geneseed 3.3.0 → 3.5.0

package/js/build/emit-claude.mjs

@@ -10,8 +10,8 @@ import { VERSION_MARKER } from '../hosts/hosts.mjs';
 import { loadAgentOverrides, writeNativeLayer } from '../hosts/native.mjs';
 import { ensureAgentOverridesStub } from '../hosts/opencode.mjs';
 import {
-  managedBlockRemove, managedBlockWrite, mergeClaudeSettings, mergeCopilotSettings,
-  unwireClaudeExcludes, unwireClaudeSettings, wireClaudeExcludes,
+  managedBlockRemove, managedBlockWrite, mergeClaudeSettings,
+  unwireClaudeExcludes, unwireClaudeSettings, unwireCopilotSettings, wireClaudeExcludes,
 } from '../hosts/settings.mjs';
 import { writeText } from '../lib/fs.mjs';
 import { isTruthy } from '../lib/json.mjs';
@@ -121,10 +121,13 @@ export function emitClaudeRender(cfg, job) {
   ensureExcludesStub(cfgDir);
 
   // Project hygiene, claim-on-create: an existing (possibly user-authored) .gitignore is
-  // never rewritten, but one we created stays owned across re-emits.
+  // never rewritten, but one we created stays owned across re-emits. The hook file is
+  // machine-specific (it names this user's hook shim): Claude's is the personal
+  // settings.local.json; Bob documents no local variant, so its settings.json is ignored.
   if (scope === 'project') {
     const gi = path.join(cfgDir, '.gitignore');
-    const giLines = (host === 'claude' ? ['settings.local.json'] : [])
+    const giLines = (host === 'claude' ? ['settings.local.json']
+      : host === 'bob' ? ['settings.json'] : [])
       .concat(['wiki.jsonc', 'agent-overrides.json']);
     if (!existsSync(gi)) {
       writeText(gi, `${giLines.join('\n')}\n`);
@@ -254,7 +257,7 @@ function claudeWire(job, claudeMdText, hasAgentText, doctrines = null, excludeRu
     // DECIDES the install's packs, so the marker on disk is still the previous build's.
     const [, managedHooks] = mergeClaudeSettings(
       settingsPath, scope, oldSf === settingsName ? get(old, 'settings_hooks') : null, hookOpts,
-      doctrines, excludeRules, host,
+      doctrines, excludeRules, host, cfgDir,
     );
     managed.settings_hooks = managedHooks;
 
@@ -288,13 +291,17 @@ function claudeWire(job, claudeMdText, hasAgentText, doctrines = null, excludeRu
       managed.settings_excludes = priorExcl;
     }
   } else if (scope === 'global') {
-    // `copilot_hooks`, not `settings_hooks`: a distinct key so the Claude-shaped unwire and
-    // integrity code, which walks `settings_hooks` as event→group arrays, never sees a
-    // Copilot record it would misread.
+    // Copilot's hooks are event → array now, so the Claude merge (append/prune by deep
+    // equality) is the Copilot merge too, recorded under `settings_hooks`. An install from
+    // before that recorded single-slot `copilot_hooks` (the dead `toolCall` event): unwire
+    // those claims first, or they linger in the file forever.
     const settingsPath = path.join(cfgDir, 'settings.json');
     managed.settings_file = 'settings.json';
-    const [, claims] = mergeCopilotSettings(settingsPath, get(old, 'copilot_hooks'), hookOpts);
-    managed.copilot_hooks = claims;
+    const legacy = get(old, 'copilot_hooks');
+    if (Array.isArray(legacy) && legacy.length) unwireCopilotSettings(settingsPath, legacy);
+    const [, managedHooks] = mergeClaudeSettings(settingsPath, scope,
+      Array.isArray(legacy) ? null : get(old, 'settings_hooks'), hookOpts, null, [], host, cfgDir);
+    managed.settings_hooks = managedHooks;
   }
   return managed;
 }

package/js/build/emit-common.mjs

@@ -2,12 +2,12 @@
  * What every emit shares — the constants that name what this tool owns, the small readers it
  * walks a tree with, and the three writers both GLOBAL emits call.
  *
- * Split out of `emit.mjs` because each of `globalMemory`, `globalNotebook`, `shipLeanLaws`
+ * Split out of the old `emit.mjs` because each of `globalMemory`, `globalNotebook`, `shipLeanLaws`
  * and `stripCapabilityLinks` has two callers in two different host emits. A helper with two
  * hosts belongs to neither, and putting it in one of them is how a file grows to 1400 lines.
  *
  * Nothing here decides WHICH host is being emitted. `emit-opencode.mjs` and
- * `emit-claude.mjs` do that; `emit.mjs` renders the bundle they read from.
+ * `emit-claude.mjs` do that; `bundle.mjs` renders the bundle they read from.
  */
 import path from 'node:path';
 import { copyFile, writeText, isFile, isDir } from '../lib/fs.mjs';
@@ -176,8 +176,8 @@ export function globalNotebook(cfgDir, items, legacy, srcRoot) {
  *
  * NO LONGER LEAN-ONLY, and the name is kept because the lean case is still the whole reason
  * it exists. `doctrines` ships at BOTH footprints, because the two footprints lose different
- * things: lean loses text (every rule is truncated to its first sentence, so the full text has
- * to be on disk), while FULL loses whole packs (only the active ones are inlined, so the
+ * things: lean loses text (each rule inlines its authored brief, so the full text has to be on
+ * disk), while FULL loses whole packs (only the active ones are inlined, so the
  * inactive ones have to be on disk). AGENT.md tells the agent it may read a rule in a pack
  * that is not active, and `src/doctrines/README.md` rests cross-pack citations on exactly
  * that — a claim the emit has to make true, not merely the `files` bundle.

package/js/build/generate.mjs

@@ -32,7 +32,7 @@
 import { existsSync, mkdirSync, statSync } from 'node:fs';
 import path from 'node:path';
 
-import { main as driverMain } from '../../bin/build-driver.mjs';
+import { main as driverMain } from './driver.mjs';
 import { makeCfg, PACK_ORDER } from './source.mjs';
 import { opencodeConfigDir, resolvePath } from '../hosts/hosts.mjs';
 import {

package/js/build/render.mjs

@@ -67,11 +67,15 @@ const TEXT_SUFFIXES = new Set(['.md', '.tmpl', '.json', '.txt', '.yml', '.yaml']
 // silently never substitutes. A leading digit stays illegal, so `{{1}}` is still not a token.
 const TOKEN_RE = /\{\{([A-Z_][A-Z0-9_]*)\}\}/g;
 const INCLUDE_RE = /^[ \t]*<!--[ \t]*INCLUDE:[ \t]*(?<path>[^ \t]+)[ \t]*-->[ \t]*$/gm;
+// Each block names its kind (`agents` | `skills`) so a host that catalogues one natively and
+// not the other — Bob — keeps exactly the table it still needs.
 const CATALOG_BLOCK_RE =
-  /[ \t]*<!-- CATALOG:begin -->\n(?<table>[\s\S]*?)[ \t]*<!-- CATALOG:else -->\n(?<pointer>[\s\S]*?)[ \t]*<!-- CATALOG:end -->\n/g;
+  /[ \t]*<!-- CATALOG:begin (?<kind>agents|skills) -->\n(?<table>[\s\S]*?)[ \t]*<!-- CATALOG:else -->\n(?<pointer>[\s\S]*?)[ \t]*<!-- CATALOG:end -->\n/g;
 // The footprint twin of CATALOG. Before it existed, `lean` could only reach the two
 // include-driven corpora (`laws/universal.md` and the doctrine packs, both truncated
-// mechanically to heading + first sentence); every other section of the root template was
+// mechanically to heading + first sentence — neither is, now: the laws, the ontology and every
+// doctrine rule reach lean through an authored half of this block); every other section of the
+// root template was
 // byte-identical across footprints, which is how ~1.5k tokens of §-level prose rode into
 // every lean install. A LEAN block ships a HAND-WRITTEN condensation instead of a
 // truncation — the objection `docs/token-footprint.md` raised against terse-ing the
@@ -154,10 +158,16 @@ export function substitute(text, theme) {
 
 /** `_build_render._resolve_catalogs`. */
 function resolveCatalogs(text, nativeCatalog) {
-  return text.replace(CATALOG_BLOCK_RE, (_m, table, pointer) => (nativeCatalog ? pointer : table));
+  // `true`/`false` still mean "both kinds", for the plain-bundle callers that pass a boolean.
+  const nat = nativeCatalog === true ? { skills: true, agents: true } : (nativeCatalog || {});
+  return text.replace(CATALOG_BLOCK_RE, (_m, kind, table, pointer) => (nat[kind] ? pointer : table));
 }
 
-/** LEAN blocks — full text or the hand-written condensation, by footprint. */
+/**
+ * LEAN blocks — full text or the hand-written condensation, by footprint. Laws, ontology,
+ * doctrine rules: every tier of the constitution authors its own lean form, and this is the
+ * one function that chooses between the halves.
+ */
 function resolveLean(text, footprint) {
   return text.replace(LEAN_BLOCK_RE, (_m, full, lean) => (footprint === 'lean' ? lean : full));
 }
@@ -182,36 +192,6 @@ function splitAtLawHeadings(text) {
   return out;
 }
 
-/**
- * Heading + first sentence, per `### ` block. DOCTRINES ONLY, now.
- *
- * The laws used to go through this too, and it made a law's lean footprint a function of its
- * punctuation: Law II shipped as one 36-character sentence and lost its stop-and-ask
- * mechanism, while a law written as one colon-chained run-on shipped nearly whole. The laws
- * now carry authored LEAN blocks in `src/laws/universal.md`, the way the ontology already did,
- * and `resolveLean` picks the half. Doctrine rules stay machine-cut: there are ~23 of them
- * across four packs, and a pack is a practice catalogue whose first sentence is written to
- * stand alone.
- */
-function terseBlocks(text) {
-  const blocks = splitAtLawHeadings(text);
-  const out = [blocks[0].trimEnd()];
-  for (const b of blocks.slice(1)) {
-    // Python's `splitlines()` also breaks on VT, FF, FS-RS, NEL, LINE SEPARATOR and
-    // PARAGRAPH SEPARATOR, where `split('\n')` does not. The law corpus is plain
-    // markdown and readText has already folded CRLF and CR to LF, so the sets coincide.
-    // (Spelling those out by name rather than by literal is not fussiness: the first
-    // draft of this comment contained the actual LINE/PARAGRAPH SEPARATOR characters,
-    // which are JS line terminators, and they ended the comment mid-sentence.)
-    const lines = b.split('\n');
-    const heading = lines[0].trimEnd();
-    const body = lines.slice(1).map((l) => l.trim()).join(' ').trim();
-    const m = /^([\s\S]+?[.!?])(?:\s|$)/.exec(body);
-    out.push(`${heading}\n${m ? m[1].trim() : body}`);
-  }
-  return out.join('\n\n');
-}
-
 /** The pointer under §1 at lean. The laws' lean text itself is authored in LEAN blocks. */
 export function lawsPointer(theme, lawsPrefix = '') {
   const law = theme.LAW ?? 'Law';
@@ -222,11 +202,29 @@ export function lawsPointer(theme, lawsPrefix = '') {
     + 'secrets, deletion, git history, scope, or untrusted content.';
 }
 
+/**
+ * SOURCE TEXT, READ ONCE PER `cfg`. One emit renders the same partials over and over — the
+ * self-improvement footer is included by ~50 specs — and `doctor --all` repeats that per theme:
+ * 91% of its file reads were repeats. Keyed on the `cfg` OBJECT, not the process: the web
+ * daemon renders in-process for days, and `makeCfg()` is called per operation, so each request
+ * sees today's source. Only files under `cfg.src` — the one tree nothing in a render writes to.
+ */
+const SRC_TEXT = new WeakMap();
+function readSource(cfg, p) {
+  const src = cfg && cfg.src ? normcase(path.resolve(cfg.src)) + path.sep : null;
+  if (!src || !normcase(p).startsWith(src)) return readText(p);
+  let seen = SRC_TEXT.get(cfg);
+  if (!seen) SRC_TEXT.set(cfg, (seen = new Map()));
+  let text = seen.get(p);
+  if (text === undefined) seen.set(p, (text = readText(p)));
+  return text;
+}
+
 /** `_build_render.render_file`. */
 export function renderFile(cfg, filePath, theme, footprint = 'full', lawsPrefix = '',
                            visiting = new Set(), nativeCatalog = false) {
   const here = path.resolve(filePath);
-  let text = readText(filePath);
+  let text = readSource(cfg, here);
 
   text = text.replace(INCLUDE_RE, (_whole, rel) => {
     const target = path.resolve(cfg.src, rel);
@@ -318,10 +316,10 @@ function activeDoctrines(cfg) {
  * `registerBody`'s single-select one.
  *
  * `registerBody` reads ONE file because a posture and a mode are scalars; a doctrine set is
- * 0-4 files, so this loops instead of wrapping it. Under `lean` each pack gets the same
- * heading + first-sentence treatment the invariants get, and the whole section — not each
- * pack — closes with one pointer at the full catalogue, which ships in every bundle whether
- * or not a pack is active.
+ * 0-4 files, so this loops instead of wrapping it. Under `lean` each rule ships the authored
+ * `LEAN:else` half of its block — `resolveLean`, the same picker the invariants go through,
+ * the first-sentence cut gone — and the whole section, not each pack, closes with one pointer
+ * at the full catalogue, which ships in every bundle whether or not a pack is active.
  */
 /** `### {{DOCTRINE}} <pack> <n> —` in the UNRENDERED source, which is where the address is. */
 const SRC_RULE_HEADING_RE = /^### \{\{DOCTRINE\}\} ([a-z]+) (\d+)\b/;
@@ -356,8 +354,11 @@ function doctrinesBody(cfg, theme, active, footprint, lawsPrefix) {
   const parts = active.map((name) => {
     const raw = dropExcludedRules(readPackText(path.join(cfg.src, 'doctrines', `${name}.md`)),
       name, excluded);
-    const body = substitute(raw, theme).trim();
-    return footprint === 'lean' ? terseBlocks(body) : body;
+    // The same picker `renderFile` runs over every other file: the authored half first, the
+    // voice second. THE ORDER IS LOAD-BEARING — `resolveLean` reads HTML markers, and
+    // substituting first would hand it prose in fourteen voices. The first-sentence cut is gone;
+    // a rule's lean text is written in `src/doctrines/<pack>.md`, not measured out of its prose.
+    return substitute(resolveLean(raw, footprint), theme).trim();
   });
   if (footprint === 'lean') {
     const doctrine = theme.DOCTRINE ?? 'Doctrine';
@@ -454,10 +455,13 @@ export function renderAll(cfg, themeName, {
   for (const file of sortedSourceFiles(cfg.src)) {
     const rel = path.relative(cfg.src, file);
     const outRel = destRel(themedRel(rel, theme)).split(path.sep).join('/');  // as_posix()
-    // The on-disk `laws/` and `ontology/` are the "complete, binding text" the lean pointer
-    // promises. They render at full whatever the footprint; only what AGENT.md INLINES leans.
+    // The on-disk `laws/`, `ontology/` and `doctrines/` are the "complete text" the two lean
+    // pointers promise — §1's and the Doctrines section's. They render at full whatever the
+    // footprint; only what AGENT.md INLINES leans. `doctrines/` joined them when its rules got
+    // authored LEAN blocks: before that a pack file carried no markers and shipped whole by
+    // accident, which is a different thing from shipping whole by contract.
     // Keyed on the SOURCE rel, not the themed one, so a DIR_* rename cannot un-exempt them.
-    const fp = /^(?:laws|ontology)[\\/]/.test(rel) ? 'full' : footprint;
+    const fp = /^(?:laws|ontology|doctrines)[\\/]/.test(rel) ? 'full' : footprint;
     items.push(TEXT_SUFFIXES.has(suffixOf(path.basename(file)))
       ? { rel: outRel, text: renderFile(cfg, file, theme, fp, lawsPrefix, new Set(), nativeCatalog), src: file }
       : { rel: outRel, text: null, src: file });

package/js/build/stubs.mjs

@@ -114,7 +114,7 @@ export const EXCLUDES_FILE = 'excludes.json';
  */
 export const EXCLUDES_STUB = `\
 {
-  "_comment": "Folders where this global Geneseed install goes dormant (hooks silent, preamble suppressed). Managed by \`harness exclude add|remove|list\`; safe to edit by hand. Paths are absolute.",
+  "_comment": "Folders where this global Geneseed install goes dormant (hooks silent, preamble suppressed). Managed by \`geneseed exclude add|remove|list\`; safe to edit by hand. Paths are absolute.",
   "excludes": []
 }
 `;

package/js/build/themes.mjs

@@ -14,10 +14,10 @@
  * `_argv` emits neither flag (argued in situ at `bin/build-driver.mjs`'s dispatch), so the
  * acceptance matrix that gates all nine emits is structurally blind to both, and the driver
  * refused them rather than crossing for exactly that reason. The gate is
- * `tests/unit/maintainer_tools.test.mjs`, replaying the frozen recording in
- * `tests/__snapshots__/sync_themes.json`: a corpus of hand-made theme directories, comparing
- * the printed output, the return value and the resulting FILE BYTES against what the reference
- * answered. Nothing can re-record it, so a change here that moves a byte is a product change.
+ * `tests/unit/maintainer_tools.test.mjs`, over the written-out cases in
+ * `tests/fixtures/sync_themes_cases.json`: hand-made theme directories, each with the output,
+ * exit status and FILE BYTES it must produce. A change that moves a byte changes a case and
+ * the sentence explaining it, in the same commit.
  *
  * WHY THIS MODULE IS NOT `js/inspect/doctor.mjs`. `--sync-themes` has no doctor dependency, so it
  * stays on the generator driver where its flag lives — and the driver is under a transitive

package/js/build/version.mjs

@@ -28,6 +28,18 @@ import { readFileSync } from 'node:fs';
  * in the output; reproducing the wrong one changes the fingerprint of every install.
  */
 export function sourceFingerprint(cfg) {
+  // Once per `cfg` — the source cannot change under one operation, and every emit (84 of them
+  // in `doctor --all`) hashed the whole tree again. Per cfg OBJECT, not per process, for the
+  // same reason as render.mjs's source cache: the web daemon is long-lived.
+  if (FINGERPRINT.has(cfg)) return FINGERPRINT.get(cfg);
+  const fp = hashSource(cfg);
+  FINGERPRINT.set(cfg, fp);
+  return fp;
+}
+
+const FINGERPRINT = new WeakMap();
+
+function hashSource(cfg) {
   const h = createHash('sha256');
   const files = [];
   for (const r of [cfg.src, cfg.themes, cfg.pluginSrc, cfg.workflowSrc]) {

package/js/cli-table.json

@@ -162,7 +162,7 @@
           ],
           "dest": "host",
           "metavar": null,
-          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) asks; 'copilot' has no ask tier, so Laws I/IV block and everything else is a stderr warning",
+          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) and 'copilot' ask, each in its own envelope; 'bob' has no ask tier, so Laws I/IV exit 2 and everything else is a stderr warning",
           "choices": null,
           "default": null,
           "required": false,
@@ -353,7 +353,7 @@
     },
     {
       "name": "git-gate",
-      "help": "PreToolUse hook: force an ASK before every git commit/push (process 5 backstop)",
+      "help": "PreToolUse hook: ASK before a history-discarding git act (Law IV) and before every git commit/push (process 5 backstop)",
       "description": "",
       "positionals": [],
       "options": [
@@ -378,7 +378,7 @@
           ],
           "dest": "host",
           "metavar": null,
-          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) asks; 'copilot' has no ask tier, so Laws I/IV block and everything else is a stderr warning",
+          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) and 'copilot' ask, each in its own envelope; 'bob' has no ask tier, so Laws I/IV exit 2 and everything else is a stderr warning",
           "choices": null,
           "default": null,
           "required": false,
@@ -386,6 +386,21 @@
           "is_flag": false,
           "type": null,
           "hidden": false
+        },
+        {
+          "names": [
+            "--no-consent"
+          ],
+          "dest": "no_consent",
+          "metavar": null,
+          "help": "skip the process-5 commit/push ask (set by the emit when the process pack or process 5 is off); Law IV still asks",
+          "choices": null,
+          "default": false,
+          "required": false,
+          "nargs": "0",
+          "is_flag": true,
+          "type": null,
+          "hidden": false
         }
       ],
       "mutex": []
@@ -641,7 +656,7 @@
           ],
           "dest": "host",
           "metavar": null,
-          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) asks; 'copilot' has no ask tier, so Laws I/IV block and everything else is a stderr warning",
+          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) and 'copilot' ask, each in its own envelope; 'bob' has no ask tier, so Laws I/IV exit 2 and everything else is a stderr warning",
           "choices": null,
           "default": null,
           "required": false,
@@ -811,7 +826,7 @@
     },
     {
       "name": "tool-gate",
-      "help": "toolCall hook (Copilot): git-gate and rule-gate fused behind one command, dispatched on the payload",
+      "help": "PreToolUse hook for hosts with no tool matcher (Copilot, Bob): git-gate and rule-gate fused behind one command, dispatched on the payload",
       "description": "",
       "positionals": [],
       "options": [
@@ -836,7 +851,7 @@
           ],
           "dest": "host",
           "metavar": null,
-          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) asks; 'copilot' has no ask tier, so Laws I/IV block and everything else is a stderr warning",
+          "help": "the host that reads the verdict (set by the emitted hook): 'claude' (default) and 'copilot' ask, each in its own envelope; 'bob' has no ask tier, so Laws I/IV exit 2 and everything else is a stderr warning",
           "choices": null,
           "default": null,
           "required": false,