chore(myco): refresh Myco integration and runtime hooks

Upgrade Myco integration to the latest runtime capabilities.
This involves:
*   Refactoring Myco hook guards for robust cross-platform execution and layered binary resolution.
*   Introducing project identity and binding through "Grove."
*   Updating the core Myco configuration schema from v6 to v9, including new Cortex and release provenance settings.
*   Migrating agent integrations (Codex, Opencode) to connect directly to the Myco daemon via URL, leveraging enriched request context (project, session, branch), and adding pre-tool-use hooks.
*   Aligning internal file management with Myco's updated structure, reflected in gitignore changes.

Author: sirkirby

.agents/myco-cli.cjs

@@ -0,0 +1,118 @@
+#!/usr/bin/env node
+// Myco hook guard — silently no-ops when myco is not installed.
+//
+// This file is committed to the repo so open-source contributors without
+// Myco don't see hook errors in their agent sessions. It stays deliberately
+// thin: its only jobs are (1) provide a cross-platform entry point that
+// works under every shell our symbionts fire hooks from, and (2) resolve
+// which myco binary to exec via the layered runtime.command pin
+// (project-scope `<project>/.myco/runtime.command` first, then machine-scope
+// `~/.myco/runtime.command`).
+//
+// Managed by: myco init / myco update
+// Safe to delete: myco remove
+'use strict';
+
+// Skip hooks for Myco's own agent pipeline sessions — they are internal
+// and should not be captured as user sessions.
+if (process.env.MYCO_AGENT_SESSION) process.exit(0);
+
+const fs = require('node:fs');
+const os = require('node:os');
+const path = require('node:path');
+const { execFileSync } = require('node:child_process');
+
+// Defensively pin cwd to the project root. Cursor's hook spawn drops stdin
+// when the command uses shell operators, so our installed hook commands
+// invoke this guard directly (no `cd "$(...)" &&` prefix). The chdir keeps
+// vault resolution working even when the spawning agent's cwd isn't set.
+try { process.chdir(path.resolve(__dirname, '..')); } catch { /* best effort */ }
+
+// Resolve which myco binary to invoke.
+//
+// `~/.myco/runtime.command` is the source of truth — a one-line plain-text
+// file holding either a PATH-resolvable name (the default for globally-
+// installed users is the file's absence) or an absolute path to a managed/
+// dev binary (what `make dev-link` writes; what the beta-channel installer
+// writes). Absolute paths bypass PATH entirely, which matters because GUI-
+// launched agents (Cursor, Claude Code desktop, etc.) run under macOS
+// launchd and inherit a minimal PATH that typically doesn't include
+// `~/.local/bin`.
+//
+// Machine-scoped: there's exactly one daemon per machine, and the runtime
+// that backs it is a machine-level choice, not per-project.
+const args = process.argv.slice(2);
+const bin = readLayeredRuntimeCommand() ?? 'myco';
+
+function readPinFile(filePath) {
+  try {
+    const raw = fs.readFileSync(filePath, 'utf-8').trim();
+    return raw || null;
+  } catch { return null; }
+}
+
+function readProjectRuntimeCommand(startDir) {
+  let dir = path.resolve(startDir);
+  while (true) {
+    const pin = readPinFile(path.join(dir, '.myco', 'runtime.command'));
+    if (pin) return pin;
+    const parent = path.dirname(dir);
+    if (parent === dir) return null;
+    dir = parent;
+  }
+}
+
+function readMachineRuntimeCommand() {
+  const home = process.env.MYCO_HOME ? expandHome(process.env.MYCO_HOME) : path.join(os.homedir(), '.myco');
+  return readPinFile(path.join(home, 'runtime.command'));
+}
+
+function readLayeredRuntimeCommand() {
+  return readProjectRuntimeCommand(process.cwd()) ?? readMachineRuntimeCommand();
+}
+
+function expandHome(value) {
+  if (value === '~') return os.homedir();
+  if (value.startsWith(`~${path.sep}`)) return path.join(os.homedir(), value.slice(2));
+  return value;
+}
+
+function toolNameFromArgs(args) {
+  if (args[0] !== 'tool' || args[1] !== 'call') return undefined;
+  for (let idx = 2; idx < args.length; idx++) {
+    const arg = args[idx];
+    if (arg === '--json') continue;
+    if (arg === '--input') {
+      idx++;
+      continue;
+    }
+    if (arg && !arg.startsWith('-')) return arg;
+  }
+  return undefined;
+}
+
+function writeToolRuntimeUnavailable(command, args) {
+  const tool = toolNameFromArgs(args);
+  const envelope = {
+    ok: false,
+    ...(tool ? { tool } : {}),
+    error: {
+      code: 'runtime_unavailable',
+      message: `Myco runtime command '${command}' could not be found. Check <project>/.myco/runtime.command and ~/.myco/runtime.command, or run Myco update from a shell where Myco is installed.`,
+    },
+  };
+  process.stdout.write(`${JSON.stringify(envelope, null, 2)}\n`);
+}
+
+try {
+  execFileSync(bin, args, { stdio: 'inherit' });
+} catch (e) {
+  if (e.code === 'ENOENT') {
+    if (args[0] === 'tool') {
+      writeToolRuntimeUnavailable(bin, args);
+      process.exit(1);
+    }
+    process.exit(0);
+  }
+  process.exit(e.status ?? 1);
+}

.agents/myco-run.cjs

@@ -5,7 +5,9 @@
 // Myco don't see hook errors in their agent sessions. It stays deliberately
 // thin: its only jobs are (1) provide a cross-platform entry point that
 // works under every shell our symbionts fire hooks from, and (2) resolve
-// which myco binary to exec via .myco/runtime.command.
+// which myco binary to exec via the layered runtime.command pin
+// (project-scope `<project>/.myco/runtime.command` first, then machine-scope
+// `~/.myco/runtime.command`).
 //
 // Managed by: myco init / myco update
 // Safe to delete: myco remove
@@ -16,6 +18,7 @@
 if (process.env.MYCO_AGENT_SESSION) process.exit(0);
 
 const fs = require('node:fs');
+const os = require('node:os');
 const path = require('node:path');
 const { execFileSync } = require('node:child_process');
 
@@ -27,27 +30,89 @@ try { process.chdir(path.resolve(__dirname, '..')); } catch { /* best effort */
 
 // Resolve which myco binary to invoke.
 //
-// `.myco/runtime.command` is the source of truth — a one-line plain-text
-// file holding either a PATH-resolvable name (`myco`, the default for
-// globally-installed users) or an absolute path (`/Users/chris/.local/
-// bin/myco-dev`, what `make dev-link` writes). Absolute paths bypass
-// PATH entirely, which matters because GUI-launched agents (Cursor,
-// Claude Code desktop, etc.) run under macOS launchd and inherit a
-// minimal PATH that typically doesn't include `~/.local/bin`.
+// `~/.myco/runtime.command` is the source of truth — a one-line plain-text
+// file holding either a PATH-resolvable name (the default for globally-
+// installed users is the file's absence) or an absolute path to a managed/
+// dev binary (what `make dev-link` writes; what the beta-channel installer
+// writes). Absolute paths bypass PATH entirely, which matters because GUI-
+// launched agents (Cursor, Claude Code desktop, etc.) run under macOS
+// launchd and inherit a minimal PATH that typically doesn't include
+// `~/.local/bin`.
 //
-// We locate the alias file via __dirname so the guard doesn't depend on
-// cwd. Hook wrappers `cd` to the project root before invoking us, but
-// not every agent keeps that contract across every shell.
-let bin = 'myco';
-try {
-  const aliasPath = path.resolve(__dirname, '..', '.myco', 'runtime.command');
-  const alias = fs.readFileSync(aliasPath, 'utf-8').trim();
-  if (alias) bin = alias;
-} catch { /* missing file → use default */ }
+// Machine-scoped: there's exactly one daemon per machine, and the runtime
+// that backs it is a machine-level choice, not per-project.
+const args = process.argv.slice(2);
+const bin = readLayeredRuntimeCommand() ?? 'myco';
+
+function readPinFile(filePath) {
+  try {
+    const raw = fs.readFileSync(filePath, 'utf-8').trim();
+    return raw || null;
+  } catch { return null; }
+}
+
+function readProjectRuntimeCommand(startDir) {
+  let dir = path.resolve(startDir);
+  while (true) {
+    const pin = readPinFile(path.join(dir, '.myco', 'runtime.command'));
+    if (pin) return pin;
+    const parent = path.dirname(dir);
+    if (parent === dir) return null;
+    dir = parent;
+  }
+}
+
+function readMachineRuntimeCommand() {
+  const home = process.env.MYCO_HOME ? expandHome(process.env.MYCO_HOME) : path.join(os.homedir(), '.myco');
+  return readPinFile(path.join(home, 'runtime.command'));
+}
+
+function readLayeredRuntimeCommand() {
+  return readProjectRuntimeCommand(process.cwd()) ?? readMachineRuntimeCommand();
+}
+
+function expandHome(value) {
+  if (value === '~') return os.homedir();
+  if (value.startsWith(`~${path.sep}`)) return path.join(os.homedir(), value.slice(2));
+  return value;
+}
+
+function toolNameFromArgs(args) {
+  if (args[0] !== 'tool' || args[1] !== 'call') return undefined;
+  for (let idx = 2; idx < args.length; idx++) {
+    const arg = args[idx];
+    if (arg === '--json') continue;
+    if (arg === '--input') {
+      idx++;
+      continue;
+    }
+    if (arg && !arg.startsWith('-')) return arg;
+  }
+  return undefined;
+}
+
+function writeToolRuntimeUnavailable(command, args) {
+  const tool = toolNameFromArgs(args);
+  const envelope = {
+    ok: false,
+    ...(tool ? { tool } : {}),
+    error: {
+      code: 'runtime_unavailable',
+      message: `Myco runtime command '${command}' could not be found. Check <project>/.myco/runtime.command and ~/.myco/runtime.command, or run Myco update from a shell where Myco is installed.`,
+    },
+  };
+  process.stdout.write(`${JSON.stringify(envelope, null, 2)}\n`);
+}
 
 try {
-  execFileSync(bin, process.argv.slice(2), { stdio: 'inherit' });
+  execFileSync(bin, args, { stdio: 'inherit' });
 } catch (e) {
-  if (e.code === 'ENOENT') process.exit(0);
+  if (e.code === 'ENOENT') {
+    if (args[0] === 'tool') {
+      writeToolRuntimeUnavailable(bin, args);
+      process.exit(1);
+    }
+    process.exit(0);
+  }
   process.exit(e.status ?? 1);
 }

.codex/config.toml

@@ -1,7 +1,5 @@
 [mcp_servers.myco]
-command = "myco-run"
-args = ["mcp"]
-cwd = "."
+url = "http://127.0.0.1:20915/mcp"
 
 [features]
-codex_hooks = true
+hooks = true

.codex/hooks.json

@@ -11,6 +11,17 @@
         ]
       }
     ],
+    "PreToolUse": [
+      {
+        "hooks": [
+          {
+            "type": "command",
+            "command": "node .agents/myco-run.cjs hook pre-tool-use --symbiont codex",
+            "timeout": 3
+          }
+        ]
+      }
+    ],
     "UserPromptSubmit": [
       {
         "hooks": [

.myco/.gitignore

@@ -26,15 +26,21 @@ team/
 # Staged files generated by the myco agent
 staging/
 
-# Runtime command alias — per-contributor override for which myco binary
-# the hook guard invokes. Default (file absent) is `myco`; `make dev-link`
-# writes `myco-dev`; users can hand-edit for PATH conflicts or pinning.
-# Never committed — different contributors use different aliases.
-runtime.command
+# Grove activation marker/state — local to this checkout and contains
+# machine-local paths and import metadata; never committed.
+migration/
 
-# Project-local managed runtime used for beta isolation
-runtime/
-runtime.tmp/
+# Grove project binding — per-machine. `project.toml` itself is committed
+# (portable project + Grove identity); the binding lives here.
+project.local.toml
 
 # Per-user appearance and settings overrides
 local.yaml
+
+# Project-scope runtime pin written by `make dev-link`. Per-machine,
+# never committed.
+runtime.command
+
+# Grove migration archive — timestamped snapshot of pre-Grove vault data
+# moved aside post-activation. Never committed; recoverable on disk.
+.archive-*/