Fix Codex hook installation to use hooks.json instead of inline TOML hooks

CHANGELOG.md

@@ -21,13 +21,15 @@ If you use GSD **as a workflow**—milestones, phases, `.planning/` artifacts, b
 
 ### Changed
 
+- **Codex install now writes the GSD SessionStart hook into `hooks.json` instead of inline `[[hooks]]` TOML** — fixes invalid `config.toml` shapes that made Codex reject model-setting updates with `invalid type: map, expected a sequence`. Install merges the exact managed GSD SessionStart command into existing `hooks.json` content without clobbering user-owned hooks, preserves malformed existing `hooks.json` files instead of rewriting them, and falls back to `hooks/` when `hooks/dist/` is absent in a source checkout. Uninstall removes only the exact managed GSD hook references from `hooks.json` and legacy inline TOML blocks, preserves user root keys and mixed user-owned entries, and deletes `hooks.json` only when it is GSD-only.
 - **SDK Phase 3 — runner hot path uses the registry directly** — When you run **phase lifecycle** or **new-project init** through the SDK, the common STATE/roadmap/plan-index/complete/commit/config calls **skip extra subprocess overhead** on the default path (workstreams and test overrides unchanged). *Contributors:* `GSDTools` → `initPhaseOp`, `phasePlanIndex`, `phaseComplete`, `initNewProject`, `configSet`, `commit` (#2302).
 - **Docs — `docs/CLI-TOOLS.md`** — New **SDK and programmatic access** section (registry-first guidance, CJS→`gsd-sdk query` examples, `GSDTools`/workstream behavior, `state load` vs registry state handlers, CLI-only commands); **See also** links to `QUERY-HANDLERS.md`, Architecture, and COMMANDS (#2302).
 - **Docs — `docs/USER-GUIDE.md`** — Programmatic CLI subsection: corrected CLI-only vs registry commands; anchor link to CLI-TOOLS SDK section; `state load` caveat cross-reference (#2302).
 - **CJS deprecation** — `get-shit-done/bin/gsd-tools.cjs` documents `@deprecated` in favor of `gsd-sdk query` and `@gsd-build/sdk` (#2302).
 
 ### Fixed
 
+- **Codex hook migration follow-up** — Codex installs refresh `gsd-file-manifest.json` after the Codex-specific hook copy/config pass so edited hook files are preserved on later updates; legacy inline hook cleanup decodes TOML literal-string doubled apostrophes before matching managed commands; and uninstall preserves `hooks/gsd-check-update.js` when `hooks.json` cannot be parsed or safely cleaned, avoiding a dangling `hooks.json` reference after users repair the file (#2637).
 - **`gsd-sdk query` now resolves parent `.planning/` root in multi-repo (`sub_repos`) workspaces** — when invoked from inside a `sub_repos`-listed child repo (e.g. `workspace/app/`), the SDK now walks up to the parent workspace that owns `.planning/`, matching the legacy `gsd-tools.cjs` `findProjectRoot` behavior. Previously `gsd-sdk query init.new-milestone` reported `project_exists: false` from the sub-repo, while `gsd-tools.cjs` resolved the parent root correctly. Resolution happens once in `cli.ts` before dispatch; if `projectDir` already owns `.planning/` (including explicit `--project-dir`), the walk is a no-op. Ported as `findProjectRoot` in `sdk/src/query/helpers.ts` with the same detection order (own `.planning/` wins, then parent `sub_repos` match, then legacy `multiRepo: true`, then `.git` heuristic), capped at 10 parent levels and never crossing `$HOME`. Closes #2623.
 - **Shell hooks falsely flagged as stale on every session** — `gsd-phase-boundary.sh`, `gsd-session-state.sh`, and `gsd-validate-commit.sh` now ship with a `# gsd-hook-version: {{GSD_VERSION}}` header; the installer substitutes `{{GSD_VERSION}}` in `.sh` hooks the same way it does for `.js` hooks; and the stale-hook detector in `gsd-check-update.js` now matches bash `#` comment syntax in addition to JS `//` syntax. All three changes are required together — neither the regex fix alone nor the install fix alone is sufficient to resolve the false positive (#2136, #2206, #2209, #2210, #2212)