(t *testing.T) {
 	assert.Less(t, elapsed, 500*time.Millisecond)
 }
 
-// TestHookClients_DisableKeepAlives asserts shared clients disable keep-alives
-// to prevent TIME_WAIT connection leaks in short-lived hook processes.
-func TestHookClients_DisableKeepAlives(t *testing.T) {
-	hTransport, ok := hookClient.Transport.(*http.Transport)
-	require.True(t, ok, "hookClient.Transport should be *http.Transport")
-	assert.True(t, hTransport.DisableKeepAlives, "hookClient must disable keep-alives")
-	assert.Equal(t, 1, hTransport.MaxIdleConns)
+// TestHTTPDo_Behaviour covers the raw HTTP/1.0 client against a real server.
+func TestHTTPDo_Behaviour(t *testing.T) {
+	big := strings.Repeat("x", 200_000)
+	srv := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		switch r.URL.Path {
+		case "/echo":
+			b, _ := io.ReadAll(r.Body)
+			assert.Equal(t, "application/json", r.Header.Get("Content-Type"))
+			_, _ = w.Write(b)
+		case "/big":
+			_, _ = w.Write([]byte(`{"v":"` + big + `"}`))
+		case "/missing":
+			w.WriteHeader(http.StatusNotFound)
+		case "/empty":
+			w.WriteHeader(http.StatusNoContent)
+		}
+	}))
+	defer srv.Close()
+	port, err := strconv.Atoi(srv.URL[strings.LastIndex(srv.URL, ":")+1:])
+	require.NoError(t, err)
 
-	hcTransport, ok := healthClient.Transport.(*http.Transport)
-	require.True(t, ok, "healthClient.Transport should be *http.Transport")
-	assert.True(t, hcTransport.DisableKeepAlives, "healthClient must disable keep-alives")
-	assert.Equal(t, 1, hcTransport.MaxIdleConns)
+	tests := []struct {
+		name       string
+		method     string
+		path       string
+		body       []byte
+		wantStatus int
+		wantLen    int
+	}{
+		{"post echoes body", "POST", "/echo", []byte(`{"a":1}`), 200, 7},
+		{"large body over server buffer", "GET", "/big", nil, 200, len(big) + 8},
+		{"not found", "GET", "/missing", nil, 404, 0},
+		{"no content", "GET", "/empty", nil, 204, 0},
+	}
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			resp, err := httpDo(context.Background(), time.Second, tt.method, port, tt.path, tt.body)
+			require.NoError(t, err)
+			assert.Equal(t, tt.wantStatus, resp.Status)
+			assert.Len(t, resp.Body, tt.wantLen)
+		})
+	}
 }
 
-// TestHookClient_Timeout verifies hookClient timeout is set.
-func TestHookClient_Timeout(t *testing.T) {
-	assert.Equal(t, 10*time.Second, hookClient.Timeout)
-	assert.Equal(t, HealthCheckTimeout, healthClient.Timeout)
+// TestHTTPDo_Failures covers connection, timeout, cancel and malformed replies.
+func TestHTTPDo_Failures(t *testing.T) {
+	t.Run("connection refused", func(t *testing.T) {
+		l, err := net.Listen("tcp", "127.0.0.1:0")
+		require.NoError(t, err)
+		port := l.Addr().(*net.TCPAddr).Port
+		require.NoError(t, l.Close())
+		_, err = httpDo(context.Background(), time.Second, "GET", port, "/", nil)
+		assert.Error(t, err)
+	})
+
+	t.Run("wedged server times out", func(t *testing.T) {
+		l, err := net.Listen("tcp", "127.0.0.1:0")
+		require.NoError(t, err)
+		defer func() { _ = l.Close() }()
+		go func() {
+			c, err := l.Accept()
+			if err == nil {
+				defer func() { _ = c.Close() }()
+				time.Sleep(2 * time.Second)
+			}
+		}()
+		start := time.Now()
+		_, err = httpDo(context.Background(), 200*time.Millisecond, "GET", l.Addr().(*net.TCPAddr).Port, "/", nil)
+		assert.Error(t, err)
+		assert.Less(t, time.Since(start), time.Second)
+	})
+
+	t.Run("cancelled context aborts", func(t *testing.T) {
+		l, err := net.Listen("tcp", "127.0.0.1:0")
+		require.NoError(t, err)
+		defer func() { _ = l.Close() }()
+		go func() {
+			c, err := l.Accept()
+			if err == nil {
+				defer func() { _ = c.Close() }()
+				time.Sleep(2 * time.Second)
+			}
+		}()
+		ctx, cancel := context.WithTimeout(context.Background(), 100*time.Millisecond)
+		defer cancel()
+		start := time.Now()
+		_, err = httpDo(ctx, 5*time.Second, "GET", l.Addr().(*net.TCPAddr).Port, "/", nil)
+		assert.Error(t, err)
+		assert.Less(t, time.Since(start), time.Second)
+	})
+
+	t.Run("malformed response", func(t *testing.T) {
+		for _, raw := range []string{"", "garbage", "HTTP/1.0\r\n\r\n", "HTTP/1.0 abc OK\r\n\r\n"} {
+			_, err := parseHTTPResponse([]byte(raw))
+			assert.Error(t, err, "input %q", raw)
+		}
+	})
 }

plugin/.claude-plugin/plugin.json.tpl

@@ -10,7 +10,6 @@
   "mcpServers": {
     "claude-mnemonic": {
       "command": "${CLAUDE_PLUGIN_ROOT}/mcp-server",
-      "args": ["--project", "${CLAUDE_PROJECT}"],
       "env": {}
     }
   },

plugin/commands/restart.md

@@ -1,3 +1,8 @@
+---
+description: Restart the Claude Mnemonic worker process
+allowed-tools: Bash(curl:*)
+---
+
 # Restart Claude Mnemonic Worker
 
 Restart the claude-mnemonic worker process. Use this command when experiencing issues with the memory system.

plugin/hooks/hooks.json

@@ -6,7 +6,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/session-start",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/session-start\"",
             "timeout": 30
           }
         ]
@@ -17,7 +17,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/user-prompt",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/user-prompt\"",
             "timeout": 10
           }
         ]
@@ -29,7 +29,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/post-tool-use",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/post-tool-use\"",
             "timeout": 10
           }
         ]
@@ -40,7 +40,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/subagent-stop",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/subagent-stop\"",
             "timeout": 10
           }
         ]
@@ -51,7 +51,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/stop",
+            "command": "\"${CLAUDE_PLUGIN_ROOT}/hooks/stop\"",
             "timeout": 30
           }
         ]

scripts/download-onnx-libs.sh

@@ -6,7 +6,7 @@
 
 set -e
 
-ONNX_VERSION="1.26.0"
+ONNX_VERSION="1.30.0"
 ASSETS_DIR="internal/embedding/assets/lib"
 PLATFORM="${1:-all}"
 FORCE_DOWNLOAD=false
@@ -51,9 +51,22 @@ get_installed_version() {
     fi
 }
 
+# Gzip the libraries: Go embeds the .gz and gunzips once at first use, which
+# shrinks the worker binary by roughly 25 MB.
+compress_libs() {
+    local plat="$1"
+    local f
+    for f in "${ASSETS_DIR}/${plat}"/*.dylib "${ASSETS_DIR}/${plat}"/*.so "${ASSETS_DIR}/${plat}"/*.dll; do
+        if [ -f "$f" ]; then
+            gzip -9 -n -f "$f"
+        fi
+    done
+}
+
 # Write version file after successful download
 write_version_file() {
     local plat="$1"
+    compress_libs "$plat"
     echo "${ONNX_VERSION}" > "${ASSETS_DIR}/${plat}/.version"
 }
 
@@ -110,9 +123,9 @@ download_windows_amd64() {
 lib_exists() {
     local plat="$1"
     case "$plat" in
-        darwin-*) [ -f "${ASSETS_DIR}/${plat}/libonnxruntime.dylib" ] ;;
-        linux-*) [ -f "${ASSETS_DIR}/${plat}/libonnxruntime.so" ] ;;
-        windows-*) [ -f "${ASSETS_DIR}/${plat}/onnxruntime.dll" ] ;;
+        darwin-*) [ -f "${ASSETS_DIR}/${plat}/libonnxruntime.dylib.gz" ] ;;
+        linux-*) [ -f "${ASSETS_DIR}/${plat}/libonnxruntime.so.gz" ] ;;
+        windows-*) [ -f "${ASSETS_DIR}/${plat}/onnxruntime.dll.gz" ] ;;
         *) return 1 ;;
     esac
 }

scripts/eval-search/corpus.json

@@ -0,0 +1,276 @@
+{
+ "docs": [
+  {
+   "type": "bugfix",
+   "title": "Fixed race in session cache",
+   "narrative": "Concurrent map writes in the session cache caused panics; guarded with a RWMutex."
+  },
+  {
+   "type": "decision",
+   "title": "Chose SQLite WAL mode",
+   "narrative": "WAL lets readers proceed while a writer commits, so hooks can query during writes."
+  },
+  {
+   "type": "feature",
+   "title": "Added Prometheus metrics endpoint",
+   "narrative": "Exposes request latency histograms and error counters at /metrics for scraping."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed memory leak in websocket hub",
+   "narrative": "Goroutines were never released when clients disconnected; added context cancellation."
+  },
+  {
+   "type": "refactor",
+   "title": "Extracted retry helper with backoff",
+   "narrative": "Exponential backoff with jitter now lives in one function used by all HTTP callers."
+  },
+  {
+   "type": "decision",
+   "title": "Use argon2id for password hashing",
+   "narrative": "bcrypt cost was too low for new hardware; argon2id with 64MB memory chosen."
+  },
+  {
+   "type": "feature",
+   "title": "Dark mode toggle in dashboard",
+   "narrative": "Theme preference persists in localStorage and follows prefers-color-scheme by default."
+  },
+  {
+   "type": "discovery",
+   "title": "Kubernetes readiness probe timing",
+   "narrative": "Pods were killed during warmup because the readiness probe fired before the model loaded."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed off-by-one in pagination",
+   "narrative": "The last page skipped one row when total count was an exact multiple of page size."
+  },
+  {
+   "type": "decision",
+   "title": "Adopted table-driven tests",
+   "narrative": "Subtests with named cases make failures easier to locate and new cases cheap to add."
+  },
+  {
+   "type": "feature",
+   "title": "Rate limiting middleware",
+   "narrative": "Token bucket per client IP returns 429 with a Retry-After header when exceeded."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed timezone bug in scheduler",
+   "narrative": "Cron jobs fired an hour late after daylight saving because times were stored in local zone."
+  },
+  {
+   "type": "discovery",
+   "title": "Slow query caused by missing index",
+   "narrative": "EXPLAIN showed a sequential scan on the events table; a composite index cut it from 900ms to 4ms."
+  },
+  {
+   "type": "refactor",
+   "title": "Split monolithic handler file",
+   "narrative": "The 3000 line handlers file was divided by domain: sessions, observations, search."
+  },
+  {
+   "type": "decision",
+   "title": "Embeddings computed locally with ONNX",
+   "narrative": "Avoids sending user text to third parties and works offline."
+  },
+  {
+   "type": "feature",
+   "title": "Export observations as JSON",
+   "narrative": "New CLI command dumps all stored observations to a portable JSON file for backup."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed CORS preflight failure",
+   "narrative": "OPTIONS requests were rejected by auth middleware; moved CORS handling before authentication."
+  },
+  {
+   "type": "discovery",
+   "title": "Docker image size dominated by build cache",
+   "narrative": "Multi-stage build with a distroless runtime reduced the image from 1.2GB to 80MB."
+  },
+  {
+   "type": "decision",
+   "title": "Structured logging with zerolog",
+   "narrative": "JSON logs with fields are easier to filter in aggregation than free-form strings."
+  },
+  {
+   "type": "feature",
+   "title": "Full text search with FTS5",
+   "narrative": "Keyword queries use SQLite FTS5 with porter stemming alongside vector similarity."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed panic on nil config",
+   "narrative": "Missing settings file returned a nil pointer; defaults are now loaded instead."
+  },
+  {
+   "type": "discovery",
+   "title": "GC pauses from large slices",
+   "narrative": "Preallocating slice capacity removed repeated growth and lowered p99 latency."
+  },
+  {
+   "type": "decision",
+   "title": "Graceful shutdown on SIGTERM",
+   "narrative": "Server drains in-flight requests for 30 seconds before exiting so deploys drop nothing."
+  },
+  {
+   "type": "refactor",
+   "title": "Replaced global state with dependency injection",
+   "narrative": "Services receive their stores through constructors, which makes tests independent."
+  },
+  {
+   "type": "feature",
+   "title": "OAuth login with GitHub",
+   "narrative": "Users authenticate via the GitHub authorization code flow and receive a session cookie."
+  },
+  {
+   "type": "bugfix",
+   "title": "Fixed flaky integration test",
+   "narrative": "The test relied on sleep; replaced with polling on a readiness condition."
+  },
+  {
+   "type": "discovery",
+   "title": "Git hooks slowed commits",
+   "narrative": "Pre-commit ran the full test suite; limited it to changed packages."
+  },
+  {
+   "type": "decision",
+   "title": "Pinned dependency versions",
+   "narrative": "Lockfile committed and CI uses frozen installs to keep builds reproducible."
+  },
+  {
+   "type": "feature",
+   "title": "Webhook retries with dead letter queue",
+   "narrative": "Failed deliveries retry five times and then land in a dead letter table for inspection."
+  },
+  {
+   "type": "discovery",
+   "title": "Unicode normalization broke search",
+   "narrative": "Accented characters did not match until queries and content were NFC normalized."
+  }
+ ],
+ "queries": [
+  {
+   "doc": 0,
+   "query": "why did concurrent writes to the cache crash the program"
+  },
+  {
+   "doc": 1,
+   "query": "how can readers keep working while the database is being written"
+  },
+  {
+   "doc": 2,
+   "query": "where do I scrape request latency numbers from"
+  },
+  {
+   "doc": 3,
+   "query": "goroutines not freed after clients drop connection"
+  },
+  {
+   "doc": 4,
+   "query": "shared function for repeating failed requests with growing delays"
+  },
+  {
+   "doc": 5,
+   "query": "which algorithm protects stored passwords"
+  },
+  {
+   "doc": 6,
+   "query": "can the UI switch to a dark theme"
+  },
+  {
+   "doc": 7,
+   "query": "containers restarted while the model was still loading"
+  },
+  {
+   "doc": 8,
+   "query": "last page of results missing an item"
+  },
+  {
+   "doc": 9,
+   "query": "why do our tests use named cases"
+  },
+  {
+   "doc": 10,
+   "query": "how are abusive clients throttled"
+  },
+  {
+   "doc": 11,
+   "query": "scheduled jobs running late after clocks changed"
+  },
+  {
+   "doc": 12,
+   "query": "query got fast after adding an index"
+  },
+  {
+   "doc": 13,
+   "query": "large source file was broken up by domain"
+  },
+  {
+   "doc": 14,
+   "query": "do we send text to an external embedding API"
+  },
+  {
+   "doc": 15,
+   "query": "how to back up everything I stored"
+  },
+  {
+   "doc": 16,
+   "query": "browser blocked cross-origin request before login check"
+  },
+  {
+   "doc": 17,
+   "query": "how did we make the container image smaller"
+  },
+  {
+   "doc": 18,
+   "query": "why are logs emitted as JSON"
+  },
+  {
+   "doc": 19,
+   "query": "keyword matching with stemming"
+  },
+  {
+   "doc": 20,
+   "query": "crash when settings file is absent"
+  },
+  {
+   "doc": 21,
+   "query": "reduce latency spikes from memory allocation"
+  },
+  {
+   "doc": 22,
+   "query": "what happens to requests during deployment shutdown"
+  },
+  {
+   "doc": 23,
+   "query": "stop using package level variables for services"
+  },
+  {
+   "doc": 24,
+   "query": "sign in with a third party identity provider"
+  },
+  {
+   "doc": 25,
+   "query": "test that fails randomly because of timing"
+  },
+  {
+   "doc": 26,
+   "query": "commit takes too long because of checks"
+  },
+  {
+   "doc": 27,
+   "query": "make builds reproducible across machines"
+  },
+  {
+   "doc": 28,
+   "query": "what happens when a callback delivery fails repeatedly"
+  },
+  {
+   "doc": 29,
+   "query": "accented letters not found when searching"
+  }
+ ]
+}

scripts/eval-search/main.go

@@ -0,0 +1,157 @@
+// Command eval-search measures search quality against a labelled corpus.
+//
+//	eval-search seed <dbdir>        writes the corpus into <dbdir>/claude-mnemonic.db
+//	eval-search run <port>          queries a running worker and prints MRR@10 and recall@5
+package main
+
+import (
+	"context"
+	_ "embed"
+	"encoding/json"
+	"fmt"
+	"io"
+	"net/http"
+	"net/url"
+	"os"
+	"path/filepath"
+	"strconv"
+	"time"
+
+	"github.com/lukaszraczylo/claude-mnemonic/internal/db/gorm"
+	"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
+)
+
+const (
+	project   = "evalproj"
+	sessionID = "eval-session"
+	dbFile    = "claude-mnemonic.db"
+	recallAt  = 5
+	mrrAt     = 10
+)
+
+//go:embed corpus.json
+var corpusJSON []byte
+
+type corpus struct {
+	Docs []struct {
+		Type      string `json:"type"`
+		Title     string `json:"title"`
+		Narrative string `json:"narrative"`
+	} `json:"docs"`
+	Queries []struct {
+		Query string `json:"query"`
+		Doc   int    `json:"doc"`
+	} `json:"queries"`
+}
+
+func main() {
+	if len(os.Args) != 3 {
+		fmt.Fprintln(os.Stderr, "usage: eval-search seed <dbdir> | run <port>")
+		os.Exit(2)
+	}
+	var c corpus
+	if err := json.Unmarshal(corpusJSON, &c); err != nil {
+		fatal(err)
+	}
+	var err error
+	switch os.Args[1] {
+	case "seed":
+		err = seed(c, os.Args[2])
+	case "run":
+		err = run(c, os.Args[2])
+	default:
+		err = fmt.Errorf("unknown mode %q", os.Args[1])
+	}
+	if err != nil {
+		fatal(err)
+	}
+}
+
+func fatal(err error) {
+	fmt.Fprintln(os.Stderr, "error:", err)
+	os.Exit(1)
+}
+
+// seed stores docs in order, so doc i gets observation id i+1.
+func seed(c corpus, dir string) error {
+	if err := os.MkdirAll(dir, 0o750); err != nil {
+		return err
+	}
+	store, err := gorm.NewStore(gorm.Config{Path: filepath.Join(dir, dbFile), MaxConns: 1})
+	if err != nil {
+		return err
+	}
+	defer func() { _ = store.Close() }()
+	obsStore := gorm.NewObservationStore(store, nil, nil, nil)
+	for i, d := range c.Docs {
+		_, _, err := obsStore.StoreObservation(context.Background(), sessionID, project, &models.ParsedObservation{
+			Type:      models.ObservationType(d.Type),
+			Title:     d.Title,
+			Narrative: d.Narrative,
+			Concepts:  []string{"eval"},
+		}, i+1, 0)
+		if err != nil {
+			return fmt.Errorf("store doc %d: %w", i, err)
+		}
+	}
+	return nil
+}
+
+type obsRef struct {
+	ID int64 `json:"id"`
+}
+
+func printRanks(query string, want int64, got []obsRef) {
+	pos := -1
+	for i, o := range got {
+		if o.ID == want {
+			pos = i + 1
+			break
+		}
+	}
+	fmt.Printf("rank=%d results=%d %q\n", pos, len(got), query)
+}
+
+func run(c corpus, port string) error {
+	client := &http.Client{Timeout: 20 * time.Second}
+	var mrr, recall, results float64
+	for _, q := range c.Queries {
+		u := fmt.Sprintf("http://127.0.0.1:%s/api/context/search?project=%s&query=%s", port, project, url.QueryEscape(q.Query))
+		resp, err := client.Get(u) // #nosec G704 -- dev tool, loopback URL from a numeric port
+		if err != nil {
+			return err
+		}
+		body, err := io.ReadAll(resp.Body)
+		_ = resp.Body.Close()
+		if err != nil {
+			return err
+		}
+		var out struct {
+			Observations []obsRef `json:"observations"`
+		}
+		if err := json.Unmarshal(body, &out); err != nil {
+			return fmt.Errorf("decode %q: %w", q.Query, err)
+		}
+		results += float64(len(out.Observations))
+		want := int64(q.Doc + 1)
+		if os.Getenv("EVAL_VERBOSE") != "" {
+			printRanks(q.Query, want, out.Observations)
+		}
+		for rank, o := range out.Observations {
+			if o.ID != want {
+				continue
+			}
+			if rank < mrrAt {
+				mrr += 1 / float64(rank+1)
+			}
+			if rank < recallAt {
+				recall++
+			}
+			break
+		}
+	}
+	n := float64(len(c.Queries))
+	fmt.Printf("queries=%d MRR@%d=%s recall@%d=%s avg_results=%s\n", len(c.Queries), mrrAt, strconv.FormatFloat(mrr/n, 'f', 4, 64),
+		recallAt, strconv.FormatFloat(recall/n, 'f', 4, 64), strconv.FormatFloat(results/n, 'f', 2, 64))
+	return nil
+}

ui/package.json

@@ -10,19 +10,19 @@
     "type-check": "vue-tsc --noEmit"
   },
   "dependencies": {
-    "vis-data": "^8.0.4",
-    "vis-network": "^10.1.0",
-    "vue": "^3.5.34"
+    "vis-data": "^8.0.5",
+    "vis-network": "^10.1.2",
+    "vue": "^3.5.43"
   },
   "devDependencies": {
-    "@fortawesome/fontawesome-free": "^7.2.0",
-    "@tailwindcss/postcss": "^4.3.0",
-    "@types/node": "^25.9.1",
-    "@vitejs/plugin-vue": "^6.0.7",
-    "postcss": "^8.5.15",
-    "tailwindcss": "^4.3.0",
+    "@fortawesome/fontawesome-free": "^7.3.1",
+    "@tailwindcss/postcss": "^4.3.3",
+    "@types/node": "^26.0.0",
+    "@vitejs/plugin-vue": "^6.0.9",
+    "postcss": "^8.5.28",
+    "tailwindcss": "^4.3.3",
     "typescript": "~6.0.3",
-    "vite": "^8.0.14",
-    "vue-tsc": "^3.3.1"
+    "vite": "^8.3.0",
+    "vue-tsc": "^3.3.11"
   }
 }

ui/package.json.tpl

@@ -10,19 +10,19 @@
     "type-check": "vue-tsc --noEmit"
   },
   "dependencies": {
-    "vis-data": "^8.0.4",
-    "vis-network": "^10.1.0",
-    "vue": "^3.5.34"
+    "vis-data": "^8.0.5",
+    "vis-network": "^10.1.2",
+    "vue": "^3.5.43"
   },
   "devDependencies": {
-    "@fortawesome/fontawesome-free": "^7.2.0",
-    "@tailwindcss/postcss": "^4.3.0",
-    "@types/node": "^25.9.1",
-    "@vitejs/plugin-vue": "^6.0.7",
-    "postcss": "^8.5.15",
-    "tailwindcss": "^4.3.0",
+    "@fortawesome/fontawesome-free": "^7.3.1",
+    "@tailwindcss/postcss": "^4.3.3",
+    "@types/node": "^26.0.0",
+    "@vitejs/plugin-vue": "^6.0.9",
+    "postcss": "^8.5.28",
+    "tailwindcss": "^4.3.3",
     "typescript": "~6.0.3",
-    "vite": "^8.0.14",
-    "vue-tsc": "^3.3.1"
+    "vite": "^8.3.0",
+    "vue-tsc": "^3.3.11"
   }
 }