diff --git a/.changeset/fierce-mice-munch.md b/.changeset/fierce-mice-munch.md
new file mode 100644
index 000000000..1df5f57b4
--- /dev/null
+++ b/.changeset/fierce-mice-munch.md
@@ -0,0 +1,5 @@
+---
+type: Removed
+pr: 3564
+---
+**Two workflow files that shipped to every runtime but were never loaded are gone** — `discovery-phase.md` and `plan-milestone-gaps.md` had no command, agent, or skill referencing them, and `docs/INVENTORY.md` claimed callers for one that did not exist. A new lint rule now fails the build if any shipped workflow becomes unreachable again. (#3560)
diff --git a/docs/INVENTORY-MANIFEST.json b/docs/INVENTORY-MANIFEST.json
index ec8ffc0da..41e8800c0 100644
--- a/docs/INVENTORY-MANIFEST.json
+++ b/docs/INVENTORY-MANIFEST.json
@@ -127,7 +127,6 @@
       "complete-milestone.md",
       "debug.md",
       "diagnose-issues.md",
-      "discovery-phase.md",
       "discuss-phase-assumptions.md",
       "discuss-phase-power.md",
       "discuss-phase.md",
@@ -163,7 +162,6 @@
       "note.md",
       "onboard.md",
       "pause-work.md",
-      "plan-milestone-gaps.md",
       "plan-phase.md",
       "plan-review-convergence.md",
       "plant-seed.md",
diff --git a/docs/INVENTORY.md b/docs/INVENTORY.md
index 16c9e25f7..b3d6e9377 100644
--- a/docs/INVENTORY.md
+++ b/docs/INVENTORY.md
@@ -193,7 +193,6 @@ Full roster at `gsd-core/workflows/*.md`. Workflows are thin orchestrators that
 | `code-review.md` | Review phase source changes via gsd-code-reviewer; produces REVIEW.md. | `/gsd-code-review` |
 | `complete-milestone.md` | Mark a shipped version as complete — MILESTONES.md entry, PROJECT.md evolution, tag. | `/gsd-complete-milestone` |
 | `diagnose-issues.md` | Orchestrate parallel debug agents to investigate UAT gaps and find root causes. | `/gsd-verify-work` (auto-diagnosis) |
-| `discovery-phase.md` | Execute discovery at the appropriate depth level. | `/gsd-new-project` (discovery path) |
 | `discuss-phase-assumptions.md` | Assumptions-mode discuss — extract implementation decisions via codebase-first analysis. | `/gsd-discuss-phase` (when `discuss_mode=assumptions`) |
 | `discuss-phase-power.md` | Power-user discuss — pre-generate all questions into a JSON state file + HTML UI. | `/gsd-discuss-phase --power` |
 | `discuss-phase.md` | Extract implementation decisions through iterative gray-area discussion. | `/gsd-discuss-phase` |
@@ -266,7 +265,7 @@ Full roster at `gsd-core/workflows/*.md`. Workflows are thin orchestrators that
 | `validate-phase.md` | Retroactively audit and fill Nyquist validation gaps for a completed phase. | `/gsd-validate-phase` |
 | `verify-work.md` | Conversational UAT with auto-diagnosis — produces UAT.md and fix plans. | `/gsd-verify-work` |
 
-> **Note:** Some workflows have no direct user-facing command (e.g. `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — they are invoked internally by orchestrator workflows. `discovery-phase.md` is an alternate entry for `/gsd-new-project`. (The former `verify-phase` workflow — goal-backward verification with no loader of its own — was deleted in #1892; its still-live gates moved to `references/verifier-phase-gates.md` behind `gsd-verifier`.)
+> **Note:** Some workflows have no direct user-facing command (e.g. `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — they are invoked internally by orchestrator workflows. (The former `verify-phase` workflow — goal-backward verification with no loader of its own — was deleted in #1892; its still-live gates moved to `references/verifier-phase-gates.md` behind `gsd-verifier`.)
 
 ### Workflow Sub-Files
 
diff --git a/docs/README.md b/docs/README.md
index e26cd532f..c76778665 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -23,6 +23,7 @@ Language versions: [English](README.md) · [Português (pt-BR)](pt-BR/README.md)
 - [Discuss a phase](how-to/discuss-a-phase.md) — capture implementation decisions before planning begins
 - [Resolve edge-coverage findings](how-to/resolve-edge-coverage-findings.md) — turn the spec phase's surfaced domain-boundary edges into covered, dismissed, or backstopped spec decisions
 - [Resolve prohibition findings](how-to/resolve-prohibition-findings.md) — turn the spec phase's surfaced must-NOT constraints into resolved, dismissed, or deferred spec decisions
+- [Resolve an unreachable-workflow finding](how-to/resolve-unreachable-workflow-findings.md) — wire or fully sweep a shipped workflow that no command, agent, or skill references
 - [Resolve unreachable-guard findings](how-to/resolve-unreachable-guard-findings.md) — fix shell guards whose fallback arm cannot run, and tell "nothing to report" apart from "could not look"
 - [Resolve an ESLint glob-coverage finding](how-to/resolve-eslint-coverage-findings.md) — bring a source file that matches no lint rule under coverage, or record a reasoned exemption
 - [Plan a phase](how-to/plan-a-phase.md) — run research, decompose work, and verify plan quality
diff --git a/docs/adr/0002-command-contract-validation-module.md b/docs/adr/0002-command-contract-validation-module.md
index fac60d04c..2a4955c5c 100644
--- a/docs/adr/0002-command-contract-validation-module.md
+++ b/docs/adr/0002-command-contract-validation-module.md
@@ -14,6 +14,13 @@ The command file contract defines what makes a valid `commands/gsd/*.md`:
 - `allowed-tools:` block present and non-empty, all entries from the canonical tool set
 - Every `@`-reference inside `<execution_context>` blocks resolves to an existing file on disk
 - `@`-references inside `<execution_context>` blocks appear on their own line (no trailing prose)
+- Every `gsd-core/workflows/*.md` file is reachable from at least one `commands/`, `agents/`, or `skills/` loader, transitively through `gsd-core/**` (#3560)
+
+The first five checks are per-file frontmatter/body rules. The sixth is a different concern in kind: a repo-level reachability graph, computed once per run rather than per command file. It walks every markdown file under `commands/`, `agents/`, and `skills/` as loader seeds, then follows references transitively through `gsd-core/**` (not just `gsd-core/workflows/`, since a `references/` or `templates/` file can itself name a workflow path) until every reachable workflow file is marked. Any `gsd-core/workflows/*.md` file left unmarked is reported as an orphan.
+
+A reference is recognized in three shapes: an eager `@`-include (the same `<execution_context>` syntax the first five checks already parse), a lazy path named only in prose or code that a command reads on demand rather than inlines, and a parent-relative sub-file path (`execute-phase/steps/post-merge-gate.md`) implicitly rooted under `workflows/`.
+
+Reachability is seeded only from loaders, never from a workflow file's own content — a workflow that references itself, or two workflows that reference only each other, must still be reported as unreachable, since no command, agent, or skill loader ever actually opens them. `docs/` and test fixtures deliberately do not count as loaders: a path merely mentioned in documentation or a test does not make it reachable by any runtime — only `commands/`, `agents/`, and `skills/` do.
 
 ## Context
 
diff --git a/docs/how-to/resolve-unreachable-workflow-findings.md b/docs/how-to/resolve-unreachable-workflow-findings.md
new file mode 100644
index 000000000..ba22e788a
--- /dev/null
+++ b/docs/how-to/resolve-unreachable-workflow-findings.md
@@ -0,0 +1,117 @@
+# How to resolve an unreachable-workflow finding
+
+**Goal:** Turn a shipped workflow that no loader references into either a wired workflow or a fully swept deletion — so the instruction layer stays a single source of truth, instead of accumulating files that install to every runtime and are never read.
+
+**Prerequisites:** A failing `npm run lint:ci` (or a direct `node scripts/lint-command-contract.cjs`) reporting one or more unreachable workflows. The check runs automatically as part of `lint:ci` — you do not invoke it separately.
+
+For what counts as a reference and why the check is shaped this way, see [ADR-0002](../adr/0002-command-contract-validation-module.md). This guide covers only how to *act* on a finding.
+
+---
+
+## Read a finding
+
+```
+ERROR lint-command-contract: 1 unreachable workflow file(s)
+
+  gsd-core/workflows/scan.md
+    ships to every runtime install tree, but no command, agent, or skill references it
+```
+
+The check walks the transitive closure from every `commands/**`, `agents/**`, and `skills/**` file, following three reference shapes:
+
+| Shape | Example | When it is used |
+|---|---|---|
+| Eager include | `@~/.claude/gsd-core/workflows/x.md` | Inlined on every invocation. Reserve for workflows the command always needs. |
+| Lazy path | `` `~/.claude/gsd-core/workflows/x.md` `` | Read on demand at the point of use. The default for flag-gated or conditional workflows. |
+| Parent-relative | `execute-phase/steps/x.md` | A sub-file under an existing workflow directory. |
+
+A finding means **none** of those reaches the file. There are exactly two correct resolutions.
+
+---
+
+## Wire it — the workflow is live and the reference is missing
+
+**Choose this when a command, flag, or agent is documented as using the workflow.** The file is not dead; the reference is.
+
+Add a reference in the loader that dispatches to it. Prefer a **lazy path** unless the workflow is needed on every invocation of that command:
+
+```markdown
+- If it is `--fast`: strip the flag, then read and execute
+  `~/.claude/gsd-core/workflows/scan.md` (passing remaining args).
+```
+
+An eager `@`-include is inlined into context on *every* invocation of that command, including the paths that never use the workflow. The progressive-disclosure split ([#717](https://github.com/open-gsd/gsd-core/issues/717)) exists specifically to keep that cost off the common path, so reach for the lazy form first.
+
+If the loader is a `commands/gsd/*.md` file, regenerate the skill surface afterward:
+
+```bash
+npm run gen:plugin-skills
+```
+
+**This was the right answer for `scan.md`** — `/gsd-map-codebase --fast` was a shipped, documented flag whose routing line named no resolvable path. Deleting the file would have removed the only implementation of a live feature ([#3561](https://github.com/open-gsd/gsd-core/issues/3561)).
+
+---
+
+## Delete it — the workflow is genuinely dead
+
+**Choose this when nothing is supposed to reach it** — typically because its command was removed and the workflow was left behind.
+
+Before deleting, confirm the fence is not load-bearing: check the file's own header for a claimed caller and verify that caller exists. The `discovery-phase` workflow's header claimed it was "called from plan-phase.md's mandatory_discovery step"; that step did not exist. `docs/INVENTORY.md` claimed it was an alternate `/gsd-new-project` entry; `new-project.md` never referenced it. **A claimed caller is not a caller.** (The `discovery-phase` workflow was deleted in #3560.)
+
+Deletion is a five-step sweep, and skipping any step leaves the tree inconsistent:
+
+```bash
+git rm gsd-core/workflows/<name>.md
+```
+
+1. **Remove its `docs/INVENTORY.md` row — in all five locales.** `docs/INVENTORY.md` plus `docs/ja-JP/`, `docs/ko-KR/`, `docs/zh-CN/`, `docs/pt-BR/`. Check the explanatory note near the bottom of each file too; a workflow is sometimes named there as well as in the table.
+2. **Regenerate the inventory manifest.** Build first — regenerating before `build:lib` silently drops modules:
+   ```bash
+   npm run build:lib && node scripts/gen-inventory-manifest.cjs --write
+   ```
+3. **Regenerate the golden install-tree fixtures.** All 19 runtimes list every shipped workflow:
+   ```bash
+   npm run gen:install-tree
+   ```
+4. **Sweep tests that name the file — allowlists *and* content assertions.** Two distinct traps live here, and #3560 hit both:
+   - An **allowlist keyed on the bare basename** will not match a full-path search. `tests/planner-language-regression.test.cjs` carried a stale entry for the `discovery-phase` workflow that a path-based sweep missed.
+   - A test that **asserts the file's existence or content** pins it. `tests/phase.test.cjs` required the `plan-milestone-gaps` workflow to exist and checked its `mkdir` patterns; deleting the file turned that into four red tests on the remote runner. Cut the coupling in the same change — but keep any sibling assertions that guard *other* files, since these blocks are often shared across several workflows.
+
+   Note that `scripts/lint-removed-but-needed.cjs` will **not** catch either: it scans `.github/workflows/`, `gsd-core/`, `docs/`, and `package.json` — not `tests/`. Search `tests/` yourself.
+5. **Add a `Removed` changeset fragment**, and remember that a `Removed` type requires a `docs/` change — which step 1 already satisfies.
+
+Then confirm the tree is consistent:
+
+```bash
+npm run lint:ci
+```
+
+---
+
+## What does *not* count as a reference
+
+The check deliberately scans only `commands/`, `agents/`, `skills/`, and `gsd-core/**`. A mention anywhere else confers no reachability:
+
+| Location | Counts? | Why |
+|---|---|---|
+| `docs/**` | **No** | Documentation is a claim about the system, not a loader. `scan.md` was documented in `docs/INVENTORY.md` while being entirely unreached. |
+| `tests/fixtures/install-tree/*.json` | **No** | A shipping manifest proves the file *ships*, which is the problem being reported, not a refutation of it. |
+| A changeset fragment | **No** | Historical record, not a load path. |
+
+If you are tempted to satisfy the check by adding a mention somewhere convenient, that is the failure mode this scoping exists to prevent — the file stays dead and the gate goes green.
+
+---
+
+## When the check passes but something still feels wrong
+
+The rule proves **structural** reachability: some loader names the file. It cannot prove the file is read on any executed path.
+
+| You see | It means |
+|---|---|
+| `151 workflow files, 151 reachable, 0 unreachable` | Every shipped workflow is named by at least one loader. Not that every one is used. |
+| A workflow reachable only from another unreachable workflow | Reported correctly — reachability is seeded only from loaders, so an unreachable file cannot confer reachability on anything else. |
+| A pair of workflows that reference only each other | Both reported. A mutual-reference island satisfies nothing. |
+| A workflow that references itself | Reported. A self-reference is not a loader. |
+| A path named only inside a fenced code block | Counted as a reference. This is a deliberate over-count: the check fails builds, and a false positive on a correct tree is worse than a missed orphan, so ambiguous references resolve toward "reachable". |
+
+A workflow that is named by a loader but never actually executed is **not** caught here. That is a semantic question this structural check does not answer.
diff --git a/docs/ja-JP/INVENTORY.md b/docs/ja-JP/INVENTORY.md
index d5ab21208..6ea9cfc38 100644
--- a/docs/ja-JP/INVENTORY.md
+++ b/docs/ja-JP/INVENTORY.md
@@ -189,7 +189,6 @@
 | `code-review.md` | gsd-code-reviewer でフェーズのソース変更をレビュー。REVIEW.md を作成。 | `/gsd-code-review` |
 | `complete-milestone.md` | 出荷されたバージョンを完了としてマーク — MILESTONES.md エントリー、PROJECT.md の進化、タグ。 | `/gsd-complete-milestone` |
 | `diagnose-issues.md` | 並列デバッグエージェントをオーケストレーションして UAT のギャップを調査し、根本原因を特定。 | `/gsd-verify-work` (auto-diagnosis) |
-| `discovery-phase.md` | 適切な深さレベルでディスカバリーを実行。 | `/gsd-new-project` (discovery path) |
 | `discuss-phase-assumptions.md` | 仮定モードの discuss — コードベースファーストの分析で実装決定を抽出。 | `/gsd-discuss-phase` (when `discuss_mode=assumptions`) |
 | `discuss-phase-power.md` | パワーユーザー discuss — すべての質問を JSON 状態ファイル + HTML UI に事前生成。 | `/gsd-discuss-phase --power` |
 | `discuss-phase.md` | 反復的なグレーゾーンの議論を通じて実装決定を抽出。 | `/gsd-discuss-phase` |
@@ -261,7 +260,7 @@
 | `validate-phase.md` | 完了したフェーズの Nyquist バリデーションのギャップを遡及監査して埋める。 | `/gsd-validate-phase` |
 | `verify-work.md` | 自動診断付きの会話型 UAT — UAT.md と修正プランを作成。 | `/gsd-verify-work` |
 
-> **注記:** 一部のワークフローには直接ユーザー向けのコマンドがありません（例: `execute-plan.md`、`transition.md`、`node-repair.md`、`diagnose-issues.md`）— これらはオーケストレーターワークフローによって内部的に呼び出されます。`discovery-phase.md` は `/gsd-new-project` の代替エントリーポイントです。
+> **注記:** 一部のワークフローには直接ユーザー向けのコマンドがありません（例: `execute-plan.md`、`transition.md`、`node-repair.md`、`diagnose-issues.md`）— これらはオーケストレーターワークフローによって内部的に呼び出されます。
 
 ---
 
diff --git a/docs/ko-KR/INVENTORY.md b/docs/ko-KR/INVENTORY.md
index 48330de87..11bf8651a 100644
--- a/docs/ko-KR/INVENTORY.md
+++ b/docs/ko-KR/INVENTORY.md
@@ -189,7 +189,6 @@
 | `code-review.md` | gsd-code-reviewer를 통한 단계 소스 변경 검토; REVIEW.md 생성. | `/gsd-code-review` |
 | `complete-milestone.md` | 출시된 버전을 완료로 표시 — MILESTONES.md 항목, PROJECT.md 발전, 태그. | `/gsd-complete-milestone` |
 | `diagnose-issues.md` | UAT 공백 조사 및 근본 원인 찾기를 위한 병렬 디버그 에이전트 오케스트레이션. | `/gsd-verify-work` (자동 진단) |
-| `discovery-phase.md` | 적절한 깊이 수준에서 탐색 실행. | `/gsd-new-project` (탐색 경로) |
 | `discuss-phase-assumptions.md` | 가정 모드 discuss — 코드베이스 우선 분석을 통한 구현 결정 추출. | `/gsd-discuss-phase` (`discuss_mode=assumptions`일 때) |
 | `discuss-phase-power.md` | 파워 유저 discuss — 모든 질문을 JSON 상태 파일 + HTML UI로 사전 생성. | `/gsd-discuss-phase --power` |
 | `discuss-phase.md` | 반복적인 회색 지대 토론을 통한 구현 결정 추출. | `/gsd-discuss-phase` |
@@ -261,7 +260,7 @@
 | `validate-phase.md` | 완료된 단계의 나이퀴스트 검증 공백을 소급 감사 및 채움. | `/gsd-validate-phase` |
 | `verify-work.md` | 자동 진단이 포함된 대화형 UAT — UAT.md 및 수정 계획 생성. | `/gsd-verify-work` |
 
-> **참고:** 일부 워크플로우는 직접적인 사용자 대면 명령어가 없습니다(예: `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — 이들은 오케스트레이터 워크플로우에 의해 내부적으로 호출됩니다. `discovery-phase.md`는 `/gsd-new-project`의 대체 진입점입니다.
+> **참고:** 일부 워크플로우는 직접적인 사용자 대면 명령어가 없습니다(예: `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — 이들은 오케스트레이터 워크플로우에 의해 내부적으로 호출됩니다.
 
 ---
 
diff --git a/docs/pt-BR/INVENTORY.md b/docs/pt-BR/INVENTORY.md
index 0b61c5cf8..3baefd60d 100644
--- a/docs/pt-BR/INVENTORY.md
+++ b/docs/pt-BR/INVENTORY.md
@@ -189,7 +189,6 @@ Registro completo em `gsd-core/workflows/*.md`. Workflows são orquestradores en
 | `code-review.md` | Revisa alterações de código-fonte da fase via gsd-code-reviewer; produz REVIEW.md. | `/gsd-code-review` |
 | `complete-milestone.md` | Marca uma versão entregue como concluída — entrada no MILESTONES.md, evolução do PROJECT.md, tag. | `/gsd-complete-milestone` |
 | `diagnose-issues.md` | Orquestra agentes de debug paralelos para investigar lacunas de UAT e encontrar causas raiz. | `/gsd-verify-work` (autodiagnóstico) |
-| `discovery-phase.md` | Executa a descoberta no nível de profundidade apropriado. | `/gsd-new-project` (caminho de descoberta) |
 | `discuss-phase-assumptions.md` | Discuss no modo de premissas — extrai decisões de implementação via análise com base no código primeiro. | `/gsd-discuss-phase` (quando `discuss_mode=assumptions`) |
 | `discuss-phase-power.md` | Discuss para usuário avançado — pré-gera todas as perguntas em um arquivo de estado JSON + UI HTML. | `/gsd-discuss-phase --power` |
 | `discuss-phase.md` | Extrai decisões de implementação por meio de discussão iterativa de zonas cinzentas. | `/gsd-discuss-phase` |
@@ -261,7 +260,7 @@ Registro completo em `gsd-core/workflows/*.md`. Workflows são orquestradores en
 | `validate-phase.md` | Audita retroativamente e preenche lacunas de validação Nyquist para uma fase concluída. | `/gsd-validate-phase` |
 | `verify-work.md` | UAT conversacional com autodiagnóstico — produz UAT.md e planos de correção. | `/gsd-verify-work` |
 
-> **Nota:** Alguns workflows não têm comando direto voltado ao usuário (p. ex. `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — eles são invocados internamente por workflows orquestradores. `discovery-phase.md` é uma entrada alternativa para `/gsd-new-project`.
+> **Nota:** Alguns workflows não têm comando direto voltado ao usuário (p. ex. `execute-plan.md`, `transition.md`, `node-repair.md`, `diagnose-issues.md`) — eles são invocados internamente por workflows orquestradores.
 
 ---
 
diff --git a/docs/zh-CN/INVENTORY.md b/docs/zh-CN/INVENTORY.md
index 4cd5c913e..1c020396a 100644
--- a/docs/zh-CN/INVENTORY.md
+++ b/docs/zh-CN/INVENTORY.md
@@ -189,7 +189,6 @@
 | `code-review.md` | 通过 gsd-code-reviewer 审查阶段源码变更；生成 REVIEW.md。 | `/gsd-code-review` |
 | `complete-milestone.md` | 将已发布版本标记为完成 — MILESTONES.md 条目、PROJECT.md 演进、标签。 | `/gsd-complete-milestone` |
 | `diagnose-issues.md` | 编排并行调试代理以调查 UAT 差距并找出根本原因。 | `/gsd-verify-work`（自动诊断） |
-| `discovery-phase.md` | 以适当的深度级别执行发现。 | `/gsd-new-project`（发现路径） |
 | `discuss-phase-assumptions.md` | 假设模式讨论 — 通过以代码库为先的分析提取实施决策。 | `/gsd-discuss-phase`（当 `discuss_mode=assumptions` 时） |
 | `discuss-phase-power.md` | 高级用户讨论 — 将所有问题预生成到 JSON 状态文件和 HTML UI 中。 | `/gsd-discuss-phase --power` |
 | `discuss-phase.md` | 通过迭代灰色地带讨论提取实施决策。 | `/gsd-discuss-phase` |
@@ -261,7 +260,7 @@
 | `validate-phase.md` | 回溯审计并填补已完成阶段的奈奎斯特验证空缺。 | `/gsd-validate-phase` |
 | `verify-work.md` | 带自动诊断的对话式 UAT — 生成 UAT.md 和修复计划。 | `/gsd-verify-work` |
 
-> **注意：** 某些工作流没有直接面向用户的命令（例如 `execute-plan.md`、`transition.md`、`node-repair.md`、`diagnose-issues.md`）— 它们由编排器工作流在内部调用。`discovery-phase.md` 是 `/gsd-new-project` 的备用入口。
+> **注意：** 某些工作流没有直接面向用户的命令（例如 `execute-plan.md`、`transition.md`、`node-repair.md`、`diagnose-issues.md`）— 它们由编排器工作流在内部调用。
 
 ---
 
diff --git a/gsd-core/workflows/discovery-phase.md b/gsd-core/workflows/discovery-phase.md
deleted file mode 100644
index b80b12339..000000000
--- a/gsd-core/workflows/discovery-phase.md
+++ /dev/null
@@ -1,298 +0,0 @@
-<purpose>
-Execute discovery at the appropriate depth level.
-Produces DISCOVERY.md (for Level 2-3) that informs PLAN.md creation.
-
-Called from plan-phase.md's mandatory_discovery step with a depth parameter.
-
-NOTE: For comprehensive ecosystem research ("how do experts build this"), use /gsd:plan-phase --research-phase instead, which produces RESEARCH.md.
-</purpose>
-```bash
-_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "${CLAUDE_CONFIG_DIR:-$HOME/.claude}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLAUDE_CONFIG_DIR:-$HOME/.claude}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi; if [ -n "${CLAUDE_ENV_FILE:-}" ] && [ -n "${GSD_TOOLS:-}" ]; then printf "export PATH='%s':\"\$PATH\"\n" "${GSD_TOOLS%/*}" >> "$CLAUDE_ENV_FILE" 2>/dev/null || true; fi
-RESPONSE_LANGUAGE=$(gsd_run query config-get response_language --default "" 2>/dev/null || echo "")
-```
-
-**If `response_language` is set:** All user-facing questions, prompts, and explanations in this workflow MUST be presented in `{response_language}`. Technical terms, code, file paths, and subagent prompts stay in English — only user-facing output is translated.
-
-
-<depth_levels>
-**This workflow supports three depth levels:**
-
-| Level | Name         | Time      | Output                                       | When                                      |
-| ----- | ------------ | --------- | -------------------------------------------- | ----------------------------------------- |
-| 1     | Quick Verify | 2-5 min   | No file, proceed with verified knowledge     | Single library, confirming current syntax |
-| 2     | Standard     | 15-30 min | DISCOVERY.md                                 | Choosing between options, new integration |
-| 3     | Deep Dive    | 1+ hour   | Detailed DISCOVERY.md with validation gates  | Architectural decisions, novel problems   |
-
-**Depth is determined by plan-phase.md before routing here.**
-</depth_levels>
-
-<source_hierarchy>
-**MANDATORY: Context7 BEFORE WebSearch**
-
-Claude's training data is 6-18 months stale. Always verify.
-
-1. **Context7 MCP FIRST** - Current docs, no hallucination
-2. **Official docs** - When Context7 lacks coverage
-3. **WebSearch LAST** - For comparisons and trends only
-
-See ~/.claude/gsd-core/templates/discovery.md `<discovery_protocol>` for full protocol.
-</source_hierarchy>
-
-<process>
-
-<step name="determine_depth">
-Check the depth parameter passed from plan-phase.md:
-- `depth=verify` → Level 1 (Quick Verification)
-- `depth=standard` → Level 2 (Standard Discovery)
-- `depth=deep` → Level 3 (Deep Dive)
-
-Route to appropriate level workflow below.
-</step>
-
-<step name="level_1_quick_verify">
-**Level 1: Quick Verification (2-5 minutes)**
-
-For: Single known library, confirming syntax/version still correct.
-
-**Process:**
-
-1. Resolve library in Context7:
-
-   ```
-   mcp__context7__resolve-library-id with libraryName: "[library]"
-   ```
-
-2. Fetch relevant docs:
-
-   ```
-   mcp__context7__query-docs with:
-   - libraryId: [from step 1]
-   - query: [specific concern]
-   ```
-
-3. Verify:
-
-   - Current version matches expectations
-   - API syntax unchanged
-   - No breaking changes in recent versions
-
-4. **If verified:** Return to plan-phase.md with confirmation. No DISCOVERY.md needed.
-
-5. **If concerns found:** Escalate to Level 2.
-
-**Output:** Verbal confirmation to proceed, or escalation to Level 2.
-</step>
-
-<step name="level_2_standard">
-**Level 2: Standard Discovery (15-30 minutes)**
-
-For: Choosing between options, new external integration.
-
-**Process:**
-
-1. **Identify what to discover:**
-
-   - What options exist?
-   - What are the key comparison criteria?
-   - What's our specific use case?
-
-2. **Context7 for each option:**
-
-   ```
-   For each library/framework:
-   - mcp__context7__resolve-library-id
-   - mcp__context7__query-docs (frame the `query` for API usage vs concepts)
-   ```
-
-3. **Official docs** for anything Context7 lacks.
-
-4. **WebSearch** for comparisons:
-
-   - "[option A] vs [option B] {current_year}"
-   - "[option] known issues"
-   - "[option] with [our stack]"
-
-5. **Cross-verify:** Any WebSearch finding → confirm with Context7/official docs.
-
-6. **Create DISCOVERY.md** using ~/.claude/gsd-core/templates/discovery.md structure:
-
-   - Summary with recommendation
-   - Key findings per option
-   - Code examples from Context7
-   - Confidence level (should be MEDIUM-HIGH for Level 2)
-
-7. Return to plan-phase.md.
-
-**Output:** `.planning/phases/XX-name/DISCOVERY.md`
-</step>
-
-<step name="level_3_deep_dive">
-**Level 3: Deep Dive (1+ hour)**
-
-For: Architectural decisions, novel problems, high-risk choices.
-
-**Process:**
-
-1. **Scope the discovery** using ~/.claude/gsd-core/templates/discovery.md:
-
-   - Define clear scope
-   - Define include/exclude boundaries
-   - List specific questions to answer
-
-2. **Exhaustive Context7 research:**
-
-   - All relevant libraries
-   - Related patterns and concepts
-   - Multiple topics per library if needed
-
-3. **Official documentation deep read:**
-
-   - Architecture guides
-   - Best practices sections
-   - Migration/upgrade guides
-   - Known limitations
-
-4. **WebSearch for ecosystem context:**
-
-   - How others solved similar problems
-   - Production experiences
-   - Gotchas and anti-patterns
-   - Recent changes/announcements
-
-5. **Cross-verify ALL findings:**
-
-   - Every WebSearch claim → verify with authoritative source
-   - Mark what's verified vs assumed
-   - Flag contradictions
-
-6. **Create comprehensive DISCOVERY.md:**
-
-   - Full structure from ~/.claude/gsd-core/templates/discovery.md
-   - Quality report with source attribution
-   - Confidence by finding
-   - If LOW confidence on any critical finding → add validation checkpoints
-
-7. **Confidence gate:** If overall confidence is LOW, present options before proceeding.
-
-8. Return to plan-phase.md.
-
-**Output:** `.planning/phases/XX-name/DISCOVERY.md` (comprehensive)
-</step>
-
-<step name="identify_unknowns">
-**For Level 2-3:** Define what we need to learn.
-
-Ask: What do we need to learn before we can plan this phase?
-
-- Technology choices?
-- Best practices?
-- API patterns?
-- Architecture approach?
-  </step>
-
-<step name="create_discovery_scope">
-Use ~/.claude/gsd-core/templates/discovery.md.
-
-Include:
-
-- Clear discovery objective
-- Scoped include/exclude lists
-- Source preferences (official docs, Context7, current year)
-- Output structure for DISCOVERY.md
-  </step>
-
-<step name="execute_discovery">
-Run the discovery:
-- Use web search for current info
-- Use Context7 MCP for library docs
-- Prefer current year sources
-- Structure findings per template
-</step>
-
-<step name="create_discovery_output">
-Write `.planning/phases/XX-name/DISCOVERY.md`:
-- Summary with recommendation
-- Key findings with sources
-- Code examples if applicable
-- Metadata (confidence, dependencies, open questions, assumptions)
-</step>
-
-<step name="confidence_gate">
-After creating DISCOVERY.md, check confidence level.
-
-If confidence is LOW:
-
-**Text mode (`workflow.text_mode: true` in config or `--text` flag):** Set `TEXT_MODE=true` if `--text` is present in `$ARGUMENTS` OR `text_mode` from init JSON is `true`. When TEXT_MODE is active, replace every `AskUserQuestion` call with a plain-text numbered list and ask the user to type their choice number. This is required for non-Claude runtimes (OpenAI Codex, Gemini CLI, etc.) where `AskUserQuestion` is not available.
-Use AskUserQuestion:
-
-- header: "Low Conf."
-- question: "Discovery confidence is LOW: [reason]. How would you like to proceed?"
-- options:
-  - "Dig deeper" - Do more research before planning
-  - "Proceed anyway" - Accept uncertainty, plan with caveats
-  - "Pause" - I need to think about this
-
-If confidence is MEDIUM:
-Inline: "Discovery complete (medium confidence). [brief reason]. Proceed to planning?"
-
-If confidence is HIGH:
-Proceed directly, just note: "Discovery complete (high confidence)."
-</step>
-
-<step name="open_questions_gate">
-If DISCOVERY.md has open_questions:
-
-Present them inline:
-"Open questions from discovery:
-
-- [Question 1]
-- [Question 2]
-
-These may affect implementation. Acknowledge and proceed? (yes / address first)"
-
-If "address first": Gather user input on questions, update discovery.
-</step>
-
-<step name="offer_next">
-```
-Discovery complete: .planning/phases/XX-name/DISCOVERY.md
-Recommendation: [one-liner]
-Confidence: [level]
-
-What's next?
-
-1. Discuss phase context (/gsd:discuss-phase [current-phase])
-2. Create phase plan (/gsd:plan-phase [current-phase])
-3. Refine discovery (dig deeper)
-4. Review discovery
-
-```
-
-NOTE: DISCOVERY.md is NOT committed separately. It will be committed with phase completion.
-</step>
-
-</process>
-
-<success_criteria>
-**Level 1 (Quick Verify):**
-- Context7 consulted for library/topic
-- Current state verified or concerns escalated
-- Verbal confirmation to proceed (no files)
-
-**Level 2 (Standard):**
-- Context7 consulted for all options
-- WebSearch findings cross-verified
-- DISCOVERY.md created with recommendation
-- Confidence level MEDIUM or higher
-- Ready to inform PLAN.md creation
-
-**Level 3 (Deep Dive):**
-- Discovery scope defined
-- Context7 exhaustively consulted
-- All WebSearch findings verified against authoritative sources
-- DISCOVERY.md created with comprehensive analysis
-- Quality report with source attribution
-- If LOW confidence findings → validation checkpoints defined
-- Confidence gate passed
-- Ready to inform PLAN.md creation
-</success_criteria>
diff --git a/gsd-core/workflows/plan-milestone-gaps.md b/gsd-core/workflows/plan-milestone-gaps.md
deleted file mode 100644
index a3078c14f..000000000
--- a/gsd-core/workflows/plan-milestone-gaps.md
+++ /dev/null
@@ -1,281 +0,0 @@
-<purpose>
-Create all phases necessary to close gaps identified by `/gsd:audit-milestone`. Reads MILESTONE-AUDIT.md, groups gaps into logical phases, creates phase entries in ROADMAP.md, and offers to plan each phase. One command creates all fix phases — no manual `/gsd-add-phase` per gap.
-</purpose>
-
-<required_reading>
-Read all files referenced by the invoking prompt's execution_context before starting.
-</required_reading>
-
-<process>
-
-## 1. Load Audit Results
-
-```bash
-# Find the most recent audit file
-(ls -t .planning/v*-MILESTONE-AUDIT.md 2>/dev/null || true) | head -1
-```
-
-Parse YAML frontmatter to extract structured gaps:
-- `gaps.requirements` — unsatisfied requirements
-- `gaps.integration` — missing cross-phase connections
-- `gaps.flows` — broken E2E flows
-
-If no audit file exists or has no gaps, error:
-```
-No audit gaps found. Run `/gsd:audit-milestone` first.
-```
-
-## 2. Prioritize Gaps
-
-Group gaps by priority from REQUIREMENTS.md:
-
-| Priority | Action |
-|----------|--------|
-| `must` | Create phase, blocks milestone |
-| `should` | Create phase, recommended |
-| `nice` | Ask user: include or defer? |
-
-For integration/flow gaps, infer priority from affected requirements.
-
-## 3. Group Gaps into Phases
-
-Cluster related gaps into logical phases:
-
-**Grouping rules:**
-- Same affected phase → combine into one fix phase
-- Same subsystem (auth, API, UI) → combine
-- Dependency order (fix stubs before wiring)
-- Keep phases focused: 2-4 tasks each
-
-**Example grouping:**
-```
-Gap: DASH-01 unsatisfied (Dashboard doesn't fetch)
-Gap: Integration Phase 1→3 (Auth not passed to API calls)
-Gap: Flow "View dashboard" broken at data fetch
-
-→ Phase 6: "Wire Dashboard to API"
-  - Add fetch to Dashboard.tsx
-  - Include auth header in fetch
-  - Handle response, update state
-  - Render user data
-```
-
-## 4. Determine Phase Numbers
-
-Find highest existing phase:
-```bash
-_GSD_SHIM_NAME="gsd-tools.cjs"; _GSD_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; GSD_TOOLS="${_GSD_RUNTIME_ROOT}/gsd-core/bin/${_GSD_SHIM_NAME}"; if [ -f "$GSD_TOOLS" ]; then gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.claude/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${_GSD_RUNTIME_ROOT}/.codex/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif command -v gsd-tools >/dev/null 2>&1; then GSD_TOOLS="$(command -v gsd-tools)"; gsd_run() { "$GSD_TOOLS" "$@"; }; elif [ -f "${CLAUDE_CONFIG_DIR:-$HOME/.claude}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLAUDE_CONFIG_DIR:-$HOME/.claude}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${HERMES_HOME:-$HOME/.hermes}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CURSOR_CONFIG_DIR:-$HOME/.cursor}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEX_HOME:-$HOME/.codex}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GEMINI_CONFIG_DIR:-$HOME/.gemini}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${COPILOT_CONFIG_DIR:-$HOME/.copilot}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${WINDSURF_CONFIG_DIR:-$HOME/.codeium/windsurf}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${AUGMENT_CONFIG_DIR:-$HOME/.augment}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${TRAE_CONFIG_DIR:-$HOME/.trae}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${QWEN_CONFIG_DIR:-$HOME/.qwen}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CODEBUDDY_CONFIG_DIR:-$HOME/.codebuddy}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${CLINE_CONFIG_DIR:-$HOME/.cline}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${GROK_AGENTS_HOME:-$HOME/.agents}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${ANTIGRAVITY_CONFIG_DIR:-$HOME/.gemini/antigravity}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${OPENCODE_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/opencode}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; elif [ -f "${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}" ]; then GSD_TOOLS="${KILO_CONFIG_DIR:-${XDG_CONFIG_HOME:-$HOME/.config}/kilo}/gsd-core/bin/${_GSD_SHIM_NAME}"; gsd_run() { node "$GSD_TOOLS" "$@"; }; else echo "ERROR: gsd-tools.cjs not found at $GSD_TOOLS and gsd-tools is not on PATH. Run: npx -y @opengsd/gsd-core@latest --claude --local" >&2; exit 1; fi; if [ -n "${CLAUDE_ENV_FILE:-}" ] && [ -n "${GSD_TOOLS:-}" ]; then printf "export PATH='%s':\"\$PATH\"\n" "${GSD_TOOLS%/*}" >> "$CLAUDE_ENV_FILE" 2>/dev/null || true; fi
-# Get sorted phase list, extract last one
-HIGHEST=$(gsd_run query phases.list --pick directories[-1])
-```
-
-New phases continue from there:
-- If Phase 5 is highest, gaps become Phase 6, 7, 8...
-
-## 5. Present Gap Closure Plan
-
-```markdown
-## Gap Closure Plan
-
-**Milestone:** {version}
-**Gaps to close:** {N} requirements, {M} integration, {K} flows
-
-### Proposed Phases
-
-**Phase {N}: {Name}**
-Closes:
-- {REQ-ID}: {description}
-- Integration: {from} → {to}
-Tasks: {count}
-
-**Phase {N+1}: {Name}**
-Closes:
-- {REQ-ID}: {description}
-- Flow: {flow name}
-Tasks: {count}
-
-{If nice-to-have gaps exist:}
-
-### Deferred (nice-to-have)
-
-These gaps are optional. Include them?
-- {gap description}
-- {gap description}
-
----
-
-Create these {X} phases? (yes / adjust / defer all optional)
-```
-
-Wait for user confirmation.
-
-## 6. Update ROADMAP.md
-
-Add new phases to current milestone:
-
-```markdown
-### Phase {N}: {Name}
-**Goal:** {derived from gaps being closed}
-**Requirements:** {REQ-IDs being satisfied}
-**Gap Closure:** Closes gaps from audit
-
-### Phase {N+1}: {Name}
-...
-```
-
-## 7. Update REQUIREMENTS.md Traceability Table (REQUIRED)
-
-For each REQ-ID assigned to a gap closure phase:
-- Update the Phase column to reflect the new gap closure phase
-- Reset Status to `Pending`
-
-Reset checked-off requirements the audit found unsatisfied:
-- Change `[x]` → `[ ]` for any requirement marked unsatisfied in the audit
-- Update coverage count at top of REQUIREMENTS.md
-
-```bash
-# Verify traceability table reflects gap closure assignments
-grep -c "Pending" .planning/REQUIREMENTS.md
-```
-
-## 8. Create Phase Directories
-
-For each new phase (N, N+1, …), resolve the directory name via `init.phase-op` so the `project_code` prefix is honoured:
-
-```bash
-INIT=$(gsd_run query init.phase-op "{NN}")
-if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi
-expected_phase_dir=$(echo "$INIT" | node -e "process.stdout.write(JSON.parse(require('fs').readFileSync('/dev/stdin','utf8')).expected_phase_dir)")
-mkdir -p "${expected_phase_dir}"
-```
-
-Repeat for each gap-closure phase number. This produces `{CODE}-{NN}-{slug}/` when `project_code` is set in `.planning/config.json`, and `{NN}-{slug}/` otherwise — consistent with all other phase-creation paths.
-
-## 9. Commit Roadmap and Requirements Update
-
-```bash
-gsd_run query commit "docs(roadmap): add gap closure phases {N}-{M}" --files .planning/ROADMAP.md .planning/REQUIREMENTS.md
-```
-
-## 10. Offer Next Steps
-
-```markdown
-## ✓ Gap Closure Phases Created
-
-**Phases added:** {N} - {M}
-**Gaps addressed:** {count} requirements, {count} integration, {count} flows
-
----
-
-## ▶ Next Up — [${PROJECT_CODE}] ${PROJECT_TITLE}
-
-**Plan first gap closure phase**
-
-`/clear` then:
-
-`/gsd:plan-phase {N}`
-
----
-
-**Also available:**
-- `/gsd:execute-phase {N}` — if plans already exist
-- `cat .planning/ROADMAP.md` — see updated roadmap
-
----
-
-**After all gap phases complete:**
-
-`/gsd:audit-milestone` — re-audit to verify gaps closed
-`/gsd:complete-milestone {version}` — archive when audit passes
-```
-
-</process>
-
-<gap_to_phase_mapping>
-
-## How Gaps Become Tasks
-
-**Requirement gap → Tasks:**
-```yaml
-gap:
-  id: DASH-01
-  description: "User sees their data"
-  reason: "Dashboard exists but doesn't fetch from API"
-  missing:
-    - "useEffect with fetch to /api/user/data"
-    - "State for user data"
-    - "Render user data in JSX"
-
-becomes:
-
-phase: "Wire Dashboard Data"
-tasks:
-  - name: "Add data fetching"
-    files: [src/components/Dashboard.tsx]
-    action: "Add useEffect that fetches /api/user/data on mount"
-
-  - name: "Add state management"
-    files: [src/components/Dashboard.tsx]
-    action: "Add useState for userData, loading, error states"
-
-  - name: "Render user data"
-    files: [src/components/Dashboard.tsx]
-    action: "Replace placeholder with userData.map rendering"
-```
-
-**Integration gap → Tasks:**
-```yaml
-gap:
-  from_phase: 1
-  to_phase: 3
-  connection: "Auth token → API calls"
-  reason: "Dashboard API calls don't include auth header"
-  missing:
-    - "Auth header in fetch calls"
-    - "Token refresh on 401"
-
-becomes:
-
-phase: "Add Auth to Dashboard API Calls"
-tasks:
-  - name: "Add auth header to fetches"
-    files: [src/components/Dashboard.tsx, src/lib/api.ts]
-    action: "Include Authorization header with token in all API calls"
-
-  - name: "Handle 401 responses"
-    files: [src/lib/api.ts]
-    action: "Add interceptor to refresh token or redirect to login on 401"
-```
-
-**Flow gap → Tasks:**
-```yaml
-gap:
-  name: "User views dashboard after login"
-  broken_at: "Dashboard data load"
-  reason: "No fetch call"
-  missing:
-    - "Fetch user data on mount"
-    - "Display loading state"
-    - "Render user data"
-
-becomes:
-
-# Usually same phase as requirement/integration gap
-# Flow gaps often overlap with other gap types
-```
-
-</gap_to_phase_mapping>
-
-<success_criteria>
-- [ ] MILESTONE-AUDIT.md loaded and gaps parsed
-- [ ] Gaps prioritized (must/should/nice)
-- [ ] Gaps grouped into logical phases
-- [ ] User confirmed phase plan
-- [ ] ROADMAP.md updated with new phases
-- [ ] REQUIREMENTS.md traceability table updated with gap closure phase assignments
-- [ ] Unsatisfied requirement checkboxes reset (`[x]` → `[ ]`)
-- [ ] Coverage count updated in REQUIREMENTS.md
-- [ ] Phase directories created
-- [ ] Changes committed (includes REQUIREMENTS.md)
-- [ ] User knows to run `/gsd:plan-phase` next
-</success_criteria>
diff --git a/scripts/command-contract-helpers.cjs b/scripts/command-contract-helpers.cjs
index 3a1179d6b..63e680774 100644
--- a/scripts/command-contract-helpers.cjs
+++ b/scripts/command-contract-helpers.cjs
@@ -124,4 +124,58 @@ function workflowPathRefs(content) {
   return refs;
 }
 
-module.exports = { CANONICAL_TOOLS, parseFrontmatter, executionContextRefs, workflowPathRefs };
+/**
+ * unreachableWorkflows(loaderContents, gsdFiles, workflowPaths)
+ *
+ * Computes reachability over the gsd-core file graph and reports which
+ * `workflowPaths` are never reached, starting only from `loaderContents`
+ * (commands/agents/skills — the files a runtime actually loads) and walking
+ * `workflowPathRefs` edges transitively through `gsdFiles`.
+ *
+ * The seed set is deliberately restricted to loaders and never includes a
+ * workflow's own content. Seeding from workflows too would let two failure
+ * modes hide: a workflow that only references itself would satisfy its own
+ * reachability, and a pair of workflows that reference only each other would
+ * form an island that looks connected from the inside but that no command,
+ * agent, or skill ever actually opens. Both are orphans in every sense that
+ * matters — nothing external can reach them — and both must be reported.
+ * Requiring every path to originate at a loader is what makes "reachable"
+ * mean "a runtime can actually get here," not merely "something points to
+ * it."
+ *
+ * `gsdFiles` covers all of `gsd-core/**`, not just `workflows/`, because a
+ * `references/` or `templates/` file can itself name a workflow path and
+ * needs to be walked through to propagate reachability — restricting the map
+ * to `workflows/` would silently break any chain that passes through a
+ * non-workflow file.
+ *
+ * `visited` guards the walk against reference cycles (including the
+ * mutual/self cases above) so traversal always terminates.
+ */
+function unreachableWorkflows(loaderContents, gsdFiles, workflowPaths) {
+  const visited = new Set();
+  const queue = [];
+
+  for (const content of loaderContents) {
+    for (const ref of workflowPathRefs(content)) queue.push(ref);
+  }
+
+  while (queue.length > 0) {
+    const p = queue.pop();
+    if (visited.has(p)) continue;
+    visited.add(p);
+    if (gsdFiles.has(p)) {
+      for (const ref of workflowPathRefs(gsdFiles.get(p))) queue.push(ref);
+    }
+  }
+
+  return workflowPaths.filter(p => !visited.has(p));
+}
+
+module.exports = {
+  CANONICAL_TOOLS,
+  parseFrontmatter,
+  executionContextRefs,
+  workflowPathRefs,
+  unreachableWorkflows,
+};
diff --git a/scripts/lint-command-contract.cjs b/scripts/lint-command-contract.cjs
index 13c2a52f4..4cce28d0f 100644
--- a/scripts/lint-command-contract.cjs
+++ b/scripts/lint-command-contract.cjs
@@ -9,6 +9,9 @@
  *   3. allowed-tools: block present, non-empty, all entries from CANONICAL_TOOLS
  *   4. execution_context @-refs: every @-reference resolves to an existing file on disk
  *   5. execution_context @-refs: each appears on its own line (no trailing prose)
+ *   6. every gsd-core/workflows/*.md file is reachable from at least one
+ *      commands/agents/skills loader, transitively through gsd-core/**
+ *      (repo-level check, runs once — not per command file)
  *
  * Exit 0 = clean. Exit 1 = violations (with diagnostics).
  */
@@ -18,7 +21,17 @@
 const fs   = require('fs');
 const path = require('path');
 
-const ROOT          = path.join(__dirname, '..');
+function resolveRoot(argv) {
+  const idx = argv.indexOf('--root');
+  if (idx === -1) return path.join(__dirname, '..');
+  const value = argv[idx + 1];
+  if (!value) {
+    throw new Error('lint-command-contract: --root requires a directory argument');
+  }
+  return path.resolve(value);
+}
+
+const ROOT          = resolveRoot(process.argv.slice(2));
 const COMMANDS_DIR  = path.join(ROOT, 'commands', 'gsd');
 const GSD_ROOT      = path.join(ROOT, 'gsd-core');
 
@@ -26,10 +39,57 @@ const {
   CANONICAL_TOOLS,
   parseFrontmatter,
   executionContextRefs: extractExecutionContextRefs,
+  unreachableWorkflows,
 } = require('./command-contract-helpers.cjs');
 
 const { runMain } = require('./lib/cli-exit.cjs');
 
+// ─── rule 6: repo-level workflow reachability ─────────────────────────────────
+
+function walkMarkdownFiles(dir, acc) {
+  let entries;
+  try {
+    entries = fs.readdirSync(dir, { withFileTypes: true });
+  } catch (e) {
+    return acc;
+  }
+  for (const entry of entries) {
+    const full = path.join(dir, entry.name);
+    if (entry.isDirectory()) {
+      walkMarkdownFiles(full, acc);
+    } else if (entry.isFile() && entry.name.endsWith('.md')) {
+      acc.push(full);
+    }
+  }
+  return acc;
+}
+
+function toGsdRelative(absPath) {
+  return path.relative(GSD_ROOT, absPath).split(path.sep).join('/');
+}
+
+function checkWorkflowReachability() {
+  const loaderFiles = [
+    ...walkMarkdownFiles(path.join(ROOT, 'commands'), []),
+    ...walkMarkdownFiles(path.join(ROOT, 'agents'), []),
+    ...walkMarkdownFiles(path.join(ROOT, 'skills'), []),
+  ];
+  const loaderContents = loaderFiles.map(f => fs.readFileSync(f, 'utf-8'));
+
+  const gsdFileAbsPaths = walkMarkdownFiles(GSD_ROOT, []);
+  const gsdFiles = new Map();
+  for (const abs of gsdFileAbsPaths) {
+    gsdFiles.set(toGsdRelative(abs), fs.readFileSync(abs, 'utf-8'));
+  }
+
+  const workflowAbsPaths = walkMarkdownFiles(path.join(GSD_ROOT, 'workflows'), []);
+  const workflowPaths = workflowAbsPaths.map(toGsdRelative);
+
+  const unreachable = unreachableWorkflows(loaderContents, gsdFiles, workflowPaths);
+
+  return { workflowCount: workflowPaths.length, unreachable };
+}
+
 // ─── check one file ───────────────────────────────────────────────────────────
 
 function check(filePath) {
@@ -88,27 +148,50 @@ function main() {
     .map(f => path.join(COMMANDS_DIR, f));
 
   const results = commandFiles.map(check).filter(Boolean);
+  const { workflowCount, unreachable } = checkWorkflowReachability();
+
+  let ok = true;
 
   if (results.length === 0) {
     console.log(
       `ok lint-command-contract: ${commandFiles.length} command files checked, 0 violations`,
     );
-    return 0;
+  } else {
+    ok = false;
+    const total = results.reduce((n, r) => n + r.violations.length, 0);
+    process.stderr.write(
+      `\nERROR lint-command-contract: ${total} violation(s) across ${results.length} file(s)\n\n`,
+    );
+    for (const r of results) {
+      process.stderr.write(`  ${r.file}\n`);
+      for (const v of r.violations) {
+        process.stderr.write(`    - ${v}\n`);
+      }
+      process.stderr.write('\n');
+    }
+    process.stderr.write('See docs/adr/0002-command-contract-validation-module.md for the contract spec.\n\n');
   }
 
-  const total = results.reduce((n, r) => n + r.violations.length, 0);
-  process.stderr.write(
-    `\nERROR lint-command-contract: ${total} violation(s) across ${results.length} file(s)\n\n`,
-  );
-  for (const r of results) {
-    process.stderr.write(`  ${r.file}\n`);
-    for (const v of r.violations) {
-      process.stderr.write(`    - ${v}\n`);
+  if (unreachable.length === 0) {
+    console.log(
+      `ok lint-command-contract: ${workflowCount} workflow files, ${workflowCount} reachable, 0 unreachable`,
+    );
+  } else {
+    ok = false;
+    process.stderr.write(
+      `\nERROR lint-command-contract: ${unreachable.length} unreachable workflow file(s) of ${workflowCount}\n\n`,
+    );
+    for (const p of unreachable) {
+      process.stderr.write(`  gsd-core/${p}\n`);
     }
-    process.stderr.write('\n');
+    process.stderr.write(
+      '\nEach file above ships to every runtime but is never referenced by any command,\n' +
+      'agent, or skill loader (directly or transitively). Either wire it to a loader\n' +
+      'or delete it — removing a command must sweep its orphaned workflow.\n\n',
+    );
   }
-  process.stderr.write('See docs/adr/0002-command-contract-validation-module.md for the contract spec.\n\n');
-  return 1;
+
+  return ok ? 0 : 1;
 }
 
 runMain(main);
diff --git a/tests/command-contract.test.cjs b/tests/command-contract.test.cjs
index 3d6f136df..7cf1f5886 100644
--- a/tests/command-contract.test.cjs
+++ b/tests/command-contract.test.cjs
@@ -33,8 +33,15 @@ const {
   parseFrontmatter,
   executionContextRefs,
   workflowPathRefs,
+  unreachableWorkflows,
 } = require('../scripts/command-contract-helpers.cjs');
 
+const { runNode, OUTCOME } = require('./helpers/process-seam.cjs');
+const { PROBE_TIMEOUT_MS } = require('./helpers/timeouts.cjs');
+const { createTempDir, cleanup } = require('./helpers.cjs');
+
+const LINT_SCRIPT = path.join(ROOT, 'scripts', 'lint-command-contract.cjs');
+
 const commandFiles = fs
   .readdirSync(COMMANDS_DIR)
   .filter(f => f.endsWith('.md'))
@@ -284,6 +291,317 @@ describe('#3561 — every workflow path referenced by a command exists on disk',
 });
 
 
+describe('#3560 — unreachableWorkflows closure', () => {
+  test('a planted orphan is reported', () => {
+    const loaderContents = ['load workflows/live.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/live.md', 'workflows/orphan.md'];
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/orphan.md'],
+    );
+  });
+
+  test('eager include reaches', () => {
+    const loaderContents = ['@~/.claude/gsd-core/workflows/a.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/a.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('lazy path reaches', () => {
+    const loaderContents = ['read `gsd-core/workflows/a.md`'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/a.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('parent-relative reaches', () => {
+    const loaderContents = ['run execute-phase/steps/s.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/execute-phase/steps/s.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('reaches transitively', () => {
+    const loaderContents = ['see workflows/a.md'];
+    const gsdFiles = new Map([['workflows/a.md', 'see workflows/b.md']]);
+    const workflowPaths = ['workflows/a.md', 'workflows/b.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('reaches at depth three', () => {
+    const loaderContents = ['see workflows/a.md'];
+    const gsdFiles = new Map([
+      ['workflows/a.md', 'see workflows/b.md'],
+      ['workflows/b.md', 'see workflows/c.md'],
+    ]);
+    const workflowPaths = ['workflows/a.md', 'workflows/b.md', 'workflows/c.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('a self-reference does not reach', () => {
+    // Nothing in loaderContents mentions self.md; the fact that self.md's
+    // own body references itself must not count as reachability.
+    const loaderContents = [];
+    const gsdFiles = new Map([['workflows/self.md', 'see workflows/self.md']]);
+    const workflowPaths = ['workflows/self.md'];
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/self.md'],
+    );
+  });
+
+  test('a mutual-reference island does not reach', () => {
+    // x and y point only at each other; no loader points at either. The
+    // island looks connected from the inside but no runtime ever opens it.
+    const loaderContents = [];
+    const gsdFiles = new Map([
+      ['workflows/x.md', 'see workflows/y.md'],
+      ['workflows/y.md', 'see workflows/x.md'],
+    ]);
+    const workflowPaths = ['workflows/x.md', 'workflows/y.md'];
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/x.md', 'workflows/y.md'],
+    );
+  });
+
+  test('terminates on a cycle', () => {
+    // a -> b -> c -> a. All three are reachable from the loader; the walk
+    // must still terminate rather than looping forever on the cycle.
+    const loaderContents = ['see workflows/a.md'];
+    const gsdFiles = new Map([
+      ['workflows/a.md', 'see workflows/b.md'],
+      ['workflows/b.md', 'see workflows/c.md'],
+      ['workflows/c.md', 'see workflows/a.md'],
+    ]);
+    const workflowPaths = ['workflows/a.md', 'workflows/b.md', 'workflows/c.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('a docs-only mention does not reach (Goodhart guard: mentioning a path is not the same as loading it)', () => {
+    // Simulates a hypothetical prose/docs file that names orphan.md — that
+    // string is simply never included in loaderContents (or gsdFiles), which
+    // is exactly what "a docs mention" looks like to this function: absent.
+    const loaderContents = [];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/orphan.md'];
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/orphan.md'],
+    );
+  });
+
+  test('a dangling reference reaches nothing', () => {
+    const loaderContents = ['see workflows/missing.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/real-orphan.md'];
+    assert.doesNotThrow(() => unreachableWorkflows(loaderContents, gsdFiles, workflowPaths));
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/real-orphan.md'],
+    );
+  });
+
+  test('empty workflow set', () => {
+    const loaderContents = ['see workflows/a.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = [];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('no loaders means nothing is reached', () => {
+    const loaderContents = [];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/a.md'];
+    assert.deepEqual(
+      unreachableWorkflows(loaderContents, gsdFiles, workflowPaths),
+      ['workflows/a.md'],
+    );
+  });
+
+  test('CRLF-tolerant', () => {
+    const loaderContents = ['workflows/a.md\r\nworkflows/b.md'];
+    const gsdFiles = new Map();
+    const workflowPaths = ['workflows/a.md', 'workflows/b.md'];
+    assert.deepEqual(unreachableWorkflows(loaderContents, gsdFiles, workflowPaths), []);
+  });
+
+  test('reports exactly the orphan among many', () => {
+    const reachable = Array.from({ length: 152 }, (_, i) => `workflows/gen-${i}.md`);
+    const loaderContents = reachable.slice();
+    const gsdFiles = new Map();
+    const orphan = 'workflows/orphan-152.md';
+    const workflowPaths = [...reachable, orphan];
+    const result = unreachableWorkflows(loaderContents, gsdFiles, workflowPaths);
+    assert.equal(result.length, 1);
+    assert.deepEqual(result, [orphan]);
+  });
+});
+
+describe('#3560 — rule 6 fails the build on a real orphan', () => {
+  // Builds the minimal fixture tree the lint CLI needs to satisfy rules 1-5
+  // for a single command file, plus an eagerly-loaded live.md workflow.
+  // `extra` lets each test layer on exactly the additional state it needs
+  // without coupling test execution order to shared mutable fixture state.
+  function buildBaseFixture(dir) {
+    fs.mkdirSync(path.join(dir, 'commands', 'gsd'), { recursive: true });
+    fs.mkdirSync(path.join(dir, 'gsd-core', 'workflows'), { recursive: true });
+    fs.mkdirSync(path.join(dir, 'agents'), { recursive: true });
+    fs.mkdirSync(path.join(dir, 'skills'), { recursive: true });
+
+    fs.writeFileSync(
+      path.join(dir, 'commands', 'gsd', 'fixture-command.md'),
+      [
+        '---',
+        'name: gsd:fixture-command',
+        'description: Fixture command for the #3560 rule-6 regression tests.',
+        'allowed-tools:',
+        '  - Read',
+        '  - Bash',
+        '---',
+        '',
+        '<execution_context>',
+        '@~/.claude/gsd-core/workflows/live.md',
+        '</execution_context>',
+        '',
+      ].join('\n'),
+    );
+
+    fs.writeFileSync(
+      path.join(dir, 'gsd-core', 'workflows', 'live.md'),
+      '# live workflow\n\nNothing special here.\n',
+    );
+  }
+
+  function runLint(dir) {
+    return runNode([LINT_SCRIPT, '--root', dir], { timeoutMs: PROBE_TIMEOUT_MS });
+  }
+
+  test('clean fixture passes', (t) => {
+    const dir = createTempDir('gsd-3560-clean-');
+    t.after(() => cleanup(dir));
+    buildBaseFixture(dir);
+
+    const result = runLint(dir);
+    assert.equal(result.outcome, OUTCOME.EXITED);
+    assert.equal(result.exitCode, 0);
+  });
+
+  test('a planted orphan fails the build', (t) => {
+    const dir = createTempDir('gsd-3560-orphan-');
+    t.after(() => cleanup(dir));
+    buildBaseFixture(dir);
+    fs.writeFileSync(
+      path.join(dir, 'gsd-core', 'workflows', 'orphan.md'),
+      '# orphan workflow\n\nNo loader references this file.\n',
+    );
+
+    const result = runLint(dir);
+    assert.equal(result.outcome, OUTCOME.EXITED);
+    assert.equal(result.exitCode, 1);
+    assert.ok(
+      (result.stdout + result.stderr).includes('gsd-core/workflows/orphan.md'),
+      'diagnostic output must name the orphaned file path',
+    );
+  });
+
+  test('an orphan referenced only from docs/ still fails', (t) => {
+    const dir = createTempDir('gsd-3560-docs-only-');
+    t.after(() => cleanup(dir));
+    buildBaseFixture(dir);
+    fs.writeFileSync(
+      path.join(dir, 'gsd-core', 'workflows', 'orphan.md'),
+      '# orphan workflow\n\nNo loader references this file.\n',
+    );
+    fs.mkdirSync(path.join(dir, 'docs'), { recursive: true });
+    fs.writeFileSync(
+      path.join(dir, 'docs', 'SOMETHING.md'),
+      'See gsd-core/workflows/orphan.md for details.\n',
+    );
+
+    const result = runLint(dir);
+    assert.equal(result.outcome, OUTCOME.EXITED);
+    assert.equal(result.exitCode, 1);
+  });
+
+  test('an orphan reachable only transitively passes', (t) => {
+    const dir = createTempDir('gsd-3560-transitive-');
+    t.after(() => cleanup(dir));
+    buildBaseFixture(dir);
+    fs.writeFileSync(
+      path.join(dir, 'gsd-core', 'workflows', 'orphan.md'),
+      '# orphan workflow\n\nReachable transitively via live.md.\n',
+    );
+    // live.md itself now names orphan.md; live.md is eagerly loaded by the
+    // fixture command, so orphan.md becomes reachable one hop out.
+    fs.writeFileSync(
+      path.join(dir, 'gsd-core', 'workflows', 'live.md'),
+      '# live workflow\n\nSee workflows/orphan.md for the follow-up.\n',
+    );
+
+    const result = runLint(dir);
+    assert.equal(result.outcome, OUTCOME.EXITED);
+    assert.equal(result.exitCode, 0);
+  });
+});
+
+describe('#3560 — deleted orphan workflows do not ship', () => {
+  const deletedBasenames = ['discovery-phase.md', 'plan-milestone-gaps.md'];
+
+  for (const basename of deletedBasenames) {
+    test(`${basename}: does not exist under gsd-core/workflows/`, () => {
+      assert.ok(
+        !fs.existsSync(path.join(GSD_ROOT, 'workflows', basename)),
+        `${basename}: expected file to be deleted from gsd-core/workflows/, but it still exists`,
+      );
+    });
+  }
+
+  const fixturesDir = path.join(ROOT, 'tests', 'fixtures', 'install-tree');
+  const fixtureFiles = fs.readdirSync(fixturesDir).filter(f => f.endsWith('.json'));
+
+  for (const fixtureFile of fixtureFiles) {
+    test(`${fixtureFile}: install-tree manifest contains no entry for a deleted workflow`, () => {
+      const manifest = JSON.parse(fs.readFileSync(path.join(fixturesDir, fixtureFile), 'utf-8'));
+      for (const basename of deletedBasenames) {
+        const gsdRelative = `gsd-core/workflows/${basename}`;
+        assert.ok(
+          !manifest.includes(gsdRelative),
+          `${fixtureFile}: manifest still lists ${gsdRelative}`,
+        );
+      }
+    });
+  }
+
+  test('scan.md is untouched by this PR', () => {
+    assert.ok(
+      fs.existsSync(path.join(GSD_ROOT, 'workflows', 'scan.md')),
+      'gsd-core/workflows/scan.md is expected to still exist — this PR only deletes ' +
+      'discovery-phase.md and plan-milestone-gaps.md',
+    );
+  });
+});
+
+describe('#3560 — INVENTORY carries no row for a deleted workflow', () => {
+  const inventoryFiles = [
+    'docs/INVENTORY.md',
+    'docs/ja-JP/INVENTORY.md',
+    'docs/ko-KR/INVENTORY.md',
+    'docs/zh-CN/INVENTORY.md',
+    'docs/pt-BR/INVENTORY.md',
+  ];
+
+  for (const rel of inventoryFiles) {
+    test(`${rel}: mentions neither discovery-phase.md nor plan-milestone-gaps.md`, () => {
+      const content = fs.readFileSync(path.join(ROOT, rel), 'utf-8');
+      assert.ok(!content.includes('discovery-phase.md'), `${rel}: still mentions discovery-phase.md`);
+      assert.ok(!content.includes('plan-milestone-gaps.md'), `${rel}: still mentions plan-milestone-gaps.md`);
+    });
+  }
+});
+
 // ────────────────────────────────────────────────────────────────────────
 // Folded from tests/bug-3168-task-to-agent-rename.test.cjs — consolidation epic #1969 (B3 #1972)
 // ────────────────────────────────────────────────────────────────────────
diff --git a/tests/fixtures/install-tree/antigravity.json b/tests/fixtures/install-tree/antigravity.json
index 26ad303b5..28947622d 100644
--- a/tests/fixtures/install-tree/antigravity.json
+++ b/tests/fixtures/install-tree/antigravity.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/augment.json b/tests/fixtures/install-tree/augment.json
index be16a7471..2962913f2 100644
--- a/tests/fixtures/install-tree/augment.json
+++ b/tests/fixtures/install-tree/augment.json
@@ -312,7 +312,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -381,7 +380,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/claude-local.json b/tests/fixtures/install-tree/claude-local.json
index ce5789006..eaddb062c 100644
--- a/tests/fixtures/install-tree/claude-local.json
+++ b/tests/fixtures/install-tree/claude-local.json
@@ -311,7 +311,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -380,7 +379,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/claude.json b/tests/fixtures/install-tree/claude.json
index 826b7a0bf..1a5a4b4f4 100644
--- a/tests/fixtures/install-tree/claude.json
+++ b/tests/fixtures/install-tree/claude.json
@@ -240,7 +240,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -309,7 +308,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/cline.json b/tests/fixtures/install-tree/cline.json
index 3d7ae077b..1ab375a67 100644
--- a/tests/fixtures/install-tree/cline.json
+++ b/tests/fixtures/install-tree/cline.json
@@ -244,7 +244,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -313,7 +312,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/codebuddy.json b/tests/fixtures/install-tree/codebuddy.json
index 310294c44..6285b7c9e 100644
--- a/tests/fixtures/install-tree/codebuddy.json
+++ b/tests/fixtures/install-tree/codebuddy.json
@@ -312,7 +312,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -381,7 +380,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/codex.json b/tests/fixtures/install-tree/codex.json
index e08a4a9f6..ad211f83a 100644
--- a/tests/fixtures/install-tree/codex.json
+++ b/tests/fixtures/install-tree/codex.json
@@ -347,7 +347,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -416,7 +415,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/copilot.json b/tests/fixtures/install-tree/copilot.json
index 632d23154..6771b5508 100644
--- a/tests/fixtures/install-tree/copilot.json
+++ b/tests/fixtures/install-tree/copilot.json
@@ -242,7 +242,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -311,7 +310,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/cursor.json b/tests/fixtures/install-tree/cursor.json
index ca150c956..eaff0bd35 100644
--- a/tests/fixtures/install-tree/cursor.json
+++ b/tests/fixtures/install-tree/cursor.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/hermes.json b/tests/fixtures/install-tree/hermes.json
index 9b441d9fb..b780830e3 100644
--- a/tests/fixtures/install-tree/hermes.json
+++ b/tests/fixtures/install-tree/hermes.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/kilo.json b/tests/fixtures/install-tree/kilo.json
index 47bd57173..0d8d99d63 100644
--- a/tests/fixtures/install-tree/kilo.json
+++ b/tests/fixtures/install-tree/kilo.json
@@ -312,7 +312,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -381,7 +380,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/kimi-code.json b/tests/fixtures/install-tree/kimi-code.json
index 1797cd1ac..00672c92d 100644
--- a/tests/fixtures/install-tree/kimi-code.json
+++ b/tests/fixtures/install-tree/kimi-code.json
@@ -274,7 +274,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -343,7 +342,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/kimi.json b/tests/fixtures/install-tree/kimi.json
index 9c0febc51..29d78ac04 100644
--- a/tests/fixtures/install-tree/kimi.json
+++ b/tests/fixtures/install-tree/kimi.json
@@ -310,7 +310,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -379,7 +378,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/opencode.json b/tests/fixtures/install-tree/opencode.json
index 476354904..ec97504e3 100644
--- a/tests/fixtures/install-tree/opencode.json
+++ b/tests/fixtures/install-tree/opencode.json
@@ -312,7 +312,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -381,7 +380,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/pi.json b/tests/fixtures/install-tree/pi.json
index d057190f1..3aeb29bad 100644
--- a/tests/fixtures/install-tree/pi.json
+++ b/tests/fixtures/install-tree/pi.json
@@ -209,7 +209,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -278,7 +277,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/qwen.json b/tests/fixtures/install-tree/qwen.json
index 1f4061faf..e88b85544 100644
--- a/tests/fixtures/install-tree/qwen.json
+++ b/tests/fixtures/install-tree/qwen.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/trae.json b/tests/fixtures/install-tree/trae.json
index 603ff7c94..fb1bc5982 100644
--- a/tests/fixtures/install-tree/trae.json
+++ b/tests/fixtures/install-tree/trae.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/windsurf.json b/tests/fixtures/install-tree/windsurf.json
index 911112d72..322930e24 100644
--- a/tests/fixtures/install-tree/windsurf.json
+++ b/tests/fixtures/install-tree/windsurf.json
@@ -241,7 +241,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -310,7 +309,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/fixtures/install-tree/zcode.json b/tests/fixtures/install-tree/zcode.json
index 6c5729610..0434cd3e5 100644
--- a/tests/fixtures/install-tree/zcode.json
+++ b/tests/fixtures/install-tree/zcode.json
@@ -312,7 +312,6 @@
   "gsd-core/workflows/complete-milestone/steps/git-tag.md",
   "gsd-core/workflows/debug.md",
   "gsd-core/workflows/diagnose-issues.md",
-  "gsd-core/workflows/discovery-phase.md",
   "gsd-core/workflows/discuss-phase-assumptions.md",
   "gsd-core/workflows/discuss-phase-assumptions/steps/auto-advance-dispatch.md",
   "gsd-core/workflows/discuss-phase-power.md",
@@ -381,7 +380,6 @@
   "gsd-core/workflows/note.md",
   "gsd-core/workflows/onboard.md",
   "gsd-core/workflows/pause-work.md",
-  "gsd-core/workflows/plan-milestone-gaps.md",
   "gsd-core/workflows/plan-phase.md",
   "gsd-core/workflows/plan-phase/steps/adr-ingest-express-path.md",
   "gsd-core/workflows/plan-phase/steps/chunked-planning-mode.md",
diff --git a/tests/phase.test.cjs b/tests/phase.test.cjs
index b9648d1f3..93d2dd85c 100644
--- a/tests/phase.test.cjs
+++ b/tests/phase.test.cjs
@@ -6069,7 +6069,6 @@ describe('bug-3287 — init plan-phase exposes expected_phase_dir with project_c
 // ─────────────────────────────────────────────────────────────────────────────
 
 {
-  const PMG_WF = path.join(__dirname, '..', 'gsd-core', 'workflows', 'plan-milestone-gaps.md');
   const IMPORT_WF = path.join(__dirname, '..', 'gsd-core', 'workflows', 'import.md');
   const BACKLOG_WF = path.join(__dirname, '..', 'gsd-core', 'workflows', 'add-backlog.md');
 
@@ -6090,29 +6089,9 @@ describe('bug-3287 — init plan-phase exposes expected_phase_dir with project_c
       || /mkdir[^`\r\n]*\.planning\/phases\/\$\{(?:NEXT|NN|PHASE)[^}]*\}-/.test(content);
   }
 
-  describe('bug-3298 — plan-milestone-gaps.md must not construct bare {NN}-{name} phase dirs', () => {
-    test('workflow file exists', () => {
-      assert.ok(fs.existsSync(PMG_WF), `plan-milestone-gaps.md must exist at ${PMG_WF}`);
-    });
-
-    test('step 8 must not use bare {NN}-{name} mkdir pattern', () => {
-      const content = readWorkflow(PMG_WF);
-      assert.ok(
-        !containsBareTemplateMkdir(content),
-        'plan-milestone-gaps.md must not contain bare mkdir .planning/phases/{NN}-{name} pattern — use phase.add or expected_phase_dir',
-      );
-    });
-
-    test('step 8 must use expected_phase_dir or phase.add for directory creation', () => {
-      const content = readWorkflow(PMG_WF);
-      const usesExpectedPhaseDir = content.includes('expected_phase_dir');
-      const usesPhaseAdd = content.includes('phase.add');
-      assert.ok(
-        usesExpectedPhaseDir || usesPhaseAdd,
-        'plan-milestone-gaps.md must use expected_phase_dir (from init.phase-op) or phase.add to create phase directories with project_code prefix',
-      );
-    });
-  });
+  // The plan-milestone-gaps arm was removed along with that workflow file in
+  // #3560 (its command was deleted by #2790). The import.md and
+  // add-backlog.md arms below still guard the same phase-dir prefix drift.
 
   describe('bug-3298 — import.md must not construct bare {NN}-{slug} phase dirs', () => {
     test('workflow file exists', () => {
diff --git a/tests/planner-language-regression.test.cjs b/tests/planner-language-regression.test.cjs
index f13eeac10..89b8fad12 100644
--- a/tests/planner-language-regression.test.cjs
+++ b/tests/planner-language-regression.test.cjs
@@ -114,8 +114,6 @@ const ALLOWLIST = {
   'gsd-debugger.md': ['time_sizing'],
   // Doc-writer uses "15 minutes" in API rate limit example, "2 minutes" for doc quality
   'gsd-doc-writer.md': ['time_sizing'],
-  // Discovery-phase uses time for level descriptions (operational, not scope)
-  'discovery-phase.md': ['time_sizing'],
   // Explore uses "~30 seconds" as operational estimate
   'explore.md': ['time_sizing'],
   // Review uses "up to 5 minutes" for CodeRabbit timeout