Merge branch 'next' into feat/1346-enhance-verify-phase-project-a-check-vio

docs/CLI-TOOLS.md

@@ -546,6 +546,20 @@ node gsd-tools.cjs worktree set-baseref
 
 **`worktree set-baseref`** applies a no-clobber write of `worktree.baseRef:"head"` to `.claude/settings.local.json`. If the file already contains an explicit `baseRef` value other than `"head"`, the existing value is preserved and `skipped:"explicit-other"` is returned. Malformed JSON causes an error rather than a silent overwrite. Both fresh installs and upgrades of GSD Core run this automatically when `workflow.use_worktrees` is enabled (the default); the command is also available for manual use — for example, to apply the setting when worktrees were toggled on after installation, or to re-apply it after a settings change.
 
+### Wave-manifest recording
+
+The execute-phase orchestrator records each spawned executor's worktree identity into a wave cleanup manifest so the matching `cleanup-wave` reader can later merge and remove exactly those worktrees.
+
+```bash
+# Append a validated per-agent entry to the wave cleanup manifest.
+# Returns JSON: { ok, reason, entry, manifest_path } (exit 0), or
+#   { ok:false, reason, hint } with a non-zero exit on a rejected entry.
+node gsd-tools.cjs worktree record-agent \
+  --manifest <path> --agent-id <id> --path <worktree> --branch <branch> --base <sha>
+```
+
+**`worktree record-agent`** appends one `{agent_id, worktree_path, branch, expected_base}` entry to an already-initialized manifest, validating every field **at write time using the same rules the `cleanup-wave` reader enforces** — `--branch` must match the disposable `^worktree-agent-[A-Za-z0-9._/-]+$` namespace, and `--path`/`--branch`/`--base` must be non-empty. `--agent-id` is required (write-strict), even though the reader treats it as optional. A missing or garbled field — or a duplicate `(worktree_path, branch)` the reader would dedup away — fails loudly with a recovery hint and a non-zero exit **without** writing, instead of appending an under-populated or silently-dropped entry. Whitespace-only `--path`/`--base` are rejected (values are trimmed). The on-disk manifest shape is unchanged (the reader re-derives `allowed_bases`); the orchestrator still initializes the empty `{orchestrator_root, worktrees: []}` shell inline before any agent is recorded.
+
 ---
 
 ## Graphify

docs/CONFIGURATION.md

@@ -248,7 +248,7 @@ All workflow toggles follow the **absent = enabled** pattern. If a key is missin
 | `workflow.max_discuss_passes` | number | `3` | Maximum number of question rounds in discuss-phase before the workflow stops asking. Useful in headless/auto mode to prevent infinite discussion loops. |
 | `workflow.skip_discuss` | boolean | `false` | When `true`, `/gsd-autonomous` bypasses the discuss-phase entirely, writing minimal CONTEXT.md from the ROADMAP phase goal. Useful for projects where developer preferences are fully captured in PROJECT.md/REQUIREMENTS.md. Added in v1.28 |
 | `workflow.text_mode` | boolean | `false` | Replaces AskUserQuestion TUI menus with plain-text numbered lists. Required for Claude Code remote sessions (`/rc` mode) where TUI menus don't render. Can also be set per-session with `--text` flag on discuss-phase. Added in v1.28 |
-| `workflow.use_worktrees` | boolean | `true` | When `false`, disables git worktree isolation for parallel execution. Users who prefer sequential execution or whose environment does not support worktrees can disable this. Added in v1.31. **Branch-divergence note:** when your branch has diverged from `origin/HEAD`, GSD auto-degrades to sequential and prints a warning. See [`worktree.baseRef`](#worktree-settings) to restore parallel execution on a diverged branch. |
+| `workflow.use_worktrees` | boolean | `true` | When `false`, disables git worktree isolation for parallel execution. Users who prefer sequential execution or whose environment does not support worktrees can disable this. Added in v1.31. **Branch-divergence note:** when your branch has diverged from `origin/HEAD`, GSD auto-degrades to sequential and prints a warning. See [`worktree.baseRef`](#worktree-settings) to restore parallel execution on a diverged branch. **Non-Claude note:** git worktree isolation uses Claude Code's `isolation="worktree"` agent primitive, which no other runtime honors. On any non-Claude install (Codex, Cursor, Gemini, Qwen, etc.) a runtime-neutral `.planning/config.json` resolves the runtime to that install's own id and defaults this key to `false`; forcing `use_worktrees: true` on a non-Claude install fails closed before any executor dispatch (#1515, #1521). |
 | `workflow.worktree_skip_hooks` | boolean | `false` | When `true`, executor agents in worktree mode pass `--no-verify` (skipping pre-commit hooks) and post-wave hook validation runs against the merged result instead. Opt-in escape hatch for projects whose hooks cannot run in agent worktrees. Default `false` runs hooks on every commit (#2924). |
 | `workflow.code_review` | boolean | `true` | Enable `/gsd-code-review` and `/gsd-code-review --fix` commands. When `false`, the commands exit with a configuration gate message. Added in v1.34 |
 | `workflow.code_review_depth` | string | `standard` | Default review depth for `/gsd-code-review`: `quick` (pattern-matching only), `standard` (per-file analysis), or `deep` (cross-file with import graphs). Can be overridden per-run with `--depth=`. Added in v1.34 |

docs/adr/1508-runtime-artifact-conversion-module.md

@@ -14,7 +14,7 @@ This is the **last upward dependency from the `.cts` source tree into the hand-a
 
 ## Decision
 
-- Promote the `[Planned]` **Runtime Artifact Conversion Module** (`src/runtime-artifact-conversion.cts`) to the single owner of per-runtime **content rewriting**: the per-runtime converters (already relocated as ADR-3660's "first slice", #1099), **plus** the rewrite engine `_applyRuntimeRewrites`, the staged-content walkers, path-prefix derivation, and commit attribution. The **Runtime Artifact Layout Module** keeps owning **placement** only.
+- Promote the `[Planned]` **Runtime Artifact Conversion Module** (`src/runtime-artifact-conversion.cts`) to the single owner of per-runtime **content rewriting**: the per-runtime converters (already relocated as ADR-3660's "first slice", #1099), **plus** the rewrite engine `_applyRuntimeRewrites`, the staged-content walkers, path-prefix derivation, and commit attribution. The **Runtime Artifact Layout Module** keeps owning **placement** only. **Exception:** opencode and kilo path-prefix rewriting remains a deliberate `bin/install.js`-owned pre-conversion step (see `applyOpencodeFamilyPathPrefix`); this is intentional per #784 and is not a violation of the single-owner rule.
 - **Public seam** — two deep calls; the caller passes only what it has, the module derives the rest:
   - `rewriteStagedSkillBodies(stagedDir, { runtime, configDir, scope }, env?)` — in-place walk (skills / kimi-agents).
   - `rewriteStagedCommandBodies(stagedDir, { runtime, configDir, scope }, env?) → tempDir` — copy-to-temp (commands).