feat(plan-phase): --research-phase flag + scrub stale slash-command refs (#3042, #3044) (#3045)

* feat(plan-phase): --research-phase flag absorbs deleted /gsd-research-phase + scrub stale refs (#3042, #3044)

#3042 (orphaned research-phase): /gsd-research-phase had a workflow file
but no slash-command stub. Rather than restore the orphan, the research-
only capability is now a flag on /gsd-plan-phase:

  /gsd-plan-phase --research-phase <N>

When set, the workflow scopes to phase N, runs the research step (Section
5 of the existing plan-phase workflow), then early-exits before the
planner/plan-checker/verifier chain.

Per RCA against the deleted standalone, the flag adds two modifiers to
fully cover the original surface (Option B from the RCA discussion):

- --view : print existing RESEARCH.md to stdout, no spawn. Cheapest mode
  for the correction-without-replanning loop the issue reporter
  explicitly called out. Errors with a clear hint if RESEARCH.md is
  missing.
- --research : reuse the existing "force re-research" semantics. In
  research-only mode this skips the existing-RESEARCH.md prompt and
  re-spawns unconditionally.
- Neither flag, RESEARCH.md exists : prompt update/view/skip. Mirrors
  the deleted standalone's existing-artifact menu (#3042 RCA).

#3044 (stale slash-command refs): scrubbed five deleted commands from
all user-facing surfaces, including English docs, 4 localized doc sets
(ja-JP, ko-KR, zh-CN, pt-BR), workflows, templates, and references.

  /gsd-check-todos          → /gsd-capture --list
  /gsd-new-workspace        → /gsd-workspace --new
  /gsd-status               → /gsd-progress
  /gsd-plan-milestone-gaps  → table rows / orphan sections removed
                              (PR #3038 only scrubbed workflows/agent;
                              missed the docs surfaces this PR covers)
  /gsd-research-phase       → /gsd-plan-phase --research-phase

Includes a fix to docs/issue-driven-orchestration.md (PR #3036)
which itself referenced /gsd-new-workspace 4 times — self-correction.

Removed:
- get-shit-done/workflows/research-phase.md (orphan, capability
  absorbed into --research-phase flag)

Tests:
- tests/bug-3042-3044-research-flag-and-stale-refs.test.cjs — 46
  structural-IR tests across both bugs:
  - argument-hint advertises --research-phase + --view
  - workflow parses --research-phase, sets RESEARCH_ONLY,
    early-exits before planner
  - --view prints RESEARCH.md without spawning
  - --research forces refresh in research-only mode
  - existing-RESEARCH.md prompt path with update/view/skip
  - workflows/research-phase.md is removed
  - 5 deleted slash-commands absent from 17 English user-facing
    surfaces + 16 localized doc surfaces (4 locales × 4 docs each)
  - replacement command tokens present where deleted ones lived

6950/6950 full suite pass. Lints clean.

Closes #3042
Closes #3044

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

* fix: address all 8 CR findings on PR #3045

Major (3):
- get-shit-done/workflows/plan-phase.md:344 — added explicit early-exit
  guard at Section 5.1: "Skip if RESEARCH_ONLY=true". Without it, an LLM
  could fall through "use existing, skip to step 6" → planner spawn,
  violating the research-only contract. The guard makes the early-exit
  unreachable from any non-research-only branch.
- get-shit-done/references/continuation-format.md (3 examples) +
  zh-CN/.../continuation-format.md (3 examples) — pointed to
  `/gsd-plan-phase --research-phase` but docs/COMMANDS.md didn't
  document the flag. Added a full --research-phase + --view + --research
  modifier section to the /gsd-plan-phase flag table in COMMANDS.md so
  the canonical reference matches the continuation examples.

Minor (5):
- docs/FEATURES.md:1632 — `/gsd-plan-phase --research-phase` →
  `/gsd-plan-phase --research-phase <N>` (include required arg).
- get-shit-done/templates/README.md:46 — NN-VALIDATION.md producer
  reverted from `/gsd-plan-phase --research-phase` (Nyquist) to plain
  `/gsd-plan-phase` (Nyquist). VALIDATION.md is created during normal
  Nyquist flow, not research-only mode — the bulk replacement was
  wrong for that line.
- get-shit-done/workflows/help.md:89 — signature line was missing
  `--research`; added it alongside `--research-phase` and `--view`.
- tests/bug-3042-3044-...:197 — promptHasView/promptHasSkip were
  tautological (matched anywhere in 1700-line workflow). Tightened
  to a proximity check anchored on "RESEARCH.md already exists" prompt
  header within a 600-char window. Updated workflow to emit that
  literal phrase.
- tests/feat-2840-...:95 — workspace assertion used `/gsd-workspace`
  but the documented replacement is `/gsd-workspace --new`. Tightened
  to require both tokens (in 3 places: requiredCommands list, regex
  in conceptPairs, error message).

6950/6950 full suite pass. Lint clean.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

docs/zh-CN/README.md

@@ -515,7 +515,6 @@ lmn012o feat(08-02): 创建注册端点
 | `/gsd-insert-phase [N]` | 在阶段之间插入紧急工作 |
 | `/gsd-remove-phase [N]` | 删除未来阶段，重新编号 |
 | `/gsd-list-phase-assumptions [N]` | 规划前查看 Claude 的预期方法 |
-| `/gsd-plan-milestone-gaps` | 创建阶段以填补审计发现的差距 |
 | `/gsd-autonomous [--from N] [--to N] [--only N]` | 自主执行所有剩余阶段（`--to N` 执行到阶段 N 停止，`--only N` 只执行单个阶段） |
 | `/gsd-analyze-dependencies` | 检测阶段间依赖关系并建议 ROADMAP.md 的 `Depends on` 条目 |
 
@@ -533,7 +532,7 @@ lmn012o feat(08-02): 创建注册端点
 | `/gsd-settings` | 配置模型配置文件和工作流代理 |
 | `/gsd-set-profile <profile>` | 切换模型配置文件（quality/balanced/budget） |
 | `/gsd-add-todo [desc]` | 捕获想法留待后用 |
-| `/gsd-check-todos` | 列出待处理事项 |
+| `/gsd-capture --list` | 列出待处理事项 |
 | `/gsd-debug [desc] [--diagnose]` | 带持久状态的系统化调试（`--diagnose` 仅诊断不修复） |
 | `/gsd-quick [--full] [--discuss] [--research]` | 用 GSD 保证执行临时任务（`--full` 启用全部阶段，`--discuss` 先收集上下文，`--research` 规划前调查方法） |
 | `/gsd-health [--repair]` | 验证 `.planning/` 目录完整性，用 `--repair` 自动修复 |

docs/zh-CN/USER-GUIDE.md

@@ -209,8 +209,7 @@
 | `/gsd-insert-phase [N]` | 插入紧急工作（小数编号） | 里程碑中途紧急修复 |
 | `/gsd-remove-phase [N]` | 删除未来阶段并重新编号 | 移除某个功能 |
 | `/gsd-list-phase-assumptions [N]` | 预览 Claude 的预期方法 | 规划前，验证方向 |
-| `/gsd-plan-milestone-gaps` | 为审计缺口创建阶段 | 审计发现缺失项后 |
-| `/gsd-research-phase [N]` | 仅深度生态研究 | 复杂或不熟悉的领域 |
+| `/gsd-plan-phase --research-phase [N]` | 仅深度生态研究 | 复杂或不熟悉的领域 |
 | `/gsd-autonomous [--from N] [--to N] [--only N]` | 自主执行剩余阶段（`--to N` 到阶段 N 停止） | 批量自动处理 |
 | `/gsd-analyze-dependencies` | 检测阶段间依赖关系 | `/gsd-manager` 前分析 |
 
@@ -231,7 +230,7 @@
 | `/gsd-quick` | 带 GSD 保证的临时任务 | Bug 修复、小功能、配置更改 |
 | `/gsd-debug [desc] [--diagnose]` | 带持久状态的系统化调试（`--diagnose` 仅诊断） | 出问题时 |
 | `/gsd-add-todo [desc]` | 捕获想法留待后用 | 会话期间想到什么 |
-| `/gsd-check-todos` | 列出待处理事项 | 查看捕获的想法 |
+| `/gsd-capture --list` | 列出待处理事项 | 查看捕获的想法 |
 | `/gsd-settings` | 配置工作流开关和模型配置 | 更改模型、切换代理 |
 | `/gsd-set-profile <profile>` | 快速切换配置 | 更改成本/质量权衡 |
 | `/gsd-update --reapply` | 更新后恢复本地修改 | 如果你有本地编辑，在 `/gsd-update` 后 |
@@ -390,7 +389,6 @@ claude --dangerously-skip-permissions
 
 ```bash
 /gsd-audit-milestone        # 检查需求覆盖率，检测存根
-/gsd-plan-milestone-gaps    # 如果审计发现缺口，创建阶段来填补
 /gsd-complete-milestone     # 归档，标记，完成
 ```
 
@@ -481,7 +479,6 @@ node gsd-tools.cjs state sync              # 从磁盘重建 STATE.md
 | 丢失上下文 / 新会话 | `/gsd-resume-work` 或 `/gsd-progress` |
 | 阶段出错 | `git revert` 阶段提交，然后重新规划 |
 | 需要更改范围 | `/gsd-add-phase`、`/gsd-insert-phase` 或 `/gsd-remove-phase` |
-| 里程碑审计发现缺口 | `/gsd-plan-milestone-gaps` |
 | 出问题了 | `/gsd-debug "描述"` |
 | STATE.md 不同步 | `state validate` 然后 `state sync` |
 | 快速针对性修复 | `/gsd-quick` |

docs/zh-CN/references/continuation-format.md

@@ -99,7 +99,7 @@
 
 **也可选：**
 - `/gsd-discuss-phase 2` — 先收集上下文
-- `/gsd-research-phase 2` — 调查未知项
+- `/gsd-plan-phase --research-phase 2` — 调查未知项
 - 审查路线图
 
 ---
@@ -128,7 +128,7 @@
 
 **也可选：**
 - `/gsd-discuss-phase 3` — 先收集上下文
-- `/gsd-research-phase 3` — 调查未知项
+- `/gsd-plan-phase --research-phase 3` — 调查未知项
 - 回顾阶段 2 构建的内容
 
 ---
@@ -149,7 +149,7 @@
 
 **先讨论上下文：** `/gsd-discuss-phase 3`
 
-**研究未知项：** `/gsd-research-phase 3`
+**研究未知项：** `/gsd-plan-phase --research-phase 3`
 
 <sub>`/clear` 优先 → 全新上下文窗口</sub>