@inetafrica/open-claudia 2.6.58 → 2.7.0

package/CHANGELOG.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## v2.7.0
+- **Tools become memory objects (tool-first architecture, Phase 1).** A tool is no longer a flat script — it's a directory: `tools/<name>/tool` (the executable), `TOOL.md` (Interface · Known issues · State · Journal — the curated, human-readable condition of the tool), and `state.json` (machine telemetry, runtime-written, gitignored). The tools dir is now a **git repository**: every add, metadata change, note, and removal auto-commits (with a per-invocation identity, never touching git config), so `git log` *is* the upgrade history and any change is one revert from undone. `tool show` is tiered disclosure: header metadata, live telemetry, TOOL.md, and the recent commit log — the source only with `--source`, so reading about a tool no longer costs its whole body in context.
+- **Risk tiers + run gate.** Every tool declares `risk: read-only | write | destructive` in its header (absent = treated as write, fail-safe). `tool run` now enforces the ask-first rule mechanically: read-only runs freely; write requires `--yes`; destructive requires `--yes-destructive` — and a plain `--yes` does **not** unlock a destructive tool. Refusals exit 3 with a clear message. The flags pass through to the tool unstripped, so tools with their own confirmation gates (e.g. prod-k8s) keep working. `tool add`/`tool set` accept `--risk`; adding without it defaults to write and says so.
+- **Run telemetry stamped at the point of use.** `tool run` itself records every execution into the tool's `state.json`: run count, last used, last exit, last success/failure, per-verb health (first non-flag arg), and a rolling history of the last 20 invocations with timing. A failing run prints a nudge to journal the defect (`tool note <name> --issue "..."`). This is the v1.2 health doctrine in code: no smoke tests, no health crons — health is verified by use, and breakage is captured automatically where it happens.
+- **`tool scaffold`, `tool note`, `tool migrate`.** `scaffold <name>` creates a ready-to-extend verb-dispatch stub (node or bash) with full header, TOOL.md skeleton, and initial telemetry — and refuses if the tool exists ("extend it instead"). `note <name> --issue|--state|--journal` maintains TOOL.md from the CLI: issues and journal lines insert newest-first; `--state` rewrites the State section (it describes *now*, not history). `migrate` converts legacy flat-file tools into directories — one commit each, sidecar telemetry carried over, TOOL.md generated — and runs automatically on first CLI use, so existing tools arrive in the new layout with their memory intact.
+- **Secrets can no longer be saved into a tool.** The add-time secret lint is now **blocking** (was advisory): `tool add`, `tool set`, and `tool note` refuse content matching credential patterns, because the git-backed dir would remember the secret forever. Other lints (requires mismatch, syntax check, dangling pack) stay advisory. Extends `test-tools.js` end to end: layout, risk gate matrix, per-verb telemetry, secret refusal, migration, scaffold, git history.
+
 ## v2.6.58
 - **Tiered recall gate — stop paying 15 seconds for "thanks".** Measured over 700+ live turns, the old discoverer pre-gate returned true whenever *any* seed matched, so it gated just 0.4% of turns — a bare "ok" with an incidental keyword hit still paid the full seed → graph → walker pass (p50 ~15s). A new `recallTier()` classifies each turn into three tiers: **skip** (pleasantries/acks up to 4 words *regardless of seeds*, emoji-only, or ≤2 words with no seeds — no recall at all), **seeds** (short command-like turns ≤4 words — user-origin keyword seeds inject directly with no graph expansion, no walker, no excerpts; the classic-engine baseline at ~ms cost), and **full** (substantive turns — the whole pipeline). The tier is logged per turn and the metrics summary now tracks the seeds-only share alongside the gated share.
 - **Walker candidate cap.** The latency deep-dive showed the walk itself dominates, not process spawn: 15–40 candidates × 600-char excerpts = 10–25KB prompts to the haiku judge on every substantive turn. Full-tier candidates are now priority-ordered — user-origin seeds by match score, then context seeds, then graph-activated nodes by activation — and capped at `RECALL_WALKER_MAX_CANDIDATES` (default 14), so the judge reads the strongest few instead of everything the graph touched.

package/README.md

@@ -267,7 +267,7 @@ Open Claudia layers three memory systems on top of the backend's native sessions
 
 **Recall engines** — how packs and entities get matched and surfaced is pluggable per chat via `/engine` (or the `RECALL_ENGINE` env default). **classic** (the default) is keyword FTS plus a relevance judge with headline injection — stable and unchanged. **discoverer** (opt-in) adds a typed-edge graph over the same corpus (`parent`/`governed-by`/`related` edges with weights in `recall-graph.db`) and runs: a pre-gate that skips recall on trivial turns → FTS seeding → spreading activation across the graph (1–2 hops — auto-pulls cross-cutting concerns the query never named) → a walker that reads each candidate and returns the genuinely-relevant set with one-line why-bullets (fail-open to keyword seeds, so it never recalls worse than classic). Edges form structurally from pack `parent` frontmatter and `[[links]]`, and strengthen via Hebbian co-use when the agent opens packs together (📖); weights decay over time. Inspect with `open-claudia recall-stats` and `open-claudia recall graph [--sync]`, or flip on `/recall` to watch — per turn — which packs/entities surfaced and why, right in the chat. Switch back any time with `/engine classic`.
 
-**Dream consolidation** — while the per-turn reviewer takes quick notes, *dream* is the slow overnight pass (default 4am, on a high-tier model — opus by default, set `DREAM_TIER` or `DREAM_MODEL`): it merges packs that drifted into the same topic, builds parent/sub pack trees with umbrella summaries, tightens descriptions and tags so the router matches with less noise, dedupes entities, cross-links notes, and tends the recall graph (structural sync, weight decay, orphan prune). Anything merged away is backed up under `~/.open-claudia/backup/dream-<stamp>/` first, and every dream that changes something reports in chat. Configure with `DREAM_CRON` / `DREAM_MODEL`, disable with `DREAM=off`.
+**Dream consolidation** — while the per-turn reviewer takes quick notes, *dream* is the slow overnight pass (default 4am, on a high-tier model — opus by default, set `DREAM_TIER` or `DREAM_MODEL`): it merges packs that drifted into the same topic, builds parent/sub pack trees with umbrella summaries, tightens descriptions and tags so the router matches with less noise, dedupes entities, cross-links notes, and tends the recall graph (structural sync, weight decay, orphan prune). The pass is *evidence-grounded*: per-turn recall telemetry (what surfaced, what got kept, what the agent actually opened) feeds the prompt, so archive/merge calls rest on usage numbers rather than vibes. Most nights run as cheap *deltas* — full pack bodies only for what changed since the last dream plus graph neighbours and pre-computed merge candidates; a full-corpus sweep runs every `DREAM_FULL_SWEEP_DAYS` (30). Deterministic phases run even if the model call fails: journal backfill dedupe, weakening of graph nodes that keep arriving but never get kept, co-rescue edge reinforcement, episodic index tending, and a memory-health report (rescue rate, noise, latency, spend) in the morning chat summary. Dream may also tune one bounded recall knob per night (`recall-tuning.json`) — every change is checked against the next window's health and auto-rolled-back if rescue drops or noise rises; env pins always win. Anything merged away is backed up under `~/.open-claudia/backup/dream-<stamp>/` first, and every dream that changes something reports in chat. Configure with `DREAM_CRON` / `DREAM_MODEL`, disable with `DREAM=off`.
 
 **Personality** — your `soul.md` holds identity and hard rules; `~/.open-claudia/persona.md` holds the voice on top — tone, quirks, emoji habits. It feeds into the system prompt and the dream pass may evolve it gently (bounded, backed up, announced). Edit it directly any time.
 
@@ -279,6 +279,7 @@ open-claudia entity list|show <slug>|match "<text>"|note <name> "<text>"|remove
 open-claudia dream [--dry-run]               # run the consolidation pass now
 open-claudia recall-stats                    # discoverer-engine metrics summary
 open-claudia recall graph [--sync]           # recall-graph node/edge stats; --sync rebuilds structural edges
+open-claudia kpi [--json|--html|--knobs]     # harness KPIs by version+model; --html writes a chart report, --knobs shows dream-tuned knob state
 open-claudia transcript-search "<query>"     # alias: ts; --all for every project
 open-claudia transcript-window "<pattern>"   # alias: tw; hits with surrounding turns
 ```
@@ -436,8 +437,11 @@ All stored in `~/.open-claudia/`:
 | `MEMORY_RECALL_MAX_CHARS` | No | Hard cap for auto-injected pack/entity memory per turn (default `9000`, `off` disables auto recall injection) |
 | `RECALL_ENGINE` | No | Default recall engine when a chat hasn't set one via `/engine` (`classic` or `discoverer`, default `classic`) |
 | `RECALL_GRAPH_DB` / `RECALL_METRICS` | No | Override the discoverer graph DB path; `off` on metrics disables per-turn recall logging |
-| `RECALL_WALKER_MAX_CANDIDATES` | No | Cap on candidates sent to the discoverer's walker judge per turn (default `14`) |
-| `RECALL_EPISODES` / `RECALL_EPISODE_LIMIT` | No | `off` disables episodic transcript candidates in recall; limit caps transcript hits per turn (default `3`) |
+| `RECALL_WALKER_MAX_CANDIDATES` | No | Cap on candidates sent to the discoverer's walker judge per turn (default `14`; dream-tunable 8–20, env pins it) |
+| `RECALL_EPISODES` / `RECALL_EPISODE_LIMIT` | No | `off` disables episodic transcript candidates in recall; limit caps transcript hits per turn (default `3`; dream-tunable 1–5) |
+| `RECALL_SEEDS_TIER_MAX_WORDS` | No | Turns at or under this word count take the fast seeds-only recall path (default `4`; dream-tunable 2–6) |
+| `RECALL_DECAY_HALF_LIFE_DAYS` | No | Half-life for recall-graph edge decay during dream tending (default `60`; dream-tunable 10–90) |
+| `RECALL_CASCADE` / `RECALL_CASCADE_SHADOW_RATE` | No | `off` disables the deterministic keep/drop cascade before the walker judge; shadow rate is the fraction of cascade verdicts also judged to audit agreement (default `0.1`) |
 | `PROJECT_TRANSCRIPTS` | No | Enable redacted project transcripts (default `true`) |
 | `TRANSCRIPT_MAX_ENTRY_CHARS` | No | Max chars per transcript entry (default `12000`) |
 | `TRANSCRIPTS_DIR` / `PACKS_DIR` / `ENTITIES_DIR` | No | Override storage directories |
@@ -448,6 +452,7 @@ All stored in `~/.open-claudia/`:
 | `DREAM_CRON` | No | Schedule for the dream pass (default `0 4 * * *`) |
 | `DREAM_MODEL` | No | Explicit model override for the dream pass (otherwise picked from `DREAM_TIER`) |
 | `DREAM_TIER` | No | Model tier for the dream pass: `low` (haiku) / `medium` (sonnet) / `high` (opus, default) |
+| `DREAM_FULL_SWEEP_DAYS` | No | Days between full-corpus dream sweeps; other nights are cheap deltas over recently-touched packs (default `30`) |
 | `PERSONA_FILE` | No | Override the persona file location |
 | `WEB_UI` / `WEB_PORT` / `WEB_PASSWORD` | No | Web UI toggle, port, and password |
 | `WHISPER_CLI` / `WHISPER_MODEL` | No | whisper.cpp binary and model for voice notes |

package/bin/cli.js

@@ -318,6 +318,10 @@ switch (command) {
     require("./recall").run(["stats", ...args.slice(1)]);
     break;
   }
+  case "kpi": {
+    require("./kpi").run(args.slice(1));
+    break;
+  }
   case "recall": {
     require("./recall").run(args.slice(1));
     break;
@@ -370,7 +374,7 @@ Memory tools:
   open-claudia transcript-window <pattern>   Search project transcript, show hits with context
                                              (alias: tw; --help for options)
   open-claudia pack list|show|match|archive|restore|archived  Context packs: living topic docs (skills + memory)
-  open-claudia tool list|search|show|add|set|edit|run|remove Reusable tools: executable scripts the agent saves & re-runs (keyring preauth)
+  open-claudia tool list|search|show|scaffold|add|set|note|edit|run|migrate|remove  Reusable tools: git-tracked dirs (exec + TOOL.md + telemetry), risk-gated runs
   open-claudia entity list|show|match|note   Entity notes: people/places/projects memory
   open-claudia lessons list|add|remove|show  Always-loaded learned rules (cross-cutting, promoted after a miss)
   open-claudia ideas list|add|remove|show    Self-improvement backlog (captured by the nightly dream)

package/bin/kpi.js

@@ -0,0 +1,55 @@
+// open-claudia kpi [--json] [--html [--out <path>]] [--knobs]
+//
+// Compare harness performance across versions and models: rescue rate, noise,
+// latency by tier, cost/turn, cascade + walker health — aggregated from the
+// version-stamped recall telemetry, plus the nightly dream KPI snapshots.
+
+const path = require("path");
+
+const HELP = `
+Harness KPIs by version.
+
+  open-claudia kpi                 Version-vs-version table
+  open-claudia kpi --json          Raw aggregates
+  open-claudia kpi --html          Write a self-contained HTML report (charts), print its path
+  open-claudia kpi --html --out p  Write the report to a specific path
+  open-claudia kpi --knobs         Current recall-knob values + dream tuning history
+
+Data sources: recall-metrics.jsonl (per-turn, version+model stamped) and
+recall-kpi.jsonl (one snapshot per dream night).
+`;
+
+function run(args) {
+  if (args.includes("--help") || args[0] === "help") { console.log(HELP); return; }
+  const kpi = require(path.join(__dirname, "..", "core", "recall", "kpi"));
+
+  if (args.includes("--knobs")) {
+    const tuning = require(path.join(__dirname, "..", "core", "recall", "tuning"));
+    console.log("Recall knobs (env pin > dream tuning > default)");
+    console.log("───────────────────────────────────────────────");
+    for (const k of tuning.knobTable()) {
+      console.log(`${k.name.padEnd(22)} ${String(k.current).padEnd(6)}${k.pinned ? " [pinned by env]" : k.current !== k.default ? " [dream-tuned]" : ""}`);
+    }
+    const hist = tuning.history();
+    if (hist.length) {
+      console.log("\nTuning history");
+      for (const h of hist.slice(-10)) console.log(`  ${h.ts.slice(0, 10)} ${h.knob}: ${h.from} → ${h.to} — ${h.reason}`);
+    }
+    return;
+  }
+
+  if (args.includes("--html")) {
+    const i = args.indexOf("--out");
+    const out = i !== -1 ? args[i + 1] : undefined;
+    console.log(kpi.writeHtmlReport(out));
+    return;
+  }
+
+  const rows = kpi.aggregate();
+  if (args.includes("--json")) { console.log(JSON.stringify({ versions: rows, snapshots: kpi.trend() }, null, 2)); return; }
+  console.log(kpi.renderTable(rows));
+  const snaps = kpi.trend();
+  if (snaps.length) console.log(`\n${snaps.length} nightly snapshot(s) in recall-kpi.jsonl — \`open-claudia kpi --html\` for charts.`);
+}
+
+module.exports = { run, HELP };

package/bin/tool.js

@@ -1,23 +1,38 @@
-// CLI: manage and run reusable tools — executable scripts the agent saves so a
-// procedure it worked out once becomes a re-runnable command, not a re-typed
-// heredoc. The executable sibling of context packs (`open-claudia pack`).
+// CLI: manage and run reusable tools — the interface operational work happens
+// through. Tool-first loop: search → exists: use it → missing a verb: extend →
+// nothing: scaffold, then work through the tool.
 //
 //   open-claudia tool list                       — index (name — description [skill])
 //   open-claudia tool search <query>             — lexical match (find before adding a dup)
-//   open-claudia tool show <name>                — full docs, path, keyring status
-//   open-claudia tool add <path> [--name n]      — register a script as a tool
-//       [--pack <dir>] [--desc "..."] [--requires "k1,k2"] [--usage "..."]
+//   open-claudia tool show <name> [--source]     — TOOL.md, telemetry, history (source with --source)
+//   open-claudia tool scaffold <name>            — create a new tool skeleton (dir + stub + TOOL.md)
+//       [--pack <dir>] [--desc "..."] [--risk read-only|write|destructive]
+//       [--requires "k1,k2"] [--usage "..."] [--lang node|bash]
+//   open-claudia tool add <path> [--name n]      — register an existing script as a tool
+//       [--pack <dir>] [--desc "..."] [--risk tier] [--requires "k1,k2"] [--usage "..."]
 //   open-claudia tool set <name> [--desc ...]    — fix a tool's metadata in place
-//       [--pack <dir>] [--requires "k1,k2"] [--usage "..."]
+//       [--pack <dir>] [--risk tier] [--requires "k1,k2"] [--usage "..."]
+//   open-claudia tool note <name>                — append to TOOL.md (auto-committed)
+//       [--issue "..."] [--state "..."] [--journal "..."]
 //   open-claudia tool edit <name>                — print the file path to open & edit
-//   open-claudia tool run <name> [args...]       — run it with keyring pre-loaded
+//   open-claudia tool run <name> [args...]       — run it (keyring pre-loaded, risk-gated)
+//   open-claudia tool migrate                    — convert legacy flat-file tools to directories
 //   open-claudia tool remove <name>              — delete one
 //   open-claudia tool path                       — print the tools directory
 //
-// Fix before fork: when a tool is wrong, prefer `tool set` (metadata) or `tool
-// edit` (open the file) over adding a near-duplicate. `add` lints the source on
-// save — flags hardcoded secrets, requires/keyring mismatches, syntax errors,
-// and dangling pack links — all advisory, never blocking.
+// A tool is a directory: executable + TOOL.md (Interface · Known issues ·
+// State · Journal) + state.json (runtime telemetry). The dir is git-tracked;
+// every change commits, so `git -C $(open-claudia tool path) log` is the
+// upgrade history.
+//
+// Risk tiers gate `tool run`: write-tier needs --yes, destructive-tier needs
+// --yes-destructive — get the user's approval first; the flag records that
+// deliberate step. Read-only tools run freely.
+//
+// Fix before fork: when a tool is wrong, prefer `tool set` (metadata), `tool
+// note` (docs), or `tool edit` (body) over adding a near-duplicate. Hardcoded
+// secrets BLOCK a save; other lints (requires/keyring mismatch, syntax,
+// dangling pack link) stay advisory.
 //
 // Credentials: a tool runs with the operational keyring merged into its env, so
 // reference creds as $NAME inside the script. `open-claudia keyring list` shows
@@ -25,6 +40,7 @@
 
 const { spawnSync } = require("child_process");
 const tools = require("../core/tools");
+const repo = require("../core/tool-repo");
 
 // Minimal flag parser: pulls --key value (and --key=value) out of argv, returns
 // { positional, flags }.
@@ -88,6 +104,17 @@ function run(args) {
   const cmd = (args[0] || "list").toLowerCase();
   const rest = args.slice(1);
 
+  // Auto-migrate legacy flat-file tools to the directory layout on first use
+  // (idempotent, one git commit per tool, telemetry carried over).
+  if (cmd !== "path") {
+    try {
+      if (repo.hasLegacyTools()) {
+        const { migrated } = repo.migrateLegacyTools();
+        if (migrated.length) console.error(`(migrated ${migrated.length} tool(s) to directory layout: ${migrated.join(", ")})`);
+      }
+    } catch (e) { /* best-effort */ }
+  }
+
   switch (cmd) {
     case "list":
     case "ls": {
@@ -98,7 +125,8 @@ function run(args) {
       console.log(`${all.length} reusable tool(s) — run via 'open-claudia tool run <name>':\n`);
       for (const t of all) {
         const skill = t.pack ? `  [skill: ${t.pack}]` : "";
-        console.log(`• ${t.name} — ${t.description || "(no description)"}${skill}`);
+        const risk = t.risk === "read-only" ? "" : `  [${t.risk || "write?"}]`;
+        console.log(`• ${t.name} — ${t.description || "(no description)"}${skill}${risk}`);
       }
       console.log(`\nDocs: open-claudia tool show <name>   ·   Dir: ${tools.TOOLS_DIR}`);
       break;
@@ -125,13 +153,15 @@ function run(args) {
 
     case "show":
     case "cat": {
-      const name = rest[0];
-      if (!name) { console.error("Usage: tool show <name>"); process.exitCode = 1; return; }
+      const { positional, flags } = parseFlags(rest);
+      const name = positional[0];
+      if (!name) { console.error("Usage: tool show <name> [--source]"); process.exitCode = 1; return; }
       const t = tools.findTool(name);
       if (!t) { console.error(`No tool named "${name}". Run: open-claudia tool list`); process.exitCode = 1; return; }
       console.log(`Tool: ${t.name}`);
       if (t.description) console.log(`Description: ${t.description}`);
       if (t.pack) console.log(`Skill pack: ${t.pack}  (open-claudia pack show ${t.pack})`);
+      console.log(`Risk: ${t.risk || "(undeclared — treated as write)"}`);
       console.log(`Usage: open-claudia tool run ${t.name}${t.usage ? "   (" + t.usage + ")" : ""}`);
       if (t.requires.length) {
         const missing = tools.missingRequires(t);
@@ -139,6 +169,22 @@ function run(args) {
         console.log(`Requires keyring keys: ${t.requires.join(", ")}  (${status})`);
       }
       console.log(`File: ${t.file}${t.executable ? "" : "  (not executable!)"}`);
+
+      // Telemetry: overall + per-verb health from state.json.
+      if (t.runCount || t.lastUsed) {
+        const exit = t.lastExit === undefined ? "" : ` · last exit ${t.lastExit}`;
+        console.log(`Runs: ${t.runCount}${t.lastUsed ? ` · last used ${t.lastUsed.slice(0, 16).replace("T", " ")}` : ""}${exit}`);
+      }
+      if (t.verbs && Object.keys(t.verbs).length) {
+        const rows = Object.entries(t.verbs).map(([v, s]) =>
+          `  • ${v}: ${s.runs} run(s), last exit ${s.lastExit}${s.lastSuccess ? `, last success ${s.lastSuccess.slice(0, 10)}` : ""}`);
+        console.log("Verbs:\n" + rows.join("\n"));
+      }
+      try {
+        const log = repo.toolLog(t.name, 5);
+        if (log.length) console.log("Recent changes:\n" + log.map((l) => "  " + l).join("\n"));
+      } catch (e) { /* git optional */ }
+
       // Directed tool-graph: what tends to run right after / before this one.
       try {
         const graph = require("../core/tool-graph");
@@ -156,7 +202,13 @@ function run(args) {
           }
         }
       } catch (e) { /* graph optional (old node) */ }
-      console.log(`\n----- source -----\n${t.content}`);
+
+      // Tiered disclosure: TOOL.md is the manual; source only when modifying.
+      const doc = tools.readToolDoc(t.name);
+      if (doc) console.log(`\n----- TOOL.md -----\n${doc.trim()}`);
+      if (flags.source) console.log(`\n----- source -----\n${t.content}`);
+      else if (!doc) console.log(`\n----- source (no TOOL.md yet) -----\n${t.content}`);
+      else console.log(`\n(source: open-claudia tool show ${t.name} --source)`);
       break;
     }
 
@@ -173,10 +225,14 @@ function run(args) {
           name: typeof flags.name === "string" ? flags.name : undefined,
           pack: typeof flags.pack === "string" ? flags.pack : undefined,
           description: typeof flags.desc === "string" ? flags.desc : (typeof flags.description === "string" ? flags.description : undefined),
+          risk: typeof flags.risk === "string" ? flags.risk : undefined,
           requires: typeof flags.requires === "string" ? flags.requires.split(/[,\s]+/).filter(Boolean) : undefined,
           usage: typeof flags.usage === "string" ? flags.usage : undefined,
         });
-        console.log(`Saved tool "${t.name}"${t.pack ? ` (skill: ${t.pack})` : ""}.`);
+        console.log(`Saved tool "${t.name}"${t.pack ? ` (skill: ${t.pack})` : ""} — risk: ${t.risk}.`);
+        if (t.defaultedRisk) {
+          console.log(`  No --risk given → defaulted to "write" (runs will demand --yes). If it only reads, fix: open-claudia tool set ${t.name} --risk read-only`);
+        }
         console.log(`Run it: open-claudia tool run ${t.name}`);
         if (t.requires.length) {
           const missing = tools.missingRequires(t);
@@ -217,17 +273,21 @@ function run(args) {
       if (typeof flags.desc === "string") patch.description = flags.desc;
       else if (typeof flags.description === "string") patch.description = flags.description;
       if (typeof flags.pack === "string") patch.pack = flags.pack;
+      if (typeof flags.risk === "string") patch.risk = flags.risk;
       if (typeof flags.requires === "string") patch.requires = flags.requires.split(/[,\s]+/).filter(Boolean);
       if (typeof flags.usage === "string") patch.usage = flags.usage;
       if (Object.keys(patch).length === 0) {
-        console.error('Nothing to set. Pass at least one of --desc / --pack / --requires / --usage. Body edits: open-claudia tool edit ' + name);
+        console.error('Nothing to set. Pass at least one of --desc / --pack / --risk / --requires / --usage. Body edits: open-claudia tool edit ' + name);
         process.exitCode = 1; return;
       }
-      const updated = tools.updateToolHeader(name, patch);
+      let updated;
+      try { updated = tools.updateToolHeader(name, patch); }
+      catch (e) { console.error(`Could not update "${name}": ${e.message}`); process.exitCode = 1; return; }
       if (!updated) { console.error(`Could not update "${name}".`); process.exitCode = 1; return; }
       console.log(`Updated tool "${updated.name}".`);
       console.log(`  Description: ${updated.description || "(none)"}`);
       if (updated.pack) console.log(`  Skill pack:  ${updated.pack}`);
+      console.log(`  Risk:        ${updated.risk || "(undeclared — treated as write)"}`);
       if (updated.requires.length) console.log(`  Requires:    ${updated.requires.join(", ")}`);
       if (updated.usage) console.log(`  Usage:       ${updated.usage}`);
       reportSafety(updated);
@@ -252,14 +312,108 @@ function run(args) {
       if (!name) { console.error("Usage: tool run <name> [args...]"); process.exitCode = 1; return; }
       const t = tools.findTool(name);
       if (!t) { console.error(`No tool named "${name}". Run: open-claudia tool list`); process.exitCode = 1; return; }
+      const toolArgs = rest.slice(1);
+
+      // Risk-tier gate: write needs --yes, destructive needs --yes-destructive.
+      // The flag is passed through to the tool (which may have its own gate).
+      const gate = tools.runGate(t, toolArgs);
+      if (!gate.ok) { console.error(gate.message); process.exitCode = 3; return; }
+
       const missing = tools.missingRequires(t);
       if (missing.length) {
         console.error(`Cannot run ${t.name}: missing keyring keys ${missing.join(", ")}. Set them with 'open-claudia keyring set <name> <value>'.`);
         process.exitCode = 1; return;
       }
-      const r = spawnSync(t.file, rest.slice(1), { stdio: "inherit", env: tools.runEnv() });
-      if (r.error) { console.error(`Failed to run ${t.name}: ${r.error.message}`); process.exitCode = 1; return; }
-      process.exitCode = typeof r.status === "number" ? r.status : 1;
+      const started = Date.now();
+      const r = spawnSync(t.file, toolArgs, { stdio: "inherit", env: tools.runEnv() });
+      const ms = Date.now() - started;
+      if (r.error) {
+        tools.recordRunResult(t.name, { args: toolArgs, exit: -1, ms });
+        console.error(`Failed to run ${t.name}: ${r.error.message}`);
+        process.exitCode = 1; return;
+      }
+      const exit = typeof r.status === "number" ? r.status : 1;
+      tools.recordRunResult(t.name, { args: toolArgs, exit, ms });
+      if (exit !== 0) {
+        console.error(`(exit ${exit} recorded in ${t.name} telemetry — if this is a real defect, journal it: ` +
+          `open-claudia tool note ${t.name} --issue "<what broke>")`);
+      }
+      process.exitCode = exit;
+      break;
+    }
+
+    case "scaffold":
+    case "new": {
+      const { positional, flags } = parseFlags(rest);
+      const name = positional[0];
+      if (!name) {
+        console.error('Usage: tool scaffold <name> [--pack dir] [--desc "..."] [--risk read-only|write|destructive] [--requires "k1,k2"] [--usage "..."] [--lang node|bash]');
+        process.exitCode = 1; return;
+      }
+      try {
+        const t = repo.scaffoldTool(name, {
+          pack: typeof flags.pack === "string" ? flags.pack : undefined,
+          description: typeof flags.desc === "string" ? flags.desc : (typeof flags.description === "string" ? flags.description : undefined),
+          risk: typeof flags.risk === "string" ? flags.risk : undefined,
+          requires: typeof flags.requires === "string" ? flags.requires.split(/[,\s]+/).filter(Boolean) : [],
+          usage: typeof flags.usage === "string" ? flags.usage : undefined,
+          lang: typeof flags.lang === "string" ? flags.lang : "node",
+        });
+        console.log(`Scaffolded tool "${t.name}" (risk: ${t.risk}).`);
+        console.log(`  Executable: ${t.file}`);
+        console.log(`  Docs:       ${t.docFile}`);
+        console.log(`Fill in the verbs, then work through it: open-claudia tool run ${t.name} <verb>`);
+      } catch (e) {
+        console.error(`Could not scaffold: ${e.message}`); process.exitCode = 1;
+      }
+      break;
+    }
+
+    case "note": {
+      const { positional, flags } = parseFlags(rest);
+      const name = positional[0];
+      const issue = typeof flags.issue === "string" ? flags.issue : null;
+      const state = typeof flags.state === "string" ? flags.state : null;
+      const journal = typeof flags.journal === "string" ? flags.journal : null;
+      if (!name || (!issue && !state && !journal)) {
+        console.error('Usage: tool note <name> [--issue "..."] [--state "..."] [--journal "..."]');
+        process.exitCode = 1; return;
+      }
+      const t = tools.findTool(name);
+      if (!t) { console.error(`No tool named "${name}". Run: open-claudia tool list`); process.exitCode = 1; return; }
+      if (!t.docFile) { console.error(`"${t.name}" is a legacy flat tool — run any tool command to migrate it first.`); process.exitCode = 1; return; }
+      try {
+        tools.assertNoSecrets([issue, state, journal].filter(Boolean).join("\n"), "note");
+        const fs = require("fs");
+        let doc = tools.readToolDoc(t.name) || repo.toolMdSkeleton(t);
+        const date = new Date().toISOString().slice(0, 10);
+        const appendUnder = (heading, line) => {
+          const re = new RegExp(`(##\\s*${heading}[^\\n]*\\n)`, "i");
+          if (re.test(doc)) doc = doc.replace(re, `$1${line}\n`);
+          else doc += `\n## ${heading}\n${line}\n`;
+        };
+        if (issue) appendUnder("Known issues", `- [${date}] ${issue}`);
+        if (state) {
+          // State is a rewrite, not an append — it describes NOW.
+          const re = /(##\s*State[^\n]*\n)([\s\S]*?)(?=\n##\s|$)/i;
+          if (re.test(doc)) doc = doc.replace(re, `$1${state}\n\n`);
+          else doc += `\n## State\n${state}\n`;
+        }
+        if (journal) appendUnder("Journal", `- [${date}] ${journal}`);
+        fs.writeFileSync(t.docFile, doc, { mode: 0o600 });
+        repo.commitTool(t.name, `note ${t.name}: ${(issue || state || journal).slice(0, 60)}`);
+        console.log(`Noted in ${t.name}/TOOL.md${issue ? " (known issue)" : ""}${state ? " (state)" : ""}${journal ? " (journal)" : ""}.`);
+      } catch (e) {
+        console.error(`Could not note: ${e.message}`); process.exitCode = 1;
+      }
+      break;
+    }
+
+    case "migrate": {
+      const { migrated, skipped } = repo.migrateLegacyTools();
+      if (!migrated.length && !skipped.length) console.log("Nothing to migrate — all tools already use the directory layout.");
+      if (migrated.length) console.log(`Migrated: ${migrated.join(", ")}`);
+      if (skipped.length) console.log(`Skipped (no tool header — left untouched): ${skipped.join(", ")}`);
       break;
     }
 
@@ -277,7 +431,7 @@ function run(args) {
       break;
 
     default:
-      console.log('Usage: open-claudia tool [list | search <query> | show <name> | add <path> [flags] | set <name> [flags] | edit <name> | run <name> [args] | remove <name> | path]');
+      console.log('Usage: open-claudia tool [list | search <query> | show <name> [--source] | scaffold <name> [flags] | add <path> [flags] | set <name> [flags] | note <name> [flags] | edit <name> | run <name> [args] | migrate | remove <name> | path]');
   }
 }