From 3943146484994e50412aa5f5ef851919be1ff5f7 Mon Sep 17 00:00:00 2001
From: Tom Boucher <trekkie@nomorestars.com>
Date: Sun, 10 May 2026 23:08:35 -0400
Subject: [PATCH 1/3] feat: migrate legacy codex hooks cleanup

---
 bin/install.js                                |  96 ++-----
 docs/ARCHITECTURE.md                          |  84 ++++--
 docs/adr/0008-installer-migration-module.md   |  17 ++
 docs/installer-migrations.md                  |  64 ++++-
 .../bin/lib/installer-migrations.cjs          | 212 +++++++++++++--
 .../001-legacy-orphan-files.cjs               |   4 +
 .../002-codex-legacy-hooks-json.cjs           |  80 ++++++
 ...codex-legacy-hooks-json-migration.test.cjs |  26 +-
 tests/installer-migrations.test.cjs           | 246 +++++++++++++++++-
 9 files changed, 708 insertions(+), 121 deletions(-)
 create mode 100644 get-shit-done/bin/lib/installer-migrations/002-codex-legacy-hooks-json.cjs

diff --git a/bin/install.js b/bin/install.js
index bdfa4e242..7cc17d601 100755
--- a/bin/install.js
+++ b/bin/install.js
@@ -777,76 +777,6 @@ function rewriteLegacyCodexHookBlock(content, absoluteRunner) {
   return { content: updated, changed };
 }
 
-function isManagedCodexHookCommand(command, targetDir) {
-  if (typeof command !== 'string') return false;
-  if (typeof targetDir !== 'string' || targetDir.length === 0) return false;
-  const normalizedCommand = command.replace(/\\/g, '/');
-  const managedHooksDir = `${path.join(targetDir, 'hooks').replace(/\\/g, '/')}/`;
-  if (!normalizedCommand.includes(managedHooksDir)) return false;
-  return /(^|[\\/\s"'])(gsd-check-update\.js|gsd-update-check\.js)(?=$|[\s"'])/.test(normalizedCommand);
-}
-
-function pruneGsdManagedHooksJsonValue(value, targetDir) {
-  if (Array.isArray(value)) {
-    let changed = false;
-    const next = [];
-    for (const item of value) {
-      const pruned = pruneGsdManagedHooksJsonValue(item, targetDir);
-      if (pruned.changed) changed = true;
-      if (!isStructurallyEmpty(pruned.value)) next.push(pruned.value);
-      else changed = true;
-    }
-    return { value: next, changed };
-  }
-
-  if (value && typeof value === 'object') {
-    if (isManagedCodexHookCommand(value.command, targetDir)) {
-      return { value: null, changed: true };
-    }
-
-    let changed = false;
-    const next = {};
-    for (const [key, child] of Object.entries(value)) {
-      const pruned = pruneGsdManagedHooksJsonValue(child, targetDir);
-      if (pruned.changed) changed = true;
-      if (!isStructurallyEmpty(pruned.value)) next[key] = pruned.value;
-      else changed = true;
-    }
-    return { value: next, changed };
-  }
-
-  return { value, changed: false };
-}
-
-function isStructurallyEmpty(value) {
-  if (value === null || value === undefined) return true;
-  if (Array.isArray(value)) return value.length === 0;
-  return typeof value === 'object' && Object.keys(value).length === 0;
-}
-
-function cleanupLegacyCodexHooksJson(targetDir) {
-  const hooksPath = path.join(targetDir, 'hooks.json');
-  if (!fs.existsSync(hooksPath)) return { changed: false, removedFile: false };
-
-  let parsed;
-  try {
-    parsed = JSON.parse(fs.readFileSync(hooksPath, 'utf8'));
-  } catch {
-    return { changed: false, removedFile: false, skipped: 'invalid_json' };
-  }
-
-  const pruned = pruneGsdManagedHooksJsonValue(parsed, targetDir);
-  if (!pruned.changed) return { changed: false, removedFile: false };
-
-  if (isStructurallyEmpty(pruned.value)) {
-    fs.unlinkSync(hooksPath);
-    return { changed: true, removedFile: true };
-  }
-
-  atomicWriteFileSync(hooksPath, JSON.stringify(pruned.value, null, 2) + '\n', 'utf8');
-  return { changed: true, removedFile: false };
-}
-
 /**
  * Build a hook command path using forward slashes for cross-platform compatibility.
  * On Windows, $HOME is not expanded by cmd.exe/PowerShell, so we use the actual path.
@@ -7620,9 +7550,6 @@ function install(isGlobal, runtime = 'claude') {
     isGlobal,
   });
 
-  // Run manifest-backed cleanup migrations before package materialization.
-  runInstallerMigrations({ configDir: targetDir });
-
   // #3245 — Codex idempotent rollback. Capture pre-install state of ALL
   // directories and files GSD will mutate so that any post-install validation
   // failure (config.toml schema check, write failure, etc.) can revert the
@@ -7653,6 +7580,13 @@ function install(isGlobal, runtime = 'claude') {
   // Map<filename, Buffer> — content snapshot of each pre-existing gsd-* agent file.
   const codexPreInstallAgentContents = new Map();
   let codexPreInstallVersionBytes = null;
+  let installerMigrationResult = null;
+  const rollbackInstallerMigrations = () => {
+    if (!installerMigrationResult || typeof installerMigrationResult.rollback !== 'function') return;
+    const rollback = installerMigrationResult.rollback;
+    installerMigrationResult = null;
+    rollback();
+  };
   if (isCodex && !isMinimalMode(installMode)) {
     const _preSkillsDir = path.join(targetDir, 'skills');
     if (fs.existsSync(_preSkillsDir)) {
@@ -7708,6 +7642,7 @@ function install(isGlobal, runtime = 'claude') {
   // The full restoreCodexSnapshot() (defined inside the config block) additionally
   // handles config.toml, which is not yet touched at this point in the pipeline.
   const _codexPreConfigRollback = !isCodex || isMinimalMode(installMode) ? null : () => {
+    rollbackInstallerMigrations();
     // skills/gsd-* — pass 1: restore snapshot entries (may be absent if deleted mid-install).
     const _earlySkillsDir = path.join(targetDir, 'skills');
     for (const skillName of codexPreInstallSkillNames) {
@@ -7784,6 +7719,15 @@ function install(isGlobal, runtime = 'claude') {
     _earlyCleanTmpFiles(targetDir);
   };
 
+  // Run manifest-backed cleanup migrations after rollback snapshots exist and
+  // before package materialization. Codex rollback paths invoke the migration
+  // rollback handle if a later install step fails.
+  installerMigrationResult = runInstallerMigrations({
+    configDir: targetDir,
+    runtime,
+    scope: isGlobal ? 'global' : 'local',
+  });
+
   // #3245 CR finding 2 — wrap the pre-config install operations in a try/catch so
   // that ANY throw between snapshot capture and the Codex config block triggers rollback.
   // Non-Codex paths are unaffected (_codexPreConfigRollback is null for them).
@@ -8445,6 +8389,7 @@ function install(isGlobal, runtime = 'claude') {
     // existence checks. Safe to call before any snapshots are captured (variables
     // default to empty Set / null). Does NOT touch non-gsd-* user content.
     const restoreCodexSnapshot = () => {
+      rollbackInstallerMigrations();
       // 1. config.toml
       if (codexConfigPreInstallSnapshot !== null) {
         try { fs.writeFileSync(codexConfigPathPreInstall, codexConfigPreInstallSnapshot); }
@@ -8708,10 +8653,6 @@ function install(isGlobal, runtime = 'claude') {
         throw wrapped;
       }
       console.log(`  ${green}✓${reset} Configured Codex hooks (SessionStart)`);
-      const legacyHooksCleanup = cleanupLegacyCodexHooksJson(targetDir);
-      if (legacyHooksCleanup.changed) {
-        console.log(`  ${green}✓${reset} Removed legacy GSD hooks.json entries`);
-      }
     } catch (e) {
       // #2760 — schema-validation and write failures must be loud and fatal
       // so the user is never left with a config Codex refuses to load (or no
@@ -10804,7 +10745,6 @@ if (process.env.GSD_TEST_MODE) {
     rewriteLegacyManagedNodeHookCommands,
     buildCodexHookBlock,
     rewriteLegacyCodexHookBlock,
-    cleanupLegacyCodexHooksJson,
   };
 } else {
 
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index e726f335b..989fb8fe0 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -484,7 +484,8 @@ UI-SPEC.md (per phase) ───────────────────
 
 ```
 ~/.claude/                          # Claude Code (global install)
-├── commands/gsd/*.md               # Slash commands (authoritative roster: docs/INVENTORY.md)
+├── skills/gsd-*/SKILL.md           # Global skills (authoritative roster: docs/INVENTORY.md)
+├── commands/gsd/*.md               # Local Claude installs use slash commands instead of global skills
 ├── get-shit-done/
 │   ├── bin/gsd-tools.cjs           # CLI utility
 │   ├── bin/lib/*.cjs               # Domain modules (authoritative roster: docs/INVENTORY.md)
@@ -500,12 +501,20 @@ UI-SPEC.md (per phase) ───────────────────
 
 Equivalent paths for other runtimes:
 
-- **OpenCode:** `~/.config/opencode/` or `~/.opencode/`
-- **Kilo:** `~/.config/kilo/` or `~/.kilo/`
-- **Gemini CLI:** `~/.gemini/`
-- **Codex:** `~/.codex/` (uses skills instead of commands)
-- **Copilot:** `~/.github/`
-- **Antigravity:** `~/.gemini/antigravity/` (global) or `./.agent/` (local)
+- **OpenCode:** `~/.config/opencode/` global or `./.opencode/` local
+- **Kilo:** `~/.config/kilo/` global or `./.kilo/` local
+- **Gemini CLI:** `~/.gemini/` global or `./.gemini/` local
+- **Codex:** `~/.codex/` global or `./.codex/` local
+- **Copilot:** `~/.copilot/` global or `./.github/` local
+- **Antigravity:** `~/.gemini/antigravity/` global or `./.agent/` local
+- **Cursor:** `~/.cursor/` global or `./.cursor/` local
+- **Windsurf:** `~/.codeium/windsurf/` global or `./.windsurf/` local
+- **Augment Code:** `~/.augment/` global or `./.augment/` local
+- **Trae:** `~/.trae/` global or `./.trae/` local
+- **Qwen Code:** `~/.qwen/` global or `./.qwen/` local
+- **Hermes Agent:** `~/.hermes/` global or `./.hermes/` local
+- **CodeBuddy:** `~/.codebuddy/` global or `./.codebuddy/` local
+- **Cline:** `~/.cline/` global or project-root `.clinerules` local
 
 ### Project Files (`.planning/`)
 
@@ -587,11 +596,11 @@ verification.
 
 ## Installer Architecture
 
-The installer (`bin/install.js`, ~3,000 lines) handles:
+The installer (`bin/install.js`, ~10,700 lines) handles:
 
-1. **Runtime detection** — Interactive prompt or CLI flags (`--claude`, `--opencode`, `--gemini`, `--kilo`, `--codex`, `--copilot`, `--antigravity`, `--cursor`, `--windsurf`, `--trae`, `--cline`, `--augment`, `--all`)
+1. **Runtime detection** — Interactive prompt or CLI flags (`--claude`, `--opencode`, `--gemini`, `--kilo`, `--codex`, `--copilot`, `--antigravity`, `--cursor`, `--windsurf`, `--augment`, `--trae`, `--qwen`, `--hermes`, `--codebuddy`, `--cline`, `--all`)
 2. **Location selection** — Global (`--global`) or local (`--local`)
-3. **File deployment** — Copies commands, workflows, references, templates, agents, hooks
+3. **File deployment** — Copies commands, skills, workflows, references, templates, agents, and hooks
 4. **Runtime adaptation** — Transforms file content per runtime:
   - Claude Code: Uses as-is
   - OpenCode: Converts commands/agents to OpenCode-compatible flat command + subagent format
@@ -600,7 +609,12 @@ The installer (`bin/install.js`, ~3,000 lines) handles:
   - Copilot: Maps tool names (Read→read, Bash→execute, etc.)
   - Gemini: Adjusts hook event names (`AfterTool` instead of `PostToolUse`)
   - Antigravity: Skills-first with Google model equivalents
+  - Cursor: Skills-first with Cursor rule references
+  - Windsurf: Skills-first with Windsurf rule references
   - Trae: Skills-first install to `~/.trae` / `./.trae` with no `settings.json` or hook integration
+  - Qwen Code: Skills-first with Qwen-branded path and prompt rewrites
+  - Hermes Agent: Category-based skills under `skills/gsd/`
+  - CodeBuddy: Skills-first with CodeBuddy path and prompt rewrites
   - Cline: Writes `.clinerules` for rule-based integration
   - Augment Code: Skills-first with full skill conversion and config management
 5. **Path normalization** — Replaces `~/.claude/` paths with runtime-specific paths
@@ -708,20 +722,46 @@ The researcher → planner → executor pipeline includes a supply-chain gate ag
 
 GSD supports multiple AI coding runtimes through a unified command/workflow architecture:
 
+### Runtime Install Contract Matrix
 
-| Runtime      | Command Format | Agent System     | Config Location          |
-| ------------ | -------------- | ---------------- | ------------------------ |
-| Claude Code  | `/gsd-command` | Task spawning    | `~/.claude/`             |
-| OpenCode     | `/gsd-command` | Subagent mode    | `~/.config/opencode/`    |
-| Kilo         | `/gsd-command` | Subagent mode    | `~/.config/kilo/`        |
-| Gemini CLI   | `/gsd-command` | Task spawning    | `~/.gemini/`             |
-| Codex        | `$gsd-command` | Skills           | `~/.codex/`              |
-| Copilot      | `/gsd-command` | Agent delegation | `~/.github/`             |
-| Antigravity  | Skills         | Skills           | `~/.gemini/antigravity/` |
-| Trae         | Skills         | Skills           | `~/.trae/`               |
-| Cline        | Rules          | Rules            | `.clinerules`            |
-| Augment Code | Skills         | Skills           | Augment config           |
+This matrix describes the runtime surfaces the installer materializes today.
+The migration-specific ownership and source snapshots live in
+[Installer Migrations](installer-migrations.md#runtime-configuration-contract-registry).
 
+| Runtime | Global root | Local root | Invocation surface | Agent surface | Config and hooks |
+| --- | --- | --- | --- | --- | --- |
+| Claude Code | `~/.claude` | `./.claude` | Global `skills/gsd-*/SKILL.md`; local `commands/gsd/*.md` | `agents/gsd-*.md` | `settings.json` hook and statusLine entries |
+| OpenCode | `~/.config/opencode` | `./.opencode` | `command/gsd-*.md` | `agents/gsd-*.md` | `opencode.json` or `opencode.jsonc`; no GSD hooks |
+| Kilo | `~/.config/kilo` | `./.kilo` | `command/gsd-*.md` | `agents/gsd-*.md` | `kilo.json` or `kilo.jsonc`; no GSD hooks |
+| Gemini CLI | `~/.gemini` | `./.gemini` | `commands/gsd/*.toml` | `agents/gsd-*.md` | `settings.json` feature flag, hooks, and statusline |
+| Codex | `~/.codex` | `./.codex` | `skills/gsd-*/SKILL.md` | `agents/` source markdown plus per-agent TOML | `config.toml` `[agents.gsd-*]`, `[features].codex_hooks`, and hook tables |
+| GitHub Copilot | `~/.copilot` | `./.github` | `skills/gsd-*/SKILL.md` and `copilot-instructions.md` | `.agent.md` files | No GSD hooks or statusline |
+| Antigravity | `~/.gemini/antigravity` | `./.agent` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Gemini-style `settings.json` hook entries when installed by GSD |
+| Cursor | `~/.cursor` | `./.cursor` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Rule references under `rules/`; no GSD hooks |
+| Windsurf | `~/.codeium/windsurf` | `./.windsurf` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Rule references under `rules/`; no GSD hooks |
+| Augment Code | `~/.augment` | `./.augment` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | No GSD hooks or statusline |
+| Trae | `~/.trae` | `./.trae` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Rule references under `rules/`; no GSD hooks |
+| Qwen Code | `~/.qwen` | `./.qwen` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Common GSD settings and hook entries where supported |
+| Hermes Agent | `~/.hermes` | `./.hermes` | `skills/gsd/DESCRIPTION.md` plus `skills/gsd/gsd-*/SKILL.md` | `agents/gsd-*.md` | Common GSD settings and hook entries where supported |
+| CodeBuddy | `~/.codebuddy` | `./.codebuddy` | `skills/gsd-*/SKILL.md` | `agents/gsd-*.md` | Common GSD settings and hook entries where supported |
+| Cline | `~/.cline` | project root | `.clinerules` | Rules only | No GSD hooks or statusline |
+
+### Upstream Contract Sources
+
+Runtime install expectations are checked against primary documentation where
+available. The current source snapshot is 2026-05-11:
+
+- Claude Code: Anthropic slash commands, settings, hooks, and subagents docs.
+- OpenCode and Kilo: OpenCode config docs and Kilo custom subagent docs.
+- Gemini CLI and Qwen Code: command/config docs; Qwen command docs were last
+  updated 2026-05-06.
+- Codex: OpenAI Codex docs and `config-schema.json`; the installer also carries
+  Codex 0.124.0 compatibility for agent table shape.
+- Copilot, Cursor, Cline, Augment, Hermes, and CodeBuddy: vendor docs for
+  custom instructions, rules, skills, or config.
+- Antigravity, Windsurf, and Trae: source-limited rows. The installer documents
+  current compatibility shims, and migrations must refresh those sources before
+  rewriting their config.
 
 ### Abstraction Points
 
diff --git a/docs/adr/0008-installer-migration-module.md b/docs/adr/0008-installer-migration-module.md
index dfeaf49cf..10883f311 100644
--- a/docs/adr/0008-installer-migration-module.md
+++ b/docs/adr/0008-installer-migration-module.md
@@ -15,6 +15,22 @@ We decided to introduce an explicit Installer Migration Module for install-time
 - Require migrations to plan first, then apply through a shared executor that owns backup, rollback, and reporting.
 - Default ambiguous or unknown files to preserve; destructive changes need managed-file evidence or explicit user choice.
 - Support dry-run output using the same planner used by apply mode.
+- Treat the runtime configuration contract registry in `docs/installer-migrations.md` as the source of truth for migrations that touch host runtime config.
+
+## Runtime Contract Decision
+
+Every migration that rewrites runtime config, moves an invocation surface, or
+retires a generated runtime artifact must cite the registry row in
+`docs/installer-migrations.md`. If the migration changes where a runtime loads
+commands, skills, agents, hooks, or rules, the PR must update both the registry
+and `docs/ARCHITECTURE.md`.
+
+The registry records what GSD installs, where it installs it, when migrations
+may touch it, who owns the surrounding config, and why the shape matches the
+host runtime. When upstream docs do not publish an API or docs version, the
+checked date is the drift sentinel. A later upstream docs or CLI release that
+changes command, skill, agent, hook, or rule loading requires a new registry
+snapshot before migration work proceeds.
 
 ## Consequences
 
@@ -23,6 +39,7 @@ We decided to introduce an explicit Installer Migration Module for install-time
 - Locally modified managed files get a consistent backup path before removal or replacement.
 - Future rollback work can become runtime-neutral instead of Codex-specific.
 - Migration authors must define ownership evidence, conflict behavior, runtime scope, and non-interactive behavior.
+- Migration authors must also define which runtime contract they are relying on and whether the upstream documentation is versioned.
 - The installer gains another state file, so tests must cover missing, legacy, and checksum-mismatch state.
 
 ## Scope
diff --git a/docs/installer-migrations.md b/docs/installer-migrations.md
index e175ec734..d8a54b635 100644
--- a/docs/installer-migrations.md
+++ b/docs/installer-migrations.md
@@ -195,11 +195,20 @@ tests for line-ending and ordering variations.
 Use for runtime config, hook registrations, feature flags, and generated
 agent registration blocks.
 
+The initial executor support is `rewrite-json`: a migration reads JSON through
+`readJson(relPath)`, returns the next parsed value in the action, and may set
+`deleteIfEmpty: true` when the remaining structure is empty. The executor owns
+the disk write, journal entry, rollback snapshot, and runtime/scope filtering.
+Use this for legacy JSON config cleanup such as Codex `hooks.json`, where GSD
+can prove ownership of individual generated hook commands but not the whole
+file.
+
 ### preserve-user
 
 Declare that a path is user-owned and must survive surrounding directory
-replacement. This action is informational in dry-run output and becomes a
-copy-through or restore operation during apply.
+replacement. This action is informational in dry-run output and blocks
+non-interactive apply until a later interactive baseline migration can ask for
+an explicit user choice.
 
 Use for profile, preferences, hand-authored instructions, and future workflow
 outputs.
@@ -279,6 +288,57 @@ sections, or hook entries, but it does not own the whole file unless the file
 was created as a GSD-only file. Config migrations should remove or rewrite
 only the owned portion.
 
+## Runtime Configuration Contract Registry
+
+Last upstream documentation check: 2026-05-11.
+
+This registry is the source of truth for migrations that touch host runtime
+configuration. Each row records:
+
+- **What:** the GSD invocation, agent, skill, rule, hook, or config surface
+- **Where:** the global and local roots the installer targets
+- **When:** install, upgrade, uninstall, and migration touch points
+- **Who:** the ownership boundary for surrounding user config
+- **Why:** the upstream loader contract or current GSD compatibility shim
+
+Migration authors must read the matching row before producing a
+`rewrite-config`, `move-managed`, or destructive cleanup action. If upstream
+docs change, update this registry, update `docs/ARCHITECTURE.md`, and add tests
+for the new shape before changing migration behavior.
+
+| Runtime | What GSD installs | Where GSD installs it | Config ownership boundary | Upstream contract snapshot |
+| --- | --- | --- | --- | --- |
+| Claude Code | Global skills in `skills/gsd-*/SKILL.md`; local slash commands in `commands/gsd/*.md`; agents in `agents/gsd-*.md`; hooks in `hooks/`; `settings.json` registrations | Global `CLAUDE_CONFIG_DIR` or `~/.claude`; local `./.claude` | GSD owns only generated skills, local commands, `gsd-*` agents, hook files, and GSD hook/statusLine entries in `settings.json` | [Slash commands](https://docs.anthropic.com/en/docs/claude-code/slash-commands), [settings](https://docs.anthropic.com/en/docs/claude-code/settings), [hooks](https://docs.anthropic.com/en/docs/claude-code/hooks), [subagents](https://docs.anthropic.com/en/docs/claude-code/sub-agents); docs not versioned, checked 2026-05-11 |
+| OpenCode | Flat markdown commands in `command/gsd-*.md`; agents in `agents/gsd-*.md`; config updates in `opencode.json` or `opencode.jsonc` | Global `OPENCODE_CONFIG_DIR`, `dirname(OPENCODE_CONFIG)`, `XDG_CONFIG_HOME/opencode`, or `~/.config/opencode`; local `./.opencode` | GSD owns generated command/agent files and GSD entries in structured config only | [Config](https://opencode.ai/docs/config/); docs published 2026-05, checked 2026-05-11 |
+| Kilo | OpenCode-style flat markdown commands in `command/gsd-*.md`; agents in `agents/gsd-*.md`; config updates in `kilo.json` or `kilo.jsonc` | Global `KILO_CONFIG_DIR`, `dirname(KILO_CONFIG)`, `XDG_CONFIG_HOME/kilo`, or `~/.config/kilo`; local `./.kilo` | GSD owns generated command/agent files and GSD entries in structured config only | [Custom subagents](https://docs.kilo.ai/docs/customize/custom-subagents); docs not versioned, checked 2026-05-11 |
+| Gemini CLI | TOML slash commands in `commands/gsd/*.toml`; agents in `agents/gsd-*.md`; `settings.json` feature flag, hooks, and statusline | Global `GEMINI_CONFIG_DIR` or `~/.gemini`; local `./.gemini` | GSD owns generated commands/agents/hooks and only GSD settings entries; local command copy may be skipped when global GSD commands already exist | [Custom commands](https://google-gemini.github.io/gemini-cli/docs/cli/custom-commands.html), [configuration](https://google-gemini.github.io/gemini-cli/docs/cli/configuration.html); docs checked 2026-05-11 |
+| Codex | Skills in `skills/gsd-*/SKILL.md`; agents as source markdown plus per-agent TOML in `agents/`; `[agents.gsd-*]` and hooks in `config.toml` | Global `CODEX_HOME` or `~/.codex`; local `./.codex` | GSD owns generated skills, generated agent TOML, `agents.gsd-*` config sections, `[features].codex_hooks` when added by GSD, and GSD hook entries | [Codex config schema](https://developers.openai.com/codex/config-schema.json), [Codex developer docs](https://developers.openai.com/codex/); docs not versioned, checked 2026-05-11; installer compatibility sentinel: Codex 0.124.0 agent table shape |
+| GitHub Copilot | Skills in `skills/gsd-*/SKILL.md`; agents as `.agent.md`; repository instructions in `copilot-instructions.md` | Global `COPILOT_CONFIG_DIR` or `~/.copilot`; local `./.github` | GSD owns generated skill/agent files and GSD-authored instruction files; no hook/statusline ownership | [Repository custom instructions](https://docs.github.com/en/copilot/how-tos/configure-custom-instructions/add-repository-instructions), [Copilot CLI custom instructions](https://docs.github.com/en/copilot/how-tos/copilot-cli/add-custom-instructions); GitHub Docs product docs, checked 2026-05-11 |
+| Antigravity | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; Gemini-style `settings.json` hooks when installed by GSD | Global `ANTIGRAVITY_CONFIG_DIR` or `~/.gemini/antigravity`; local `./.agent` | GSD owns generated skills/agents/hooks and GSD settings entries only | Public Antigravity install/config docs for this file layout were not stable or complete as of 2026-05-11; GSD uses the Gemini-compatible settings contract as a compatibility shim |
+| Cursor | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; rule references under `rules/` | Global `CURSOR_CONFIG_DIR` or `~/.cursor`; local `./.cursor` | GSD owns generated skills/agents and GSD rule files or references; no hook/statusline ownership | [Cursor rules](https://docs.cursor.com/context/rules); docs not versioned, checked 2026-05-11 |
+| Windsurf | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; rule references under `rules/` | Global `WINDSURF_CONFIG_DIR` or `~/.codeium/windsurf`; local `./.windsurf` | GSD owns generated skills/agents and GSD rule files or references; no hook/statusline ownership | Windsurf public rule docs were source-limited in search results as of 2026-05-11; installer targets the common workspace rules convention `./.windsurf/rules` and must be rechecked before migrations rewrite rules |
+| Augment Code | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/` | Global `AUGMENT_CONFIG_DIR` or `~/.augment`; local `./.augment` | GSD owns generated skills/agents only; no hook/statusline ownership | [Augment Agent Skills](https://docs.augmentcode.com/cli/skills), [Augment IDE skills](https://docs.augmentcode.com/using-augment/skills); IDE skills public beta in VS Code 0.789.0+, checked 2026-05-11 |
+| Trae | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; rule references under `rules/` | Global `TRAE_CONFIG_DIR` or `~/.trae`; local `./.trae` | GSD owns generated skills/agents and GSD rule files or references; no hook/statusline ownership | Public Trae docs expose AI settings and `.rules` announcements, but no stable skills/config API was found as of 2026-05-11; migrations must treat this row as source-limited |
+| Qwen Code | Claude-compatible skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; optional common hook/settings integration through GSD | Global `QWEN_CONFIG_DIR` or `~/.qwen`; local `./.qwen` | GSD owns generated skills/agents/hooks and GSD settings entries only | [Qwen commands and skills](https://qwenlm.github.io/qwen-code-docs/en/users/features/commands/); docs last updated 2026-05-06 |
+| Hermes Agent | Category skills under `skills/gsd/` with `DESCRIPTION.md` plus nested `gsd-*/SKILL.md`; agents in `agents/`; optional common hook/settings integration through GSD | Global `HERMES_HOME` or `~/.hermes`; local `./.hermes` | GSD owns generated `skills/gsd/` category content, generated agents, and GSD settings entries only | [Hermes configuration](https://hermes-agent.nousresearch.com/docs/user-guide/configuration), [Hermes skills](https://hermes-agent.nousresearch.com/docs/zh-Hans/user-guide/features/skills), [working with skills](https://hermes-agent.nousresearch.com/docs/guides/work-with-skills); docs checked 2026-05-11 |
+| CodeBuddy | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; optional common hook/settings integration through GSD | Global `CODEBUDDY_CONFIG_DIR` or `~/.codebuddy`; local `./.codebuddy` | GSD owns generated skills/agents/hooks and GSD settings entries only | [CodeBuddy CLI skills](https://www.codebuddy.ai/docs/cli/skills), [CodeBuddy IDE skills](https://www.codebuddy.ai/docs/ide/Features/Skills); docs checked 2026-05-11 |
+| Cline | Rule-based integration via `.clinerules` for current installer output | Global `CLINE_CONFIG_DIR` or `~/.cline`; local project root `.clinerules` | GSD owns the generated `.clinerules` file only when it created or manifest-tracked it; no hooks/statusline ownership | [Cline rules](https://docs.cline.bot/customization/cline-rules); docs prefer `.clinerules/` directory and still detect legacy rule files, checked 2026-05-11 |
+
+### Registry Authoring Rules
+
+- Use structured parsers for config files whenever the runtime provides JSON,
+  JSONC, TOML, or YAML. Marker-block rewrites need line-ending and ordering
+  tests.
+- Do not claim ownership of a mixed config file. Own only generated entries,
+  generated files, and explicit marker blocks.
+- Preserve unknown user config, even when it sits inside a GSD-managed runtime
+  root.
+- Add or update the upstream snapshot date and version note when a runtime's
+  docs, CLI schema, or loader behavior changes.
+- Treat source-limited rows as high-risk. A migration that rewrites those
+  runtimes needs either a new primary source or an installer-level probe with
+  tests.
+
 ### Rollback
 
 Before applying a migration, the executor records enough data to restore:
diff --git a/get-shit-done/bin/lib/installer-migrations.cjs b/get-shit-done/bin/lib/installer-migrations.cjs
index fba3f81eb..ac2c6a243 100644
--- a/get-shit-done/bin/lib/installer-migrations.cjs
+++ b/get-shit-done/bin/lib/installer-migrations.cjs
@@ -12,6 +12,10 @@ function sha256File(filePath) {
   return crypto.createHash('sha256').update(fs.readFileSync(filePath)).digest('hex');
 }
 
+function sha256Text(value) {
+  return crypto.createHash('sha256').update(value).digest('hex');
+}
+
 function readJsonIfPresent(filePath, fallback) {
   if (!fs.existsSync(filePath)) return fallback;
   try {
@@ -47,10 +51,22 @@ function readInstallState(configDir) {
 
 function writeInstallState(configDir, state) {
   fs.mkdirSync(configDir, { recursive: true });
-  fs.writeFileSync(path.join(configDir, INSTALL_STATE_NAME), JSON.stringify(state, null, 2) + '\n', 'utf8');
+  writeFileAtomicSync(path.join(configDir, INSTALL_STATE_NAME), JSON.stringify(state, null, 2) + '\n');
   return state;
 }
 
+function readJson(configDir, relPath) {
+  const { fullPath } = ensureInsideConfig(configDir, relPath);
+  if (!fs.existsSync(fullPath)) {
+    return { exists: false, value: null, error: null };
+  }
+  try {
+    return { exists: true, value: JSON.parse(fs.readFileSync(fullPath, 'utf8')), error: null };
+  } catch (error) {
+    return { exists: true, value: null, error };
+  }
+}
+
 function normalizeRelPath(relPath) {
   if (typeof relPath !== 'string' || relPath.trim() === '') {
     throw new Error('migration action relPath must be a non-empty string');
@@ -87,6 +103,56 @@ function appliedMigrationIds(state) {
   );
 }
 
+function appliedMigrationEntries(state) {
+  const entries = new Map();
+  for (const entry of state.appliedMigrations) {
+    if (entry && typeof entry.id === 'string' && !entries.has(entry.id)) {
+      entries.set(entry.id, entry);
+    }
+  }
+  return entries;
+}
+
+function migrationChecksum(migration) {
+  if (typeof migration.checksum === 'string' && migration.checksum) return migration.checksum;
+  const serializable = {
+    id: migration.id,
+    title: migration.title || null,
+    description: migration.description || null,
+    introducedIn: migration.introducedIn || null,
+    runtimes: migration.runtimes || null,
+    scopes: migration.scopes || null,
+    destructive: migration.destructive === true,
+    runtimeContract: migration.runtimeContract || null,
+    plan: typeof migration.plan === 'function' ? migration.plan.toString() : null,
+  };
+  return `sha256:${sha256Text(JSON.stringify(serializable))}`;
+}
+
+function assertAppliedMigrationChecksums(state, migrations) {
+  const applied = appliedMigrationEntries(state);
+  for (const migration of migrations) {
+    const entry = applied.get(migration.id);
+    if (!entry || !entry.checksum) continue;
+    const checksum = migrationChecksum(migration);
+    if (entry.checksum !== checksum) {
+      throw new Error(
+        `applied migration checksum changed for ${migration.id}; create a new fix-forward migration id`
+      );
+    }
+  }
+}
+
+function migrationMatchesContext(migration, { runtime, scope }) {
+  if (Array.isArray(migration.runtimes) && migration.runtimes.length > 0) {
+    if (!runtime || !migration.runtimes.includes(runtime)) return false;
+  }
+  if (Array.isArray(migration.scopes) && migration.scopes.length > 0) {
+    if (!scope || !migration.scopes.includes(scope)) return false;
+  }
+  return true;
+}
+
 function validateMigrationRecord(record, source) {
   if (!record || typeof record !== 'object') {
     throw new Error(`migration record must export an object: ${source}`);
@@ -108,10 +174,11 @@ function discoverInstallerMigrations({ migrationsDir }) {
     .sort()
     .flatMap((fileName) => {
       const source = path.join(migrationsDir, fileName);
+      const checksum = `sha256:${sha256File(source)}`;
       delete require.cache[require.resolve(source)];
       const exported = require(source);
       const records = Array.isArray(exported) ? exported : [exported];
-      return records.map((record) => validateMigrationRecord(record, source));
+      return records.map((record) => validateMigrationRecord({ ...record, checksum: record.checksum || checksum }, source));
     });
 }
 
@@ -129,14 +196,44 @@ function ensureInsideConfig(configDir, relPath) {
   return { normalized, fullPath };
 }
 
-function planInstallerMigrations({ configDir, migrations, now = () => new Date().toISOString() }) {
+function isStructurallyEmpty(value) {
+  if (value === null || value === undefined) return true;
+  if (Array.isArray(value)) return value.length === 0;
+  return typeof value === 'object' && Object.keys(value).length === 0;
+}
+
+function writeFileAtomicSync(filePath, content) {
+  const tmpPath = `${filePath}.tmp-${process.pid}-${Date.now()}`;
+  try {
+    fs.writeFileSync(tmpPath, content, 'utf8');
+    fs.renameSync(tmpPath, filePath);
+  } catch (error) {
+    try {
+      fs.rmSync(tmpPath, { force: true });
+    } catch {
+      // best-effort cleanup only; preserve the original write failure
+    }
+    throw error;
+  }
+}
+
+function journalAction(action, status, extras = {}) {
+  const { value, ...safeAction } = action;
+  return { ...safeAction, ...extras, status };
+}
+
+function planInstallerMigrations({ configDir, runtime = null, scope = null, migrations, now = () => new Date().toISOString() }) {
   if (!configDir) throw new Error('configDir is required');
   if (!Array.isArray(migrations)) throw new Error('migrations must be an array');
 
   const manifest = readInstallManifest(configDir);
   const state = readInstallState(configDir);
+  const scopedMigrations = migrations.filter((migration) =>
+    migration && migrationMatchesContext(migration, { runtime, scope })
+  );
+  assertAppliedMigrationChecksums(state, scopedMigrations);
   const applied = appliedMigrationIds(state);
-  const pending = migrations.filter((migration) => migration && !applied.has(migration.id));
+  const pending = scopedMigrations.filter((migration) => !applied.has(migration.id));
   const actions = [];
   const blocked = [];
   const classifications = new Map();
@@ -157,10 +254,13 @@ function planInstallerMigrations({ configDir, migrations, now = () => new Date()
     }
     const plannedActions = migration.plan({
       configDir,
+      runtime,
+      scope,
       manifest,
       state,
       now,
       classifyArtifact: classify,
+      readJson: (relPath) => readJson(configDir, relPath),
     });
     if (!Array.isArray(plannedActions)) {
       throw new Error(`migration ${migration.id} plan must return an array`);
@@ -177,6 +277,7 @@ function planInstallerMigrations({ configDir, migrations, now = () => new Date()
       }
       const action = {
         migrationId: migration.id,
+        migrationChecksum: migrationChecksum(migration),
         type: protectedType,
         relPath,
         reason: rawAction.reason || migration.description || '',
@@ -190,7 +291,11 @@ function planInstallerMigrations({ configDir, migrations, now = () => new Date()
       if (action.type === 'backup-and-remove') {
         action.backupRelPath = path.posix.join('gsd-migration-backups', migration.id, relPath);
       }
-      if (action.classification === 'unknown') blocked.push(action);
+      if (action.type === 'rewrite-json') {
+        action.value = rawAction.value;
+        action.deleteIfEmpty = rawAction.deleteIfEmpty === true;
+      }
+      if (action.classification === 'unknown' && action.type !== 'rewrite-json') blocked.push(action);
       actions.push(action);
     }
   }
@@ -209,6 +314,54 @@ function uniqueActionMigrationIds(actions) {
   return [...new Set(actions.map((action) => action.migrationId).filter(Boolean))];
 }
 
+function rollbackAppliedMigrationResult({ configDir, journal, journalPath, rollbackRoot, previousInstallStateBytes }) {
+  const failures = [];
+  for (const action of [...journal.actions].reverse()) {
+    if (!action.rollbackRelPath) continue;
+    const rollbackPath = path.join(configDir, action.rollbackRelPath);
+    const dest = path.join(configDir, action.relPath);
+    try {
+      if (fs.existsSync(rollbackPath)) {
+        fs.mkdirSync(path.dirname(dest), { recursive: true });
+        fs.copyFileSync(rollbackPath, dest);
+      }
+    } catch (error) {
+      failures.push({ relPath: action.relPath, error: error.message });
+    }
+    if (action.backupRelPath) {
+      try {
+        fs.rmSync(path.join(configDir, action.backupRelPath), { force: true });
+      } catch {
+        // backup cleanup is best-effort; preserve restore failures above
+      }
+    }
+  }
+
+  try {
+    if (previousInstallStateBytes === null) {
+      fs.rmSync(path.join(configDir, INSTALL_STATE_NAME), { force: true });
+    } else {
+      fs.mkdirSync(configDir, { recursive: true });
+      writeFileAtomicSync(path.join(configDir, INSTALL_STATE_NAME), previousInstallStateBytes);
+    }
+  } catch (error) {
+    failures.push({ relPath: INSTALL_STATE_NAME, error: error.message });
+  }
+
+  try {
+    fs.rmSync(journalPath, { force: true });
+    fs.rmSync(rollbackRoot, { recursive: true, force: true });
+  } catch {
+    // journal cleanup is best-effort; the rollback above is the safety-critical part
+  }
+
+  if (failures.length > 0) {
+    const error = new Error('migration rollback incomplete');
+    error.rollbackFailures = failures;
+    throw error;
+  }
+}
+
 function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().toISOString() }) {
   if (!configDir) throw new Error('configDir is required');
   if (!plan || !Array.isArray(plan.actions)) throw new Error('plan with actions is required');
@@ -228,20 +381,20 @@ function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().t
     actions: [],
   };
   const rollback = [];
+  const installStatePath = path.join(configDir, INSTALL_STATE_NAME);
+  const previousInstallStateBytes = fs.existsSync(installStatePath)
+    ? fs.readFileSync(installStatePath)
+    : null;
 
   try {
     for (const action of plan.actions) {
-      if (action.type === 'preserve-user') {
-        journal.actions.push({ ...action, status: 'preserved' });
-        continue;
-      }
-      if (action.type !== 'remove-managed' && action.type !== 'backup-and-remove') {
+      if (action.type !== 'remove-managed' && action.type !== 'backup-and-remove' && action.type !== 'rewrite-json') {
         throw new Error(`unsupported migration action type: ${action.type}`);
       }
 
       const { normalized, fullPath } = ensureInsideConfig(configDir, action.relPath);
       if (!fs.existsSync(fullPath)) {
-        journal.actions.push({ ...action, status: 'missing' });
+        journal.actions.push(journalAction(action, 'missing'));
         continue;
       }
 
@@ -250,14 +403,34 @@ function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().t
       fs.copyFileSync(fullPath, rollbackPath);
       rollback.push({ relPath: normalized, rollbackPath });
 
+      if (action.type === 'rewrite-json') {
+        if (action.deleteIfEmpty && isStructurallyEmpty(action.value)) {
+          fs.rmSync(fullPath, { force: true });
+          journal.actions.push(journalAction(action, 'removed', {
+            rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized),
+          }));
+        } else {
+          writeFileAtomicSync(fullPath, JSON.stringify(action.value, null, 2) + '\n');
+          journal.actions.push(journalAction(action, 'rewritten', {
+            rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized),
+          }));
+        }
+        continue;
+      }
+
       if (action.type === 'backup-and-remove') {
         const backupRelPath = action.backupRelPath || path.posix.join('gsd-migration-backups', action.migrationId, normalized);
         const backupPath = path.join(configDir, backupRelPath);
         fs.mkdirSync(path.dirname(backupPath), { recursive: true });
         fs.copyFileSync(fullPath, backupPath);
-        journal.actions.push({ ...action, backupRelPath, rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized), status: 'removed' });
+        journal.actions.push(journalAction(action, 'removed', {
+          backupRelPath,
+          rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized),
+        }));
       } else {
-        journal.actions.push({ ...action, rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized), status: 'removed' });
+        journal.actions.push(journalAction(action, 'removed', {
+          rollbackRelPath: path.posix.join(rollbackRootRelPath, normalized),
+        }));
       }
       fs.rmSync(fullPath, { force: true });
     }
@@ -270,7 +443,13 @@ function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().t
     const nextApplied = [...state.appliedMigrations];
     for (const id of journal.appliedMigrationIds) {
       if (!applied.has(id)) {
-        nextApplied.push({ id, appliedAt, journal: journalRelPath });
+        const action = plan.actions.find((candidate) => candidate.migrationId === id);
+        nextApplied.push({
+          id,
+          appliedAt,
+          journal: journalRelPath,
+          checksum: action && action.migrationChecksum ? action.migrationChecksum : null,
+        });
       }
     }
     writeInstallState(configDir, {
@@ -281,6 +460,7 @@ function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().t
     return {
       appliedMigrationIds: journal.appliedMigrationIds,
       journalRelPath,
+      rollback: () => rollbackAppliedMigrationResult({ configDir, journal, journalPath, rollbackRoot, previousInstallStateBytes }),
     };
   } catch (error) {
     const rollbackFailures = [];
@@ -309,11 +489,13 @@ function applyInstallerMigrationPlan({ configDir, plan, now = () => new Date().t
 
 function runInstallerMigrations({
   configDir,
+  runtime = null,
+  scope = null,
   migrationsDir = DEFAULT_MIGRATIONS_DIR,
   migrations = discoverInstallerMigrations({ migrationsDir }),
   now = () => new Date().toISOString(),
 } = {}) {
-  const plan = planInstallerMigrations({ configDir, migrations, now });
+  const plan = planInstallerMigrations({ configDir, runtime, scope, migrations, now });
   if (plan.actions.length === 0) {
     return {
       appliedMigrationIds: [],
diff --git a/get-shit-done/bin/lib/installer-migrations/001-legacy-orphan-files.cjs b/get-shit-done/bin/lib/installer-migrations/001-legacy-orphan-files.cjs
index 2540d901d..d216bb366 100644
--- a/get-shit-done/bin/lib/installer-migrations/001-legacy-orphan-files.cjs
+++ b/get-shit-done/bin/lib/installer-migrations/001-legacy-orphan-files.cjs
@@ -7,7 +7,11 @@ const LEGACY_ORPHAN_FILES = [
 
 module.exports = {
   id: '2026-05-11-legacy-orphan-files',
+  title: 'Remove manifest-managed legacy orphan hook files',
   description: 'Remove legacy orphan hook files that are still manifest-managed.',
+  introducedIn: '1.50.0',
+  scopes: ['global', 'local'],
+  destructive: true,
   plan: ({ classifyArtifact }) => {
     const actions = [];
     for (const relPath of LEGACY_ORPHAN_FILES) {
diff --git a/get-shit-done/bin/lib/installer-migrations/002-codex-legacy-hooks-json.cjs b/get-shit-done/bin/lib/installer-migrations/002-codex-legacy-hooks-json.cjs
new file mode 100644
index 000000000..6a7d9fe1d
--- /dev/null
+++ b/get-shit-done/bin/lib/installer-migrations/002-codex-legacy-hooks-json.cjs
@@ -0,0 +1,80 @@
+'use strict';
+
+const path = require('path');
+
+function isStructurallyEmpty(value) {
+  if (value === null || value === undefined) return true;
+  if (Array.isArray(value)) return value.length === 0;
+  if (typeof value !== 'object') return false;
+  for (const _key in value) return false;
+  return true;
+}
+
+function isManagedCodexHookCommand(command, configDir) {
+  if (typeof command !== 'string') return false;
+  if (typeof configDir !== 'string' || configDir.length === 0) return false;
+  const normalizedCommand = command.replace(/\\/g, '/');
+  const managedHooksDir = `${path.join(configDir, 'hooks').replace(/\\/g, '/')}/`;
+  if (!normalizedCommand.includes(managedHooksDir)) return false;
+  return /(^|[\\/\s"'])(gsd-check-update\.js|gsd-update-check\.js)(?=$|[\s"'])/.test(normalizedCommand);
+}
+
+function pruneLegacyCodexHooksJsonValue(value, configDir) {
+  if (Array.isArray(value)) {
+    let changed = false;
+    const next = [];
+    for (const item of value) {
+      const pruned = pruneLegacyCodexHooksJsonValue(item, configDir);
+      if (pruned.changed) changed = true;
+      if (!isStructurallyEmpty(pruned.value)) next.push(pruned.value);
+      else changed = true;
+    }
+    return { value: next, changed };
+  }
+
+  if (value && typeof value === 'object') {
+    if (isManagedCodexHookCommand(value.command, configDir)) {
+      return { value: null, changed: true };
+    }
+
+    let changed = false;
+    const next = {};
+    for (const [key, child] of Object.entries(value)) {
+      const pruned = pruneLegacyCodexHooksJsonValue(child, configDir);
+      if (pruned.changed) changed = true;
+      if (!isStructurallyEmpty(pruned.value)) next[key] = pruned.value;
+      else changed = true;
+    }
+    return { value: next, changed };
+  }
+
+  return { value, changed: false };
+}
+
+module.exports = {
+  id: '2026-05-11-codex-legacy-hooks-json',
+  title: 'Remove legacy Codex hooks.json GSD hook registrations',
+  description: 'Remove legacy Codex hooks.json GSD hook registrations after config.toml migration.',
+  introducedIn: '1.50.0',
+  runtimes: ['codex'],
+  scopes: ['global', 'local'],
+  destructive: true,
+  runtimeContract: 'docs/installer-migrations.md#runtime-configuration-contract-registry Codex row',
+  plan: ({ configDir, readJson }) => {
+    const hooksJson = readJson('hooks.json');
+    if (!hooksJson.exists || hooksJson.error) return [];
+
+    const pruned = pruneLegacyCodexHooksJsonValue(hooksJson.value, configDir);
+    if (!pruned.changed) return [];
+
+    return [
+      {
+        type: 'rewrite-json',
+        relPath: 'hooks.json',
+        value: pruned.value,
+        deleteIfEmpty: true,
+        reason: 'legacy Codex hooks.json GSD registration retired by installer migration',
+      },
+    ];
+  },
+};
diff --git a/tests/bug-3357-codex-legacy-hooks-json-migration.test.cjs b/tests/bug-3357-codex-legacy-hooks-json-migration.test.cjs
index 7bb0a3768..b88c15831 100644
--- a/tests/bug-3357-codex-legacy-hooks-json-migration.test.cjs
+++ b/tests/bug-3357-codex-legacy-hooks-json-migration.test.cjs
@@ -15,7 +15,9 @@ const assert = require('node:assert/strict');
 const fs = require('node:fs');
 const path = require('node:path');
 
-const { install, parseTomlToObject } = require('../bin/install.js');
+const installModule = require('../bin/install.js');
+const { readInstallState } = require('../get-shit-done/bin/lib/installer-migrations.cjs');
+const { install, parseTomlToObject } = installModule;
 const { createTempDir, cleanup } = require('./helpers.cjs');
 
 function withCodexHome(codexHome, fn) {
@@ -67,6 +69,7 @@ describe('#3357 — Codex install removes legacy GSD hooks.json entries', { conc
   });
 
   afterEach(() => {
+    delete installModule.__codexSchemaValidator;
     cleanup(tmpRoot);
   });
 
@@ -104,4 +107,25 @@ describe('#3357 — Codex install removes legacy GSD hooks.json entries', { conc
     ]);
     assert.equal(tomlGsdHookCount(codexHome), 1);
   });
+
+  test('restores migrated hooks.json and install state when later Codex validation fails', () => {
+    const before = JSON.stringify({ SessionStart: [legacyGsdHook(codexHome)] }, null, 2);
+    fs.writeFileSync(path.join(codexHome, 'hooks.json'), before);
+
+    installModule.__codexSchemaValidator = () => ({
+      ok: false,
+      reason: 'forced migration rollback test',
+    });
+
+    assert.throws(
+      () => withCodexHome(codexHome, () => install(true, 'codex')),
+      /forced migration rollback test/
+    );
+
+    assert.equal(fs.readFileSync(path.join(codexHome, 'hooks.json'), 'utf8'), before);
+    assert.equal(
+      readInstallState(codexHome).appliedMigrations.some((entry) => entry.id === '2026-05-11-codex-legacy-hooks-json'),
+      false
+    );
+  });
 });
diff --git a/tests/installer-migrations.test.cjs b/tests/installer-migrations.test.cjs
index 8796dd328..6ba99a390 100644
--- a/tests/installer-migrations.test.cjs
+++ b/tests/installer-migrations.test.cjs
@@ -8,6 +8,7 @@ const crypto = require('crypto');
 const {
   applyInstallerMigrationPlan,
   discoverInstallerMigrations,
+  INSTALL_STATE_NAME,
   planInstallerMigrations,
   readInstallState,
   runInstallerMigrations,
@@ -45,6 +46,28 @@ function writeManifest(root, files) {
   );
 }
 
+function legacyCodexHook(configDir) {
+  return {
+    hooks: [
+      {
+        type: 'command',
+        command: `node "${path.join(configDir, 'hooks', 'gsd-check-update.js')}"`,
+      },
+    ],
+  };
+}
+
+function userHook(command) {
+  return {
+    hooks: [
+      {
+        type: 'command',
+        command,
+      },
+    ],
+  };
+}
+
 test('plans a pending migration against an unchanged managed file', () => {
   const configDir = createTempInstall();
   try {
@@ -73,7 +96,17 @@ test('plans a pending migration against an unchanged managed file', () => {
 
     assert.deepEqual(plan.pendingMigrationIds, ['2026-05-11-remove-old-hook']);
     assert.equal(plan.blocked.length, 0);
-    assert.deepEqual(plan.actions, [
+    assert.equal(plan.actions.length, 1);
+    assert.deepEqual(
+      {
+        migrationId: plan.actions[0].migrationId,
+        type: plan.actions[0].type,
+        relPath: plan.actions[0].relPath,
+        reason: plan.actions[0].reason,
+        classification: plan.actions[0].classification,
+        originalHash: plan.actions[0].originalHash,
+        currentHash: plan.actions[0].currentHash,
+      },
       {
         migrationId: '2026-05-11-remove-old-hook',
         type: 'remove-managed',
@@ -82,8 +115,9 @@ test('plans a pending migration against an unchanged managed file', () => {
         classification: 'managed-pristine',
         originalHash: sha256('managed hook\n'),
         currentHash: sha256('managed hook\n'),
-      },
-    ]);
+      }
+    );
+    assert.match(plan.actions[0].migrationChecksum, /^sha256:/);
   } finally {
     cleanup(configDir);
   }
@@ -203,6 +237,7 @@ test('applies an unblocked plan with a journal and install-state update', () =>
 
     const state = readInstallState(configDir);
     assert.deepEqual(state.appliedMigrations.map((entry) => entry.id), ['2026-05-11-remove-old-hook']);
+    assert.match(state.appliedMigrations[0].checksum, /^sha256:/);
   } finally {
     cleanup(configDir);
   }
@@ -317,6 +352,70 @@ test('reports rollback restore failures instead of swallowing them', () => {
   }
 });
 
+test('rejects executable preserve-user actions because preservation blocks non-interactive apply', () => {
+  const configDir = createTempInstall();
+  try {
+    writeManifest(configDir, {});
+
+    assert.throws(
+      () => applyInstallerMigrationPlan({
+        configDir,
+        plan: {
+          blocked: [],
+          actions: [
+            {
+              migrationId: '2026-05-11-preserve-user',
+              type: 'preserve-user',
+              relPath: 'hooks/custom-user-hook.js',
+              reason: 'unknown user hook',
+              classification: 'unknown',
+              originalHash: null,
+              currentHash: sha256('user hook\n'),
+            },
+          ],
+        },
+      }),
+      /unsupported migration action type: preserve-user/
+    );
+  } finally {
+    cleanup(configDir);
+  }
+});
+
+test('keeps prior install state intact when a state write fails mid-write', () => {
+  const configDir = createTempInstall();
+  const originalWriteFileSync = fs.writeFileSync;
+  try {
+    writeInstallState(configDir, {
+      schemaVersion: 1,
+      appliedMigrations: [{ id: 'already-safe', appliedAt: '2026-05-11T00:00:00.000Z' }],
+    });
+
+    fs.writeFileSync = (filePath, content, ...rest) => {
+      if (path.basename(filePath).startsWith(`${INSTALL_STATE_NAME}.tmp-`)) {
+        throw new Error('simulated temp state write failure');
+      }
+      return originalWriteFileSync(filePath, content, ...rest);
+    };
+
+    assert.throws(
+      () => writeInstallState(configDir, {
+        schemaVersion: 1,
+        appliedMigrations: [{ id: 'new-migration', appliedAt: '2026-05-11T00:00:01.000Z' }],
+      }),
+      /simulated temp state write failure/
+    );
+  } finally {
+    fs.writeFileSync = originalWriteFileSync;
+  }
+
+  try {
+    assert.deepEqual(readInstallState(configDir).appliedMigrations.map((entry) => entry.id), ['already-safe']);
+  } finally {
+    cleanup(configDir);
+  }
+});
+
 test('skips migration records already present in install state', () => {
   const configDir = createTempInstall();
   try {
@@ -354,6 +453,83 @@ test('skips migration records already present in install state', () => {
   }
 });
 
+test('refuses to plan an already-applied migration whose checksum changed', () => {
+  const configDir = createTempInstall();
+  try {
+    writeManifest(configDir, {});
+    writeInstallState(configDir, {
+      schemaVersion: 1,
+      appliedMigrations: [
+        {
+          id: '2026-05-11-remove-old-hook',
+          checksum: 'sha256:old-definition',
+          appliedAt: '2026-05-11T00:00:00.000Z',
+          journal: 'gsd-migration-journal/prior.json',
+        },
+      ],
+    });
+
+    assert.throws(
+      () => planInstallerMigrations({
+        configDir,
+        migrations: [
+          {
+            id: '2026-05-11-remove-old-hook',
+            checksum: 'sha256:new-definition',
+            description: 'Remove retired hook',
+            plan: () => [],
+          },
+        ],
+      }),
+      /applied migration checksum changed/
+    );
+  } finally {
+    cleanup(configDir);
+  }
+});
+
+test('ignores checksum drift for applied migrations outside the active runtime scope', () => {
+  const configDir = createTempInstall();
+  try {
+    writeManifest(configDir, {});
+    writeInstallState(configDir, {
+      schemaVersion: 1,
+      appliedMigrations: [
+        {
+          id: '2026-05-11-codex-only',
+          checksum: 'sha256:old-definition',
+          appliedAt: '2026-05-11T00:00:00.000Z',
+          journal: 'gsd-migration-journal/prior.json',
+        },
+      ],
+    });
+
+    const plan = planInstallerMigrations({
+      configDir,
+      runtime: 'claude',
+      scope: 'global',
+      migrations: [
+        {
+          id: '2026-05-11-codex-only',
+          checksum: 'sha256:new-definition',
+          runtimes: ['codex'],
+          scopes: ['global'],
+          description: 'Codex-only migration',
+          plan: () => {
+            throw new Error('out-of-scope migration planner must not run');
+          },
+        },
+      ],
+    });
+
+    assert.deepEqual(plan.pendingMigrationIds, []);
+    assert.deepEqual(plan.actions, []);
+    assert.deepEqual(plan.blocked, []);
+  } finally {
+    cleanup(configDir);
+  }
+});
+
 test('discovers migration records from a directory in filename order', () => {
   const configDir = createTempInstall();
   try {
@@ -418,6 +594,7 @@ test('runs discovered installer migrations against manifest-managed legacy orpha
 
     const result = runInstallerMigrations({
       configDir,
+      scope: 'global',
       now: () => '2026-05-11T00:00:05.000Z',
     });
 
@@ -429,3 +606,66 @@ test('runs discovered installer migrations against manifest-managed legacy orpha
     cleanup(configDir);
   }
 });
+
+test('runs a Codex legacy hooks.json cleanup migration without removing user hooks', () => {
+  const configDir = createTempInstall();
+  try {
+    writeFile(
+      configDir,
+      'hooks.json',
+      JSON.stringify({
+        SessionStart: [
+          legacyCodexHook(configDir),
+          userHook('node "/Users/example/bin/user-hook.js"'),
+          userHook('node "/Users/example/bin/gsd-check-update.js"'),
+        ],
+      }, null, 2)
+    );
+    writeManifest(configDir, {});
+
+    const result = runInstallerMigrations({
+      configDir,
+      runtime: 'codex',
+      scope: 'global',
+      now: () => '2026-05-11T00:00:06.000Z',
+    });
+
+    const hooksJson = JSON.parse(fs.readFileSync(path.join(configDir, 'hooks.json'), 'utf8'));
+    const commands = hooksJson.SessionStart.flatMap((entry) => entry.hooks).map((hook) => hook.command);
+
+    assert.deepEqual(commands, [
+      'node "/Users/example/bin/user-hook.js"',
+      'node "/Users/example/bin/gsd-check-update.js"',
+    ]);
+    assert.ok(result.appliedMigrationIds.includes('2026-05-11-codex-legacy-hooks-json'));
+  } finally {
+    cleanup(configDir);
+  }
+});
+
+test('skips runtime-specific migration records for other runtimes', () => {
+  const configDir = createTempInstall();
+  try {
+    writeFile(
+      configDir,
+      'hooks.json',
+      JSON.stringify({
+        SessionStart: [legacyCodexHook(configDir)],
+      }, null, 2)
+    );
+    writeManifest(configDir, {});
+
+    const result = runInstallerMigrations({
+      configDir,
+      runtime: 'claude',
+      scope: 'global',
+      now: () => '2026-05-11T00:00:07.000Z',
+    });
+
+    const hooksJson = JSON.parse(fs.readFileSync(path.join(configDir, 'hooks.json'), 'utf8'));
+    assert.equal(hooksJson.SessionStart[0].hooks[0].command, `node "${path.join(configDir, 'hooks', 'gsd-check-update.js')}"`);
+    assert.equal(result.appliedMigrationIds.includes('2026-05-11-codex-legacy-hooks-json'), false);
+  } finally {
+    cleanup(configDir);
+  }
+});

From 9889d0a9aa569072ba59a4885feccef526b1247e Mon Sep 17 00:00:00 2001
From: Tom Boucher <trekkie@nomorestars.com>
Date: Sun, 10 May 2026 23:10:10 -0400
Subject: [PATCH 2/3] docs: add changeset for installer migration phase two

---
 .changeset/gentle-jays-zip.md | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .changeset/gentle-jays-zip.md

diff --git a/.changeset/gentle-jays-zip.md b/.changeset/gentle-jays-zip.md
new file mode 100644
index 000000000..82c581f8e
--- /dev/null
+++ b/.changeset/gentle-jays-zip.md
@@ -0,0 +1,5 @@
+---
+type: Added
+pr: 3399
+---
+**Installer migrations now handle legacy Codex hooks cleanup transactionally** - GSD-owned hooks.json entries are removed through the migration runner with runtime filtering, rollback, and checksum drift protection.

From 5002d51d92ce5a8bc9343655d42a50d9a220ff3b Mon Sep 17 00:00:00 2001
From: Tom Boucher <trekkie@nomorestars.com>
Date: Mon, 11 May 2026 14:59:33 -0400
Subject: [PATCH 3/3] Docs(installer): reword Antigravity migration contract
 note

---
 docs/installer-migrations.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/installer-migrations.md b/docs/installer-migrations.md
index d8a54b635..c9701c4c3 100644
--- a/docs/installer-migrations.md
+++ b/docs/installer-migrations.md
@@ -314,7 +314,7 @@ for the new shape before changing migration behavior.
 | Gemini CLI | TOML slash commands in `commands/gsd/*.toml`; agents in `agents/gsd-*.md`; `settings.json` feature flag, hooks, and statusline | Global `GEMINI_CONFIG_DIR` or `~/.gemini`; local `./.gemini` | GSD owns generated commands/agents/hooks and only GSD settings entries; local command copy may be skipped when global GSD commands already exist | [Custom commands](https://google-gemini.github.io/gemini-cli/docs/cli/custom-commands.html), [configuration](https://google-gemini.github.io/gemini-cli/docs/cli/configuration.html); docs checked 2026-05-11 |
 | Codex | Skills in `skills/gsd-*/SKILL.md`; agents as source markdown plus per-agent TOML in `agents/`; `[agents.gsd-*]` and hooks in `config.toml` | Global `CODEX_HOME` or `~/.codex`; local `./.codex` | GSD owns generated skills, generated agent TOML, `agents.gsd-*` config sections, `[features].codex_hooks` when added by GSD, and GSD hook entries | [Codex config schema](https://developers.openai.com/codex/config-schema.json), [Codex developer docs](https://developers.openai.com/codex/); docs not versioned, checked 2026-05-11; installer compatibility sentinel: Codex 0.124.0 agent table shape |
 | GitHub Copilot | Skills in `skills/gsd-*/SKILL.md`; agents as `.agent.md`; repository instructions in `copilot-instructions.md` | Global `COPILOT_CONFIG_DIR` or `~/.copilot`; local `./.github` | GSD owns generated skill/agent files and GSD-authored instruction files; no hook/statusline ownership | [Repository custom instructions](https://docs.github.com/en/copilot/how-tos/configure-custom-instructions/add-repository-instructions), [Copilot CLI custom instructions](https://docs.github.com/en/copilot/how-tos/copilot-cli/add-custom-instructions); GitHub Docs product docs, checked 2026-05-11 |
-| Antigravity | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; Gemini-style `settings.json` hooks when installed by GSD | Global `ANTIGRAVITY_CONFIG_DIR` or `~/.gemini/antigravity`; local `./.agent` | GSD owns generated skills/agents/hooks and GSD settings entries only | Public Antigravity install/config docs for this file layout were not stable or complete as of 2026-05-11; GSD uses the Gemini-compatible settings contract as a compatibility shim |
+| Antigravity | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; Gemini-style `settings.json` hooks when installed by GSD | Global `ANTIGRAVITY_CONFIG_DIR` or `~/.gemini/antigravity`; local `./.agent` | GSD owns generated skills/agents/hooks and GSD settings entries only | Checked 2026-05-11 against available Antigravity install/config material; this row records GSD's Gemini-compatible settings contract as the compatibility baseline for installer migrations. |
 | Cursor | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; rule references under `rules/` | Global `CURSOR_CONFIG_DIR` or `~/.cursor`; local `./.cursor` | GSD owns generated skills/agents and GSD rule files or references; no hook/statusline ownership | [Cursor rules](https://docs.cursor.com/context/rules); docs not versioned, checked 2026-05-11 |
 | Windsurf | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/`; rule references under `rules/` | Global `WINDSURF_CONFIG_DIR` or `~/.codeium/windsurf`; local `./.windsurf` | GSD owns generated skills/agents and GSD rule files or references; no hook/statusline ownership | Windsurf public rule docs were source-limited in search results as of 2026-05-11; installer targets the common workspace rules convention `./.windsurf/rules` and must be rechecked before migrations rewrite rules |
 | Augment Code | Skills in `skills/gsd-*/SKILL.md`; agents in `agents/` | Global `AUGMENT_CONFIG_DIR` or `~/.augment`; local `./.augment` | GSD owns generated skills/agents only; no hook/statusline ownership | [Augment Agent Skills](https://docs.augmentcode.com/cli/skills), [Augment IDE skills](https://docs.augmentcode.com/using-augment/skills); IDE skills public beta in VS Code 0.789.0+, checked 2026-05-11 |