geneseed 4.0.0 → 4.2.0

package/js/README.md

@@ -73,6 +73,7 @@ user co-owns, and the hook verbs those emitted configs then run.
 | `hooks-context.mjs` | The `context` verb — SessionStart: session files plus the repo's context docs |
 | `hooks-learn.mjs` | The `learn` verb — Stop/SubagentStop/PreCompact distiller; the hook path's ONE spawn (`$GENESEED_LLM`) |
 | `hooks-prims.mjs` | The Python path/text primitives the hook verbs share (`splitLines`, `readStdin`, a never-throwing `isFile`) |
+| `usage.mjs` | The usage counter `tool-gate` runs: one `{day, kind, name}` line per Skill or subagent call into `notebook/usage.jsonl`. Hook path: builtins only, silent, never throws |
 | `memory-files.mjs` | The memory store's file format — `frontmatter`, `MEMORY.md` index writes, agent lessons, consolidate. No spawn: the CLI and web console import it |
 | `gitref.mjs` | fs/path-only: `gitRootOf`, `gitDirOf`, `currentBranch`, `loopLaunched` — read straight off `.git`, never spawn git. Shared by `hooks.mjs`'s git-gate and `js/loop/cli.mjs`'s commit-message writer |
 | `settings.mjs` | Merges into user-owned `settings.json`/`opencode.json` (one `loadJsonObject` reader for all of them) and the managed blocks |
@@ -82,6 +83,7 @@ user co-owns, and the hook verbs those emitted configs then run.
 | `installs.mjs` | Detects deployed installs and reads back their theme, footprint, posture, mode and loop trust preset |
 | `mcp.mjs` | MCP server presets, the per-host `mcpServers` config read/write, and toggle state |
 | `link.mjs` | `geneseed link`/`unlink` — the PATH shim, and the only Windows USER-Path registry edit |
+| `owned.mjs` | Manifest rel -> path on disk decisions: `ownedWithin`, the containment boundary `uninstall.mjs` and the driver's prune both go through before acting on an `owned` list entry |
 
 **Before editing:** `hooks*.mjs` **are the hook path** — the verdict travels as JSON on stdout and
 every arm exits 0, so one stray printed byte turns a blocking gate silently permissive, and anything
@@ -106,6 +108,7 @@ Everything that inspects an already-built or already-deployed harness and report
 | `validate.mjs` | The `--validate-only` verb: renders a sandbox, scans it for tokens and dead links, own exit contract |
 | `inventory.mjs` | The one catalog walk and its taxonomy tables, read by status, the TUI and the web console |
 | `status.mjs` | `geneseed status` and `version` — the panel data, counts, accent colour, version verdict |
+| `cost.mjs` | What one install injects every session, by part (root file, skill and agent lists, session files), in characters; owns `CARRIER_CEILING`, which the smoke test gates and the console draws |
 | `diff.mjs` | `geneseed diff` — what a deployed install has that a fresh render of `src/` does not |
 | `excludes.mjs` | `geneseed exclude add|remove|list` — the WRITER for `excludes.json`; `hooks.mjs` only reads it |
 | `registry.mjs` | `installs.json` under XDG — the persistent deploy-root list `rebuild-all` re-emits into |
@@ -211,6 +214,9 @@ the deployed harness as JSON.
 | `state.mjs` | `webState` — the resolved install view every endpoint reads, with its cached inventory and doctor |
 | `catalog.mjs` | The Library read model: inventory, constitution tiers, memory/notebook/wiki/config items, `apiCatalog`/`apiItem`, `NotFound` |
 | `api.mjs` | The dashboard and settings reads: overview, recent, themes, setup, doctor, diff, installs, excludes, loops |
+| `update-check.mjs` | Is a newer release on npm? Answers from memory, refreshes in the background (a day when it got an answer, an hour when it did not), `null` on any failure, never asked under `node --test` |
+| `gates-api.mjs` | `GET /api/gates`: gate asks per rule per day over 30 days, read off every installed harness's `notebook/gates.jsonl` (the Overview's sparklines) |
+| `usage-api.mjs` | `GET /api/usage`: the 30-day skill and agent call counts across every installed harness, the never-fired list, and the 90-day prune of each `notebook/usage.jsonl` |
 | `user-files.mjs` | The fingerprint-guarded editors for `user-rules.md` (incl. memory promotion) and `PROFILE.md`, read and write |
 | `actions.mjs` | The other mutating endpoints — memory delete, MCP, excludes, installs, view, restore — plus install/deploy argv |
 | `daemon.mjs` | Detached web start/stop/status/restart, the `.geneseed-web.json` record, and `openUrl` |

package/js/build/driver.mjs

@@ -50,6 +50,9 @@ import {
   GLOBAL_MANIFEST, HOSTS, resolvePath, opencodeConfigDir, claudeConfigDir, bobConfigDir,
   openclaudeConfigDir, hostCatalogsNatively,
 } from '../hosts/hosts.mjs';
+import {
+  hashesOf, ownedHashes, ownedState, ownedWithin,
+} from '../hosts/owned.mjs';
 
 // P5d moved these out of this file for the reason P5c moved the host resolvers: `harness
 // status` renders to count, so `bin/geneseed-cli.mjs` needs the same checkout paths and the
@@ -185,11 +188,38 @@ function writeManifestAtomic(file, data) {
  * Runs AFTER the whole current set is on disk, so a live file is never momentarily absent
  * part-way through an emit. A pre-existing file that was never in the manifest is the
  * user's and is not reachable from here at all.
+ *
+ * `ownedWithin` filters the stale rels before this ever joins one with `oc` — F3
+ * (`docs/specs/2026-10-13-borrowed-hardening.md`): this loop used to `path.join` a manifest
+ * rel straight in, with no containment check, so a crafted per-repo manifest entry of
+ * `../victim.txt` deleted a file outside the install the moment a re-emit called it stale.
+ * `uninstall.mjs`'s owned-file walk already drew this boundary; the prune now goes through it.
+ *
+ * `oldHashes` (Task 4): a stale rel the user has EDITED is kept rather than deleted — the
+ * same "never clobber an edit" rule `claimer` enforces on the write side, applied to the
+ * delete side. `'unknown'`/`'unmodified'` fall straight through to the ordinary delete below,
+ * which is what keeps a pre-Task-3 manifest (no `hashes` at all) behaving exactly as before.
+ *
+ * `editRefused` (Task 4, fix round 1): the rels `claimer` already refused to (over)write this
+ * SAME emit because the user had edited them. Such a rel drops out of `owned` (never written),
+ * which makes it look exactly like `stale` — a rel this build stopped shipping — and without
+ * this exclusion `pruneOwned` would independently re-run `ownedState`, see `'modified'` again,
+ * and print its OWN "kept your edited... (no longer shipped)" right under `claimer`'s "kept
+ * your edited... delete it to get Geneseed's copy back": two warnings about one rel that is in
+ * fact still shipped. Excluded from `stale` before anything is checked or printed — silently,
+ * because `claimer` already said everything there is to say about it.
  */
-function pruneOwned(oc, oldOwned, owned) {
+function pruneOwned(oc, oldOwned, owned, oldHashes = {}, editRefused = []) {
   const now = new Set(owned);
+  const alreadyWarned = new Set(editRefused);
+  const stale = [...new Set(oldOwned)]
+    .filter((r) => !now.has(r) && !alreadyWarned.has(r)).sort();
   const failed = [];
-  for (const rel of [...new Set(oldOwned)].filter((r) => !now.has(r)).sort()) {
+  for (const rel of ownedWithin(oc, stale)) {
+    if (ownedState(oc, rel, oldHashes) === 'modified') {
+      process.stderr.write(`[geneseed] kept your edited ${rel} (no longer shipped)\n`);
+      continue;
+    }
     const victim = path.join(oc, rel);
     try {
       if (isFile(victim)) {
@@ -282,6 +312,7 @@ function emitOpencode(cfg, args, out) {
   const { existed: manifestExisted, doc } = readManifest(manifestPath);
   const oldOwned = (doc && doc.owned) || [];
   const oldDenies = recordedDenies(doc);
+  const oldHashes = hashesOf(doc);
 
   const agentPathRel = relUnder(out, root);
   const agentPath = agentPathRel ? `${agentPathRel}/AGENT.md` : 'AGENT.md';
@@ -293,12 +324,12 @@ function emitOpencode(cfg, args, out) {
     {
       theme: args.theme, out, root, footprint: args.footprint,
       nativeCatalog: hostCatalogsNatively('opencode'), oldOwned, manifestExisted, agentPath,
-      oldDenies,
+      oldDenies, oldHashes,
     });
-  const { owned, stats, cfgName, skillDenies } = rendered;
+  const { owned, stats, cfgName, skillDenies, editRefused } = rendered;
 
   phaseLog('PRUNE');
-  pruneOwned(oc, oldOwned, owned);
+  pruneOwned(oc, oldOwned, owned, oldHashes, editRefused);
 
   phaseLog('MANIFEST');
   writeManifestAtomic(manifestPath, {
@@ -306,6 +337,7 @@ function emitOpencode(cfg, args, out) {
       + 'Do not edit; removed on re-emit. A pre-existing file not in this '
       + 'list is yours and is never touched.',
     owned: [...owned].sort(),
+    hashes: ownedHashes(oc, owned),
     scope: 'project',
     ...(skillDenies.length ? { skill_denies: skillDenies } : {}),
   });
@@ -341,6 +373,7 @@ function emitOpencodeGlobal(cfg, args, out) {
   const { doc } = readManifest(manifestPath);
   const oldOwned = (doc && doc.owned) || [];
   const oldDenies = recordedDenies(doc);
+  const oldHashes = hashesOf(doc);
 
   const agentPath = path.join(cfgDir, 'AGENT.md').split(path.sep).join('/');
 
@@ -349,12 +382,12 @@ function emitOpencodeGlobal(cfg, args, out) {
     {
       theme: args.theme, cfgDir, out,
       footprint: args.footprint, nativeCatalog: hostCatalogsNatively('opencode'),
-      oldOwned, agentPath, oldDenies,
+      oldOwned, agentPath, oldDenies, oldHashes,
     });
-  const { owned, stats, memStatus, nbStatus, cfgName, skillDenies } = rendered;
+  const { owned, stats, memStatus, nbStatus, cfgName, skillDenies, editRefused } = rendered;
 
   phaseLog('PRUNE');
-  pruneOwned(cfgDir, oldOwned, owned);
+  pruneOwned(cfgDir, oldOwned, owned, oldHashes, editRefused);
 
   phaseLog('MANIFEST');
   writeManifestAtomic(manifestPath, {
@@ -362,6 +395,7 @@ function emitOpencodeGlobal(cfg, args, out) {
       + 'Do not edit; removed on re-emit. The memory and notebook '
       + 'stores are NOT listed — they are never deleted.',
     owned: [...owned].sort(),
+    hashes: ownedHashes(cfgDir, owned),
     ...(skillDenies.length ? { skill_denies: skillDenies } : {}),
   });
 
@@ -391,6 +425,7 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
   const oldOwned = (doc && doc.owned) || [];
   const oldManaged = (doc && doc.managed && typeof doc.managed === 'object'
     && !Array.isArray(doc.managed)) ? doc.managed : {};
+  const oldHashes = hashesOf(doc);
 
   // RENDER + WIRE in one child's worth of work. `preambleExclude` is null for every
   // carrier but `CLAUDE.md`, so Bob's `AGENTS.md` does not resolve to one; for a `CLAUDE.md`
@@ -402,12 +437,12 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
     out,
     footprint: args.footprint, nativeCatalog: hostCatalogsNatively(host),
     oldOwned, oldManaged, preambleExclude: preambleExclude(claudeMd, host),
-    hookOpts,
+    hookOpts, oldHashes,
   });
-  const { owned, stats, memStatus, nbStatus, managed } = rendered;
+  const { owned, stats, memStatus, nbStatus, managed, editRefused } = rendered;
 
   phaseLog('PRUNE');
-  pruneOwned(cfgDir, oldOwned, owned);
+  pruneOwned(cfgDir, oldOwned, owned, oldHashes, editRefused);
 
   phaseLog('MANIFEST');
   writeManifestAtomic(manifestPath, {
@@ -417,6 +452,7 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
       + '(settings.json, or settings.local.json at PROJECT scope on Claude/OpenClaude) '
       + 'hooks so uninstall removes exactly those.',
     owned: [...owned].sort(),
+    hashes: ownedHashes(cfgDir, owned),
     managed,
     scope,
   });

package/js/build/emit-claude.mjs

@@ -13,6 +13,7 @@ import {
   managedBlockRemove, managedBlockWrite, mergeClaudeSettings,
   unwireClaudeExcludes, unwireClaudeSettings, wireClaudeExcludes,
 } from '../hosts/settings.mjs';
+import { claimLeaf } from '../hosts/owned.mjs';
 import { writeText } from '../lib/fs.mjs';
 import { get, isDict, isTruthy } from '../lib/json.mjs';
 import { relPosix } from '../lib/text.mjs';
@@ -51,7 +52,7 @@ export function emitClaudeRender(cfg, job) {
   phaseLog('RENDER');
   const {
     theme: themeName, cfgDir, claudeMd, scope, out, footprint, host, nativeCatalog,
-    oldOwned,
+    oldOwned, oldHashes = {},
   } = job;
 
   // `os.path.relpath(cfg, claude_md.parent)` — note the reversed argument order, and
@@ -98,10 +99,16 @@ export function emitClaudeRender(cfg, job) {
   // slim shadow stub whose only job is to have the same filename.
   if (isBob && agentText !== null) {
     const rulesMd = path.join(cfgDir, 'rules', 'geneseed.md');
-    mkdirSync(path.dirname(rulesMd), { recursive: true });
-    writeText(rulesMd, scope === 'project' ? BOB_RULES_STUB
-      : stripCapabilityLinks(prefixedAgentText('../') || agentText));
-    owned.push('rules/geneseed.md');
+    // `claimLeaf` BEFORE `mkdirSync`: `safeLeaf` walks up to the nearest EXISTING ancestor
+    // (`resolvePath`'s own contract), so it needs no directory created first — and creating
+    // `rules/` first would plant an empty directory at a linked ancestor's target the moment
+    // before the refusal fires.
+    if (claimLeaf(cfgDir, rulesMd, 'rules/geneseed.md')) {
+      mkdirSync(path.dirname(rulesMd), { recursive: true });
+      writeText(rulesMd, scope === 'project' ? BOB_RULES_STUB
+        : stripCapabilityLinks(prefixedAgentText('../') || agentText));
+      owned.push('rules/geneseed.md');
+    }
   }
 
   ensureAgentOverridesStub(cfg, cfgDir);
@@ -119,7 +126,7 @@ export function emitClaudeRender(cfg, job) {
   // One shared `claim` (see `claimer`): the skills/agents writer and the Bob command writer
   // below both push into the same `owned` list, so a pre-manifest-install warning still
   // prints once across the whole emit rather than once per writer.
-  const claim = claimer(oldOwned, cfgDir, true);
+  const claim = claimer(oldOwned, cfgDir, true, oldHashes);
   const { nAgents, nSkills, written } = writeNativeLayer(
     items, path.join(cfgDir, 'agents'), path.join(cfgDir, 'skills'),
     loadAgentOverrides(cfgDir),
@@ -160,15 +167,19 @@ export function emitClaudeRender(cfg, job) {
       : host === 'bob' ? ['settings.json'] : [])
       .concat(['context.json', WIKI_FILE, 'agent-overrides.json']);
     if (!existsSync(gi)) {
-      writeText(gi, `${giLines.join('\n')}\n`);
-      owned.push('.gitignore');
+      // `!existsSync(gi)` is exactly the case a DANGLING symlink also satisfies — it reads
+      // as absent — so `claimLeaf` (which lstats) runs before the write, not instead of
+      // this check.
+      if (claimLeaf(cfgDir, gi, '.gitignore')) {
+        writeText(gi, `${giLines.join('\n')}\n`);
+        owned.push('.gitignore');
+      }
     } else if (oldOwned.includes('.gitignore')) {
       owned.push('.gitignore');
     }
   }
 
-  writeVersion(cfg, cfgDir);
-  owned.push(VERSION_MARKER);
+  if (writeVersion(cfg, cfgDir) !== null) owned.push(VERSION_MARKER);
 
   shipLeanLaws(items, theme, cfgDir, owned, footprint);
 
@@ -192,6 +203,7 @@ export function emitClaudeRender(cfg, job) {
     memStatus,
     nbStatus,
     managed,
+    editRefused: [...claim.editRefused],
   };
 }
 

package/js/build/emit-common.mjs

@@ -10,6 +10,7 @@
  * `emit-claude.mjs` do that; `bundle.mjs` renders the bundle they read from.
  */
 import path from 'node:path';
+import { claimLeaf } from '../hosts/owned.mjs';
 import { copyFile, writeText, isDir } from '../lib/fs.mjs';
 import { relPosix } from '../lib/text.mjs';
 import { SRC_DIR_TOKENS, destRel } from './render.mjs';
@@ -183,9 +184,14 @@ export function shipLeanLaws(items, theme, cfgDir, owned, footprint) {
     // nothing to detect, not because the gate cannot see it.
     if (text !== null && parts.length && dirs.has(parts[0])) {
       const dest = path.join(cfgDir, ...parts);
-      mkdirSync(path.dirname(dest), { recursive: true });
-      writeText(dest, text);
-      owned.push(rel);
+      // `claimLeaf` BEFORE `mkdirSync`, for the same reason `emitClaudeRender`'s rules stub
+      // does: `safeLeaf` needs no directory created first, and creating one ahead of the
+      // refusal would plant it at a linked ancestor's target.
+      if (claimLeaf(cfgDir, dest, rel)) {
+        mkdirSync(path.dirname(dest), { recursive: true });
+        writeText(dest, text);
+        owned.push(rel);
+      }
     }
   }
 }

package/js/build/emit-opencode.mjs

@@ -14,6 +14,7 @@ import {
   writeAliasCommands, writePonytailCommand, writePrimaryAgent, writeTheme,
 } from '../hosts/opencode.mjs';
 import { mergeOpencodeJson, opencodeSentinelWrite } from '../hosts/settings.mjs';
+import { claimLeaf } from '../hosts/owned.mjs';
 import { isFile, readText, writeText } from '../lib/fs.mjs';
 import { relPosix } from '../lib/text.mjs';
 import { assertSourceComplete, build, phaseLog } from './bundle.mjs';
@@ -54,11 +55,12 @@ import { mkdirSync } from 'node:fs';
 function opencodeLayer(cfg, items, themeName, theme, dir, owned, opts) {
   const {
     oldOwned, manifestExisted, agentPath, wireBase, overridesDir, oldDenies = [],
+    oldHashes = {},
   } = opts;
   ensureAgentOverridesStub(cfg, overridesDir);
   const overrides = loadAgentOverrides(overridesDir);
   // One claim for every writer below whose path lands in `owned` — see `claimer`.
-  const claim = claimer(oldOwned, dir, manifestExisted);
+  const claim = claimer(oldOwned, dir, manifestExisted, oldHashes);
 
   const { nAgents, nSkills, written, userOnlySkills } = writeNativeLayer(
     items, path.join(dir, 'agents'), path.join(dir, 'skills'), overrides,
@@ -105,7 +107,7 @@ function opencodeLayer(cfg, items, themeName, theme, dir, owned, opts) {
 
   return {
     nAgents, nSkills, nPlugins, nWorkflows, primary, nCommands: commands.length, cfgName,
-    skillDenies,
+    skillDenies, editRefused: [...claim.editRefused],
   };
 }
 
@@ -129,7 +131,7 @@ export function emitOpencodeRender(cfg, job) {
   phaseLog('RENDER');
   const {
     theme: _theme, out, root, footprint, nativeCatalog, oldOwned, manifestExisted, agentPath,
-    oldDenies,
+    oldDenies, oldHashes = {},
   } = job;
   const oc = path.join(root, '.opencode');
 
@@ -144,9 +146,9 @@ export function emitOpencodeRender(cfg, job) {
   const { theme, items } = renderAll(cfg, _theme, { footprint, nativeCatalog });
 
   const {
-    nAgents, nSkills, nPlugins, nWorkflows, primary, nCommands, cfgName, skillDenies,
+    nAgents, nSkills, nPlugins, nWorkflows, primary, nCommands, cfgName, skillDenies, editRefused,
   } = opencodeLayer(cfg, items, _theme, theme, oc, owned, {
-    oldOwned, manifestExisted, agentPath, wireBase: root, overridesDir: out, oldDenies,
+    oldOwned, manifestExisted, agentPath, wireBase: root, overridesDir: out, oldDenies, oldHashes,
   });
 
   return {
@@ -156,6 +158,7 @@ export function emitOpencodeRender(cfg, job) {
     },
     cfgName,
     skillDenies,
+    editRefused,
   };
 }
 
@@ -195,6 +198,7 @@ export function emitOpencodeGlobalRender(cfg, job) {
   phaseLog('RENDER');
   const {
     theme: themeName, cfgDir, out, footprint, nativeCatalog, oldOwned, agentPath, oldDenies,
+    oldHashes = {},
   } = job;
 
   // No `lawsPrefix`: the standalone laws dir sits beside AGENT.md in <cfg>, so the lean
@@ -210,8 +214,11 @@ export function emitOpencodeGlobalRender(cfg, job) {
     // plain names. Memory links stay RELATIVE: in the global layout AGENT.md and the
     // store are siblings, so `memory/` resolves from AGENT.md's own location and stays
     // hermetic — no absolute path a doctor check would flag as an escape.
-    writeText(path.join(cfgDir, 'AGENT.md'), stripCapabilityLinks(agentText));
-    owned.push('AGENT.md');
+    const agentDest = path.join(cfgDir, 'AGENT.md');
+    if (claimLeaf(cfgDir, agentDest, 'AGENT.md')) {
+      writeText(agentDest, stripCapabilityLinks(agentText));
+      owned.push('AGENT.md');
+    }
   }
   // Co-owned, so never in `owned` — see `opencodeSentinelWrite`.
   opencodeSentinelWrite(cfgDir);
@@ -219,9 +226,9 @@ export function emitOpencodeGlobalRender(cfg, job) {
   // `manifestExisted` is deliberately not passed — the Python does not pass it either, so
   // the pre-manifest header line is unreachable from this emit on both sides.
   const {
-    nAgents, nSkills, nPlugins, nWorkflows, primary, nCommands, cfgName, skillDenies,
+    nAgents, nSkills, nPlugins, nWorkflows, primary, nCommands, cfgName, skillDenies, editRefused,
   } = opencodeLayer(cfg, items, themeName, theme, cfgDir, owned, {
-    oldOwned, agentPath, wireBase: cfgDir, overridesDir: cfgDir, oldDenies,
+    oldOwned, agentPath, wireBase: cfgDir, overridesDir: cfgDir, oldDenies, oldHashes,
   });
 
   const memStatus = globalMemory(cfgDir, items, out, cfg.src);
@@ -233,8 +240,7 @@ export function emitOpencodeGlobalRender(cfg, job) {
   ensureProfileStub(cfgDir);
   ensureExcludesStub(cfgDir);
 
-  writeVersion(cfg, cfgDir);
-  owned.push(VERSION_MARKER);
+  if (writeVersion(cfg, cfgDir) !== null) owned.push(VERSION_MARKER);
 
   shipLeanLaws(items, theme, cfgDir, owned, footprint);
 
@@ -247,5 +253,6 @@ export function emitOpencodeGlobalRender(cfg, job) {
     nbStatus,
     cfgName,
     skillDenies,
+    editRefused,
   };
 }

package/js/build/source.mjs

@@ -348,6 +348,7 @@ export function skillAliases(src = SRC) {
  */
 export const RETIRED_SKILL_IDS = {
   tickets: 'removed in the 2026-10 sharpen; plan slices the work now',
+  herdr: 'removed 2026-10; Orca covers multi-pane and multi-agent work',
 };
 
 /**

package/js/build/version.mjs

@@ -9,6 +9,7 @@
 import path from 'node:path';
 import { VERSION_MARKER } from '../hosts/hosts.mjs';
 import { readText, writeText } from '../lib/fs.mjs';
+import { claimLeaf } from '../hosts/owned.mjs';
 import { parseJson } from '../lib/json.mjs';
 import { isDir } from '../lib/fs.mjs';
 import { relPosix } from '../lib/text.mjs';
@@ -162,8 +163,15 @@ function warnIfDowngrade(cfg, out) {
   }
 }
 
-/** `_build_render.write_version`. */
+/**
+ * `_build_render.write_version`. Returns the fingerprint on a successful write, or `null` when
+ * `claimLeaf` refuses `out`'s marker (a symlinked or hard-linked `VERSION_MARKER`) — every
+ * caller pushes `VERSION_MARKER` into `owned` only when this is not `null`, the same
+ * "skip the write, keep it out of owned" shape `claimer` uses.
+ */
 export function writeVersion(cfg, out) {
+  const dest = path.join(out, VERSION_MARKER);
+  if (!claimLeaf(out, dest, VERSION_MARKER)) return null;
   warnIfDowngrade(cfg, out);
   const fp = sourceFingerprint(cfg);
   const release = sourceReleaseVersion(cfg);
@@ -177,8 +185,7 @@ export function writeVersion(cfg, out) {
   // clock across a process boundary is not something the harness can do — which is
   // exactly why the choice is spelled out instead of relying on the comparison.
   const today = new Date().toLocaleDateString('sv-SE');
-  writeText(path.join(out, VERSION_MARKER),
-    `${fp} (built ${today}) [release ${release}]\n`);
+  writeText(dest, `${fp} (built ${today}) [release ${release}]\n`);
   return fp;
 }
 

package/js/cli-table.json

@@ -901,7 +901,7 @@
     },
     {
       "name": "mcp",
-      "help": "list the MCP servers wired into each active install, and the presets available to add",
+      "help": "list the MCP servers wired into each active install, read-only",
       "description": "",
       "positionals": [],
       "options": [],
@@ -1415,6 +1415,21 @@
           "is_flag": true,
           "type": null,
           "hidden": false
+        },
+        {
+          "names": [
+            "--force"
+          ],
+          "dest": "force",
+          "metavar": null,
+          "help": "also delete owned files you edited since install",
+          "choices": null,
+          "default": false,
+          "required": false,
+          "nargs": "0",
+          "is_flag": true,
+          "type": null,
+          "hidden": false
         }
       ],
       "mutex": []

package/js/hosts/hooks.mjs

@@ -59,6 +59,7 @@ import {
 } from './hosts.mjs';
 import { currentBranch, gitRootOf, loopLaunched } from './gitref.mjs';
 import { selfAndParents, readStdin } from './hooks-prims.mjs';
+import { recordUse } from './usage.mjs';
 
 // ======================================================================================
 // git-gate — Doctrine process 5's tool-boundary backstop
@@ -627,6 +628,9 @@ function normaliseBobPayload(payload) {
 function toolGate(args) {
   if (sovereignBypass(args.root)) return 0;
   const payload = normaliseBobPayload(readPayload());
+  // Count a skill or subagent call before judging it: Bob runs this verb on every tool and
+  // Claude/OpenClaude route their `Skill|Agent|Task` matcher here (js/hosts/usage.mjs).
+  recordUse(args.root, payload);
   const ti = (payload && payload.tool_input) || {};
   return typeof ti.command === 'string' ? gitDecide(args, payload) : ruleDecide(args, payload);
 }

package/js/hosts/installs.mjs

@@ -181,7 +181,7 @@ const CARRIERS = [
  * `AGENTS.md` (`CLAUDE_SHAPED['bob-global']`'s summary says so) — which `HOSTS` has no column
  * for and this hard-codes, same as the un-narrowed `CARRIERS` above always did.
  */
-function carriersFor(host) {
+export function carriersFor(host) {
   const row = HOSTS.find((h) => h.host === host);
   if (!row) return CARRIERS;
   if (host === 'bob') return [path.join('rules', 'geneseed.md'), row.agentFile];