geneseed 3.9.0 → 3.11.0

package/docs/understand/on-your-machine.md

@@ -0,0 +1,76 @@
+---
+group: understand
+order: 2
+title: "What lands on your machine"
+kind: "map"
+---
+An install writes a handful of files into your host's config folder and, where the host allows it, wires small programs that run at fixed moments: when a session starts, before a tool call, when a session ends. Everything below says what each piece does for you, when it runs, what it costs, and how to turn it off. The **Kind** column uses four words:
+
+- **enforced**: code runs before the action and can stop it. The model cannot argue past it.
+- **automatic**: runs by itself at a fixed moment, such as session start or session end.
+- **asked**: text the model reads every session. It usually follows it, but nothing makes it.
+- **on demand**: loads only when you or the agent call it by name.
+
+Token costs are for the default *lean* footprint. Before you type anything, a session carries about 12k tokens of harness. That is roughly 6% of a 200k window. A `--footprint full` build adds about 5k on the rules file. For a live figure on your own install, ask the agent to use the `token-report` skill.
+
+<!--harness:claude-->
+*(Claude Code only)*
+
+| Piece | What it does for you | Kind | Cost | Turn it off |
+|---|---|---|---|---|
+| `CLAUDE.md` (managed block) | The rules, the pointers to agents and skills, and how memory works. Geneseed writes only its own block; your own lines in the file stay | asked | ~7.2k tokens every session | Shrink it with fewer doctrine packs (`--doctrines`); remove it with `geneseed uninstall` |
+| `user-rules.md` | Your own standing rules, read every session. Seeded empty | asked | 0 until you write in it | Leave it empty |
+| `PROFILE.md` | Who you are and how you like answers pitched. Fill it with the `profile` skill | asked | 0 until you fill it | Leave the seeded text untouched |
+| context hook | At session start, and again after a resume or compaction, puts your repo's README, CONTRIBUTING and a listing of `docs/` in front of the agent, with your rules, profile, memory index and wiki | automatic | Your docs, capped at 16 KB a file and 48 KB a session | `geneseed exclude add <folder>` silences every hook in that folder |
+| git-gate hook | Before each shell command: asks you before any `git commit` or `git push`, and before a force-push, `reset --hard`, `clean -f`, `branch -D` or `checkout --` | enforced | ~14 ms per shell call | The commit/push question goes away if you build without the **process** pack; the destructive-git question has no switch except `geneseed exclude` |
+| rule-gate hook | Before each write or edit: asks you when the file would carry a credential-shaped string (outside `.env`), or when the agent writes to `user-rules.md` or memory | enforced | ~14 ms per write | `geneseed exclude add <folder>` |
+| learn hook | When the agent finishes a reply, and before compaction, distils durable facts from the recent conversation into `memory/`. Off until you set `GENESEED_LLM` to a model command such as `claude -p` | automatic | One model call each time it runs, once enabled | Leave `GENESEED_LLM` unset (the default) |
+| `skills/` | Written procedures you call by name, such as `brainstorm` or `plan` | on demand | ~4.1k tokens for names and descriptions; a skill's body loads only when called | No per-skill switch; `geneseed uninstall` removes them all |
+| `agents/` | Specialists the agent can delegate to, such as `reviewer` or `tester` | on demand | ~0.5k tokens | `geneseed uninstall` |
+| `memory/` | Durable facts, one per file, with a `MEMORY.md` index the context hook injects | automatic | 0 when fresh; grows as facts accumulate | `geneseed memory list`, then `geneseed memory rm <name>` |
+| `notebook/` | The agent's own working space: plans, scratch notes, and the gate log `gates.jsonl` | automatic | 0 when fresh; its index grows with use | Delete what you do not want; it is git-ignored and yours |
+| hook shim | `~/.geneseed/bin/geneseed-hook`, the one stable path every hook calls, so moving the Geneseed checkout does not break your hooks | automatic | Nothing on its own | Not removed by uninstall, since every install on the machine shares it. `GENESEED_HOME` moves it |
+
+<!--/harness-->
+<!--harness:opencode-->
+*(OpenCode only)*
+
+| Piece | What it does for you | Kind | Cost | Turn it off |
+|---|---|---|---|---|
+| `AGENT.md` | The rules, the pointers to agents and skills, and how memory works | asked | ~7.2k tokens every session | Shrink it with fewer doctrine packs (`--doctrines`); remove it with `geneseed uninstall` |
+| `user-rules.md` | Your own standing rules, read every session. Seeded empty | asked | 0 until you write in it | Leave it empty |
+| `PROFILE.md` | Who you are and how you like answers pitched. Fill it with the `profile` skill | asked | 0 until you fill it | Leave the seeded text untouched |
+| `opencode.json` entries | `instructions` points OpenCode at `AGENT.md`. `permission.bash` makes OpenCode ask before `rm -rf`, a force-push, `reset --hard`, `clean -f`, `branch -D` or `checkout --`, and before every commit and push when the **process** pack is on | enforced | No tokens | Edit the `permission` block yourself. The commit/push questions follow the **process** pack |
+| context plugin | Puts your repo's README, CONTRIBUTING and a listing of `docs/` in front of the agent, with your rules, profile, memory index and wiki | automatic | Your docs, capped at 16 KB a file and 48 KB a session | `GENESEED_CONTEXT_INJECT=off` |
+| guard plugin | Blocks writes to key and credential files (`id_rsa`, `.pem`, `.ssh/`…), catastrophic commands (`rm -rf /`, formatting a disk), and changes inside your wiki's protected folders. Refuses the first write to `user-rules.md` or memory once, so the choice is yours | enforced | No tokens | `GENESEED_GUARD=off`, or `GENESEED_GUARD=warn` to log instead of block |
+| learn plugin | Once a session has been quiet for 60 seconds, distils durable facts into `memory/` with the model the session already uses | automatic | One model call per quiet session | `geneseed exclude add <folder>` silences it in that folder |
+| activity plugin | Writes one small file per session that the web console's Activity view shows | automatic | No tokens | `GENESEED_ACTIVITY=off` |
+| notify plugin | A desktop notification when a turn took longer than 30 seconds | automatic | No tokens | `GENESEED_NOTIFY=off` |
+| ponytail plugin | Minimal-code mode. `/ponytail lite`, `full` or `ultra` adds a short ruleset to every turn until you switch it off | on demand | 0 while off, which is the default | `/ponytail off` |
+| workflow plugin | Adds a `workflow` tool that runs saved orchestration scripts | on demand | Runs only when called | `geneseed uninstall` |
+| `skills/` | Written procedures you call by name, such as `brainstorm` or `plan` | on demand | ~4.1k tokens for names and descriptions; a skill's body loads only when called | No per-skill switch; `geneseed uninstall` removes them all |
+| `agents/` | Specialists the agent can delegate to, such as `reviewer` or `tester` | on demand | ~0.5k tokens | `geneseed uninstall` |
+| `memory/` | Durable facts, one per file, with a `MEMORY.md` index the context plugin injects | automatic | 0 when fresh; grows as facts accumulate | `geneseed memory list`, then `geneseed memory rm <name>` |
+| `notebook/` | The agent's own working space: plans, scratch notes, and the gate log `gates.jsonl` | automatic | 0 when fresh; its index grows with use | Delete what you do not want; it is git-ignored and yours |
+
+<!--/harness-->
+
+### Where the files are
+
+**OpenCode.** A global install writes to `~/.config/opencode/`. Setting `OPENCODE_CONFIG_DIR` or `XDG_CONFIG_HOME` moves it. Geneseed merges its entries into your existing `opencode.json` and keeps every other key. A per-repo install writes into the repo instead.
+
+**Claude Code.** A global install writes to `~/.claude/`, and its hooks go into `~/.claude/settings.json`, next to any hooks of your own. A per-repo install uses the repo's `.claude/` folder, with the hooks in `.claude/settings.local.json`.
+
+**Bob.** A global install writes to `~/.bob/`, or `BOB_CONFIG_DIR`. Bob does not load a global `AGENTS.md`, so the rules go into `~/.bob/rules/geneseed.md`. A per-repo install writes `AGENTS.md` instead. Hooks live in `~/.bob/settings/settings.json`. Bob runs three of them: context at session start, one combined gate before each tool call, and learn at session end. Bob has no "ask" prompt, so the gate refuses outright, and only for credentials and destructive git. The commit/push and memory questions become log lines.
+
+**OpenClaude.** Same pieces as Claude Code, under `~/.openclaude/` or `OPENCLAUDE_CONFIG_DIR`. A per-repo install uses `.openclaude/`, with the hooks in `.openclaude/settings.local.json`.
+
+**Plain bundle.** The `files` target writes `AGENT.md` and the same folders into `./Harness/` for any tool that reads `AGENT.md`. It installs no hooks and no plugins, so nothing in it is enforced.
+
+### Taking it back out
+
+`geneseed uninstall` removes only what Geneseed recorded writing: the rules file or its managed block, `agents/`, `skills/`, plugins, and Geneseed's own hook and config entries. It keeps `memory/` and `notebook/` in place, along with the files it seeded for you to edit (`user-rules.md`, `PROFILE.md`, `wiki.jsonc`). Add `--archive-memory` to move memory and notebook aside instead. It still deletes nothing. See [Uninstall](../guides/uninstall.md).
+
+---
+
+**Next:** [A day with the harness](a-day.md)

package/docs/web-ui.md

@@ -4,7 +4,7 @@
 
 **Every view in the local browser console, what it shows, and how to drive it.**
 
-[← README](../README.md) · [Setup](../SETUP.md) · [What's shipped](../SHIPPED.md)
+[← README](../README.md) · [Docs](README.md) · [What's shipped](../SHIPPED.md)
 
 </div>
 
@@ -120,7 +120,7 @@ streams the output of background jobs and keeps their history across reloads.
 - **Docs** (`#/docs`) — rendered documentation: markdown pages, concept pages, a CLI
   reference (generated from the harness argument parser), and a glossary, grouped into
   Get started / Core concepts / How-to / MCP servers / Plugins / Reference / Deeper. Filtered
-  for one host family (OpenCode, or Claude Code — which Bob, Copilot and OpenClaude share); with no
+  for one host family (OpenCode, or Claude Code — which Bob and OpenClaude share); with no
   choice stored it follows the deployed install.
 
 ### 🩺 Care

package/harness.config.json

@@ -2,5 +2,5 @@
   "_comment": "version is a human-readable release label only; the canonical identity of an installed harness is the source fingerprint stamped in .geneseed-version (see `harness version`), not this string.",
   "theme": "neutral",
   "product": "Geneseed",
-  "version": "3.9.0"
+  "version": "3.11.0"
 }

package/js/README.md

@@ -40,12 +40,12 @@ as a per-host install at project or global scope.
 | `source.mjs` | Where the SOURCE is: `ROOT`/`SRC`/`THEMES`/`CONFIG`, `PACK_ORDER`, the rule canon (stable ids → positional numbers, citations → names), the cfg object |
 | `render.mjs` | The pure text pipeline: theme load, `INCLUDE` inlining, CATALOG blocks, `{{TOKENS}}`, dest paths |
 | `bundle.mjs` | `build` — render a theme into a bundle dir, plus the source-completeness refusal. Sits UNDER both emits |
-| `emit-claude.mjs` | The Claude/Bob/Copilot/OpenClaude emit — the render half plus the settings + CLAUDE.md managed-block wire |
+| `emit-claude.mjs` | The Claude/Bob/OpenClaude emit — the render half plus the settings + CLAUDE.md managed-block wire |
 | `emit-opencode.mjs` | The OpenCode emits — a project's `.opencode/` and the global config dir. Deliberate twin of the above |
 | `emit-common.mjs` | Constants, tree walkers, and the three writers BOTH global emits share. Decides no host |
 | `stubs.mjs` | Write-once seed files: context, wiki, rules, excludes, profile, `.gitignore`, memory/notebook indexes |
 | `version.mjs` | The release marker: fingerprint the sources, read/compare/write an install's version, warn on downgrade |
-| `driver.mjs` | The generator driver: `--emit`/`--theme`/`--footprint` flag parsing, the eleven emit targets, per-host emit orchestration, the prune and the manifest. `bin/build-driver.mjs` is only its entry |
+| `driver.mjs` | The generator driver: `--emit`/`--theme`/`--footprint` flag parsing, the nine emit targets, per-host emit orchestration, the prune and the manifest. `bin/build-driver.mjs` is only its entry |
 | `generate.mjs` | CLI verbs `build`, `prompt`, `theme`, `rebuild-all` — the thin face over `driver.mjs` |
 | `catalog.mjs` | `geneseed catalog` — prints the shipped roster. Classifies nothing itself |
 | `themes.mjs` | Maintainer-only `--sync-themes`: inserts `_TEMPLATE.json`'s missing keys into the committed themes |
@@ -66,8 +66,8 @@ user co-owns, and the hook verbs those emitted configs then run.
 
 | module | owns |
 |---|---|
-| `hosts.mjs` | The five host config dirs (opencode/claude/bob/copilot/openclaude), plus `resolvePath`/`expanduser` |
-| `hooks.mjs` | The verbs the emitted hooks run every session: `context`, `git-gate`, `rule-gate`, `tool-gate` (the two gates fused, for Copilot), `learn`. `--host` picks the verdict dialect |
+| `hosts.mjs` | The four host config dirs (opencode/claude/bob/openclaude), plus `resolvePath`/`expanduser` |
+| `hooks.mjs` | The verbs the emitted hooks run every session: `context`, `git-gate`, `rule-gate`, `tool-gate` (the two gates fused, for Bob), `learn`. `--host` picks the verdict dialect |
 | `settings.mjs` | Merges into user-owned `settings.json`/`opencode.json`; owns the hook shim and the managed blocks |
 | `native.mjs` | Capability specs → host-native subagents and skills. The impure half of the emit |
 | `opencode.mjs` | OpenCode-only extras: colour themes, primary agent, `/commands`, plugins, overrides stub |
@@ -118,6 +118,7 @@ into files users have committed, so change the test that states it in the same c
 | `text.mjs` | String primitives: `codePointLength`, `WHITESPACE`, `parseIntStrict`, `percentDecode` |
 | `udiff.mjs` | `geneseed diff`'s own difflib clone — the alignment IS the printed hunks — plus `splitLines` |
 | `proc.mjs` | One constant: the `windowsHide` flag every spawn in `js/` must reuse |
+| `node-floor.mjs` | The first import of all three binaries: below Node 22.3, one sentence on stderr and exit 1 (0 in the hook) instead of a stack trace |
 
 **Before editing:** parse with `parseJson`, never `JSON.parse` — the latter collapses int `1` and
 float `1.0` into one double, and that value gets written into a user's file. Do not swap in a diff
@@ -168,7 +169,7 @@ the deployed harness as JSON.
 | `actions.mjs` | The mutating endpoints — rules, profile, memory, MCP, excludes — plus install/deploy argv |
 | `daemon.mjs` | Detached web start/stop/status/restart, the `.geneseed-web.json` record, and `openUrl` |
 | `jobs.mjs` | `JobManager` and the action→argv table. The only module here that spawns job children |
-| `docs.mjs` | The Docs tab: the `docs/web/` page registry, `?harness=` filtering, the five page kinds |
+| `docs.mjs` | The Docs tab: the `docs/<folder>/` page registry, `?harness=` filtering, link rewriting, the six page kinds |
 | `activity.mjs` | The `activity/` session files: pid-liveness prune, list, detail, and the on/off flag |
 
 **Before editing:** `makeHandler(state, jm, token, dist, holder)`'s arity is load-bearing — three
@@ -190,6 +191,6 @@ and inline lists are held against a surface list written out in
 | a web endpoint | GET → `js/web/api.mjs`; POST → `js/web/actions.mjs` | declare it in `js/web/routes.mjs`; the partition test probes the real handler |
 | a CLI verb | `js/cli-table.json` — the table IS the parser | the `VERBS` row in `bin/geneseed-cli.mjs`, the row count in `cli_table.test.mjs`, `NATIVE` in **two** test files |
 | a hook verb | `js/hosts/hooks.mjs` | `claudeHookGroups` in `settings.mjs`, `VERBS` in `bin/geneseed-hook.mjs`. Keep the import graph tiny |
-| a console doc page | `docs/web/<id>.md` — the stem is the id | `docs/extending.md` §4c. Only `kind: "concept"` gets `{N_*}` substitution |
+| a console doc page | `docs/<understand|guides|concepts|reference>/<id>.md` — the stem is the id | `docs/extending.md` §4c. Only `kind: "concept"` gets `{N_*}` substitution |
 | an OpenCode plugin | `adapters/opencode/plugins/geneseed-<name>.js` | `docs/extending.md` §4a — the `geneseed-` prefix is mechanically load-bearing |
 | to change a `js/lib/` primitive | `tests/fixtures/pure_probe.mjs` **first** | the docblock says which Node default it deliberately departs from — change that sentence too, or the next reader restores the default |

package/js/build/driver.mjs

@@ -1,5 +1,5 @@
 /**
- * The generator driver — flag parsing, the eleven emit targets, and the per-host emit orchestration.
+ * The generator driver — flag parsing, the nine emit targets, and the per-host emit orchestration.
  * `bin/build-driver.mjs` (`geneseed-build`) is only its entry; this module is what the CLI verbs
  * (`build`, `setup`, `migrate`, `doctor`, `diff`, `validate`, the web console) import. It lived in
  * `bin/` until 2026-09, which made nine `js/` modules import upward from a binary.
@@ -51,7 +51,7 @@ import { parseJson, jsonDumpsIndent } from '../lib/json.mjs';
 // that should exist twice. golden.py's 259 cells are what made the move safe to attempt.
 import {
   GLOBAL_MANIFEST, resolvePath, opencodeConfigDir, claudeConfigDir, bobConfigDir,
-  copilotConfigDir, openclaudeConfigDir, hostCatalogsNatively,
+  openclaudeConfigDir, hostCatalogsNatively,
 } from '../hosts/hosts.mjs';
 
 // P5d moved these out of this file for the reason P5c moved the host resolvers: `harness
@@ -71,9 +71,9 @@ import { registryRecord, registryRoots } from '../inspect/registry.mjs';
 // maintainer pair that needs nothing this driver is banned from having.
 import { syncThemes } from './themes.mjs';
 
-/** The eleven `--emit` choices: build.py:337-338's nine, then OpenClaude's pair. */
+/** The nine `--emit` choices: a plain bundle, then a project and a global emit per host. */
 const EMITS = ['files', 'opencode', 'opencode-global', 'claude', 'claude-global',
-  'bob', 'bob-global', 'copilot', 'copilot-global', 'openclaude', 'openclaude-global'];
+  'bob', 'bob-global', 'openclaude', 'openclaude-global'];
 
 /** `_build_emit.PRIMARY_AGENT_SRC`. */
 const PRIMARY_AGENT_SRC = path.join(ROOT, 'adapters', 'opencode', 'agents', 'orchestrator.md');
@@ -497,7 +497,7 @@ export function hookRunnerEntry() {
  * to suppress the GLOBAL preamble of the same host, or null for a host that gets none.
  *
  * `_PREAMBLE_CONFIG_DIR` has exactly one key, so only a `CLAUDE.md` carrier resolves to a
- * value: Bob's and Copilot's `AGENTS.md`, and Copilot's `copilot-instructions.md`, get null.
+ * value: Bob's `AGENTS.md` gets null.
  *
  * Computed HERE and not in the render child, and that is the inverted boundary rule doing
  * real work rather than being restated. P3b's note on the Python original: it resolves
@@ -519,10 +519,8 @@ function preambleExclude(claudeMd, host) {
 /**
  * `_build_global._warn_bob_global_over_project` — informational, never auto-removes.
  *
- * Same shape as `warnCopilotGlobalOverProject` and a DIFFERENT message, because the two
- * hosts differ in what they can promise: Copilot simply stacks both preambles, while Bob's
- * workspace rules may or may not shadow the global copy depending on precedence nothing can
- * verify at emit time — so this text hedges where Copilot's asserts.
+ * The text hedges on purpose: Bob's workspace rules may or may not shadow the global copy,
+ * depending on a precedence nothing can verify at emit time.
  */
 function warnBobGlobalOverProject() {
   const survivors = projectSurvivors('bob');
@@ -646,27 +644,6 @@ function projectSurvivors(emitName) {
   return out;
 }
 
-/**
- * `_build_global._warn_copilot_global_over_project` — purely informational.
- *
- * Copilot documents no exclude or shadow mechanism, so a global preamble and a project
- * one simply stack. UNREACHABLE from every golden cell: each emits into a fresh sandbox
- * whose registry is empty, so `projectSurvivors` is always `[]` and this never prints.
- * Reaching it needs a project emit registered BEFORE a global one in the same sandbox.
- */
-function warnCopilotGlobalOverProject() {
-  const survivors = projectSurvivors('copilot');
-  if (!survivors.length) return;
-  process.stderr.write(
-    `[geneseed] WARN: ${survivors.length} project Copilot install(s) already exist — `
-    + 'emitting GLOBAL now means BOTH preambles load together in those repos '
-    + '(doubled context): Copilot stacks ~/.copilot/copilot-instructions.md on top '
-    + "of a repo's own AGENTS.md. Review and remove what you don't want:\n");
-  for (const root of survivors) {
-    process.stderr.write(`  - ${root}  ->  geneseed uninstall --target "${root}"\n`);
-  }
-}
-
 /**
  * `_build_emit.emit_opencode` — the driver body, which is what this phase actually ports.
  *
@@ -776,22 +753,14 @@ function emitOpencodeGlobal(cfg, args, out) {
 }
 
 /**
- * `_build_global._emit_claude_core` — the shared engine behind six emits.
- *
- * Only the two Copilot ones run through it so far, and that is a deliberate split rather
- * than an arbitrary stopping point: `js/build/emit-claude.mjs's wire` gates the entire settings/hook path
- * behind `if (!isCopilot)`, so a Copilot emit never reaches `hookPrefix` and therefore never
- * needs `hookOpts` — the pair of machine-absolute values (`sys.executable` and the harness
- * entry point) that a Node driver has no way to produce. Copilot crossing first isolates
- * this driver body from that question entirely.
+ * `_build_global._emit_claude_core` — the shared engine behind six emits (Claude, Bob and
+ * OpenClaude, each per-repo and global).
  *
- * `hookOpts` is OMITTED for a host that does not wire hooks, rather than passed as `{}` or
- * `null`. If a future change ever routed a Copilot emit into the hook path, `hookPrefix()`
- * would receive `undefined`, hit its own default and throw the error it was built to throw
- * — where `null` would raise an unrelated TypeError and `{}` would bake the literal string
- * `"undefined"` into the shim and silently kill every hook in the install. Fail loud, on
- * purpose. The four hook-writing hosts pass a real pair from `hookRunnerEntry()`, which
- * cannot fail to produce one — `process.execPath` is the node already running.
+ * Every caller passes a real `hookOpts` pair from `hookRunnerEntry()`, which cannot fail to
+ * produce one — `process.execPath` is the node already running. Were it ever omitted,
+ * `hookPrefix()` would receive `undefined`, hit its own default and throw the error it was
+ * built to throw — where `null` would raise an unrelated TypeError and `{}` would bake the
+ * literal string `"undefined"` into the shim and silently kill every hook in the install.
  */
 function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpts }) {
   const manifestPath = path.join(cfgDir, GLOBAL_MANIFEST);
@@ -799,12 +768,10 @@ 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 isCopilot = host === 'copilot';
 
-  // RENDER + WIRE in one child's worth of work. `preambleExclude` is null for every host
-  // but Claude — `_PREAMBLE_CONFIG_DIR` has exactly one key, `CLAUDE.md` — so neither
-  // Copilot carrier filename (copilot-instructions.md, AGENTS.md) resolves to one, and
-  // neither does Bob's. Spelling it as a call rather than a literal is what makes that a
+  // RENDER + WIRE in one child's worth of work. `preambleExclude` is null for every
+  // carrier but `CLAUDE.md` — `_PREAMBLE_CONFIG_DIR` has exactly one key — so Bob's
+  // `AGENTS.md` does not resolve to one. Spelling it as a call rather than a literal is what makes that a
   // measured `null` instead of an assumed one.
   const rendered = emitClaudeRender(cfg, {
     theme: args.theme, cfgDir, claudeMd, scope, host,
@@ -832,8 +799,7 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
   // VERIFY — re-read the settings file just written and match it against the claims just
   // recorded, so a merge that silently did not stick (a commented file, a mid-flight
   // external edit, a bug in the merge) is loud now instead of surfacing as hooks that
-  // quietly never fire. Copilot's settings have their own shape and their own check; a
-  // Copilot PROJECT emit records no hooks and so checks nothing.
+  // quietly never fire.
   //
   // On the Python driver this stage runs in Python AFTER a Node child did the wiring, which
   // makes it a live cross-implementation check on every build. Here both halves are Node, so
@@ -845,10 +811,8 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
   // deleting this call is byte-identical in all 259 cells. `test_verify_reports_an_orphaned
   // _geneseed_hook` plants the fault that makes it speak.
   phaseLog('VERIFY');
-  if (!isCopilot || managed.settings_hooks) {
-    settingsIntegrityCheck(
-      path.join(cfgDir, managed.settings_file || 'settings.json'), managed, 'present');
-  }
+  settingsIntegrityCheck(
+    path.join(cfgDir, managed.settings_file || 'settings.json'), managed, 'present');
   return {
     nAgents: stats.nAgents,
     nSkills: stats.nSkills,
@@ -858,38 +822,6 @@ function emitClaudeCore(cfg, args, { cfgDir, claudeMd, scope, host, out, hookOpt
   };
 }
 
-/** `_build_global.emit_copilot` — per-repo: AGENTS.md at the repo root + a `.github/` layer. */
-function emitCopilot(cfg, args, out) {
-  const root = args.root ? resolveOut(args.root) : out;
-  const cfgDir = path.join(root, '.github');
-  const r = emitClaudeCore(cfg, args, {
-    cfgDir, claudeMd: path.join(root, 'AGENTS.md'), scope: 'project', host: 'copilot', out,
-  });
-  process.stdout.write(`[geneseed] copilot (folder) -> ${root}: AGENTS.md + .github/ `
-    + `(${r.nAgents} agents (.agent.md), ${r.nSkills} skills), ${r.memStatus}, `
-    + `${r.nbStatus}. No hooks at project scope (Copilot reads hooks from `
-    + '~/.copilot/settings.json only — the global emit wires them).\n');
-  return cfgDir;
-}
-
-/** `_build_global.emit_copilot_global` — into Copilot's personal config dir (~/.copilot). */
-function emitCopilotGlobal(cfg, args, out) {
-  const cfgDir = args.cfgDir ?? copilotConfigDir();
-  warnCopilotGlobalOverProject();
-  // The hook runner pair, as for Claude and Bob: the global emit is the one Copilot scope
-  // that wires hooks (`~/.copilot/settings.json`), and the shim it bakes is machine-wide.
-  const hookOpts = hookRunnerEntry();
-  const r = emitClaudeCore(cfg, args, {
-    cfgDir, claudeMd: path.join(cfgDir, 'copilot-instructions.md'),
-    scope: 'global', host: 'copilot', out, hookOpts,
-  });
-  process.stdout.write(`[geneseed] copilot-global -> ${cfgDir}: ${r.nAgents} agents (.agent.md), `
-    + `${r.nSkills} skills, copilot-instructions.md, ${r.memStatus}, ${r.nbStatus}, `
-    + `${r.nHooks} hooks (settings.json: sessionStart context, preToolUse gate, agentStop + `
-    + 'preCompact learn); MCP servers go in mcp-config.json.\n');
-  return cfgDir;
-}
-
 /**
  * `_build_global.emit_claude_global` — into Claude Code's global config dir (~/.claude).
  *
@@ -1018,7 +950,7 @@ function writeMarkers(markerDir, emit, footprint) {
     mkdirSync(markerDir, { recursive: true });
     writeText(path.join(markerDir, '.geneseed-emit'), `${emit}\n`);
     // Written for EVERY emit (build.py:443, unconditional), unlike the theme marker:
-    // the claude/bob/copilot PROJECT installs never call build(), so this is their only
+    // the claude/bob/openclaude PROJECT installs never call build(), so this is their only
     // footprint record. Read by harness._footprint_of_dir, which defaults to 'full'.
     writeText(path.join(markerDir, '.geneseed-footprint'), `${footprint}\n`);
   } catch { /* best-effort, exactly as build.py:444-445 — a marker hiccup never fails a build */ }
@@ -1049,14 +981,13 @@ const GLOBAL_EMITS = {
   opencode: emitOpencodeGlobal,
   claude: emitClaudeGlobal,
   bob: emitBobGlobal,
-  copilot: emitCopilotGlobal,
   openclaude: emitOpenclaudeGlobal,
 };
 
 /**
  * The PER-REPO half of the same idea, and `doctor` is its only caller.
  *
- * `_claude_bob_emit_problems` renders `emit_claude`, `emit_bob` and `emit_copilot` into
+ * `_claude_bob_emit_problems` renders `emit_claude`, `emit_bob` and `emit_openclaude` into
  * throwaway sandboxes and scans each — the three emits that write CLAUDE.md/AGENTS.md
  * straight into a repo, and the ones outside doctor's sweep when the skill-table dead links
  * shipped.
@@ -1072,7 +1003,7 @@ const GLOBAL_EMITS = {
  * three-positional call leaves in place, inherited here rather than re-decided.
  */
 const PROJECT_EMITS = {
-  claude: emitClaude, bob: emitBob, copilot: emitCopilot, openclaude: emitOpenclaude,
+  claude: emitClaude, bob: emitBob, openclaude: emitOpenclaude,
   // P2. `opencode` joins the three for `cmdValidate`, which has to be able to render EVERY
   // `--emit` choice into its sandbox and not only the three doctor already scans. Its call
   // shape is `emitClaude`'s exactly — `(cfg, args, out)` — so the row is the whole change.
@@ -1210,7 +1141,7 @@ function run(argv) {
     markerDir = GLOBAL_EMITS[args.emit.slice(0, -'-global'.length)](cfg, args, out);
   } else if (args.emit !== 'files') {
     // The PROJECT emits keep their markers in `out`, not in the host config dir the emit
-    // wrote to (build.py:435-436) — `.github/` is the layer, `out` is the install.
+    // wrote to (build.py:435-436) — `.claude/` is the layer, `out` is the install.
     PROJECT_EMITS[args.emit](cfg, args, out);
   } else {
     // The ninth choice, a plain bundle: `nativeCatalog: false` is build.py:421's
@@ -1223,7 +1154,7 @@ function run(argv) {
   writeMarkers(markerDir, args.emit, args.footprint);
   // build() drops a .geneseed-theme in `out` for the emits that call it; the global emits
   // render into the config dir WITHOUT calling build(), so the theme is recorded here.
-  // Deliberately not written for the claude/bob/copilot PROJECT emits — they carry none,
+  // Deliberately not written for the claude/bob/openclaude PROJECT emits — they carry none,
   // and `_harness_setup._installed_defaults` detects those by an AGENT.md sigil scan
   // instead. Writing one for them would change the emitted tree.
   if (args.emit.endsWith('-global')) {
@@ -1234,7 +1165,7 @@ function run(argv) {
   // An ALLOW-LIST, not "everything that is not global": a plain `--emit files` dev build —
   // the default — must never pollute the registry, and only the four per-repo host emits
   // are ones `_EMIT_HOST_SCOPE` can map back to a row. Records `out`, where the marker is.
-  if (['opencode', 'claude', 'bob', 'copilot', 'openclaude'].includes(args.emit)) {
+  if (['opencode', 'claude', 'bob', 'openclaude'].includes(args.emit)) {
     registryRecord(markerDir);
   }
   return 0;