msd-core/docs/USER-GUIDE.md

# GSD User Guide

A narrative companion guide to GSD Core — orient yourself here, then follow the links into the dedicated docs.

> **GSD Core's documentation is organised by [Diataxis](https://diataxis.fr).**
> Browse by goal: [Tutorials](README.md#tutorials) · [How-to guides](README.md#how-to-guides) · [Reference](README.md#reference) · [Explanation](README.md#explanation) · [Docs index](README.md)

---

## Table of Contents

- [Slash-command forms](#slash-command-form)
- [Namespace routing primer](#namespace-routing-primer-gsd-ns--v140)
- [Reading GSD's output](#reading-gsds-output)
- [Project lifecycle overview](#project-lifecycle-overview)
- [Workflow Diagrams](#workflow-diagrams)
- [UI Design Contract](#ui-design-contract)
- [Spiking & Sketching](#spiking--sketching)
- [Backlog & Threads](#backlog--threads)
- [Workstreams & Workspaces](#workstreams--workspaces)
- [Security](#security)
- [Usage Examples](#usage-examples)
- [Troubleshooting](#troubleshooting)
- [Recovery Quick Reference](#recovery-quick-reference)
- [Project File Structure](#project-file-structure)
- [Related](#related)

For driving GSD directly from a GitHub / Linear / Jira issue, see the
[Issue-driven orchestration](issue-driven-orchestration.md) guide — a
recipe that maps tracker issues onto the workspace → discuss → plan →
execute → verify → review → ship loop using existing GSD primitives.

---

## Slash-command form

GSD ships **the same set of skills** to every supported runtime, using the hyphen slash-form spelling:

- **Hyphen form** — `/gsd-command-name` — used by Claude Code, Copilot, OpenCode, Kilo, Cursor, Windsurf, Augment, Antigravity, and Trae.

The installer writes this form into the command directory of each runtime you target.

## Namespace routing primer (`gsd-ns-*`, v1.40+)

### Architecture

GSD ships six **namespace router bundles** (`gsd-ns-workflow`, `gsd-ns-project`, `gsd-ns-review`, `gsd-ns-context`, `gsd-ns-ideate`, `gsd-ns-manage`). On runtimes with non-recursive skill loaders, the installer emits these 6 routers as the **only top-level skill entries**; the ~61 concrete skills are nested under each router at `<router>/skills/<name>/SKILL.md`. This reduces the eager skill-listing overhead to ≈6 entries instead of ≈67.

Each router's body contains a routing table. When the model receives a request, it reads the router, identifies the relevant sub-skill by name, then opens `skills/<name>/SKILL.md` via a file-path `Read`. The concrete skill is fully available — it is not invocable by bare name through the Skill tool's top-level listing, but is reachable through the router.

The nested layout applies only to runtimes with confirmed non-recursive skill loaders: **Cline, Qwen, Hermes, Augment, Trae**. Claude's loader is also non-recursive, but #924 reverted it flat because the Skill tool hard-errors on unknown names rather than re-routing via the router. Antigravity's loader is also non-recursive, but #1614 moved it flat because `agy` scans only `skills/<name>/SKILL.md` — nested sub-skills were unreachable. Other recursive or unconfirmed loaders (Cursor, Codex, Copilot, Windsurf, CodeBuddy, OpenCode, Kilo) retain the flat layout unchanged.

| Namespace | Router bundle | Routes to |
|-----------|--------------|-----------|
| Phase pipeline | `gsd-ns-workflow` | discuss / plan / execute / verify / phase / progress |
| Project lifecycle | `gsd-ns-project` | milestones, audits, summary |
| Quality gates | `gsd-ns-review` | code review, debug, audit, security, eval, ui |
| Codebase intelligence | `gsd-ns-context` | map, graphify, docs, learnings |
| Exploration & capture | `gsd-ns-ideate` | explore, sketch, spike, spec, capture |
| Management | `gsd-ns-manage` | config, workspace, workstreams, thread, update, ship, inbox |

### Slash commands are unaffected

On runtimes that install a commands surface (`commands/gsd`), slash commands such as `/gsd-plan-phase` continue to work directly — the nesting applies only to the Skill tool's top-level listing, not to the commands directory.

### Migration note (breaking change on nesting runtimes)

On the seven nesting runtimes listed above, upgrading to v1.40 changes skill invocation behaviour:

- **Before:** each of the ~67 concrete `gsd-<name>` skills appeared at the top level and was invocable by bare name through the Skill tool.
- **After:** only the 6 `gsd-ns-*` router bundles appear at the top level. Concrete skills are reachable via the router's routing table and a `Read skills/<name>/SKILL.md` call. Direct bare-name invocation of concrete skills through the Skill tool's listing no longer works.
- **Slash commands unchanged:** `/gsd-plan-phase`, `/gsd-discuss-phase`, etc. still work directly where a commands surface is installed.
- **Upgrade prune:** the installer's existing prune step removes the legacy top-level `gsd-<concrete>/` skill directories on upgrade — no manual cleanup is needed.

---

## Reading GSD's output

GSD marks its sections with Markdown, not with drawn borders. There are exactly
three forms, and every workflow, checkpoint and report uses them:

| You see | It means |
|---|---|
| `### GSD ► {STAGE NAME}` | A major workflow transition — planning, executing a wave, verifying, completing |
| `### CHECKPOINT: {Type}` | GSD is waiting on you. The bolded `**→ …**` line at the bottom tells you what to type |
| `---` | A break between two sections — most often before the **▶ Next Up** block at the end of a completion |

Panels that used to be drawn with box characters are now a heading followed by
their rows as ordinary lines. A checkpoint reads:

```
### CHECKPOINT: Verification Required

Progress: 5/8 tasks complete
Task: Responsive dashboard layout

How to verify:
  1. Visit: http://localhost:3000/dashboard

---

**→ YOUR ACTION: Type "approved" or describe issues**
```

### Why there are no drawn borders

Earlier releases framed stage banners between two 53-character runs
of `━`, and checkpoints were a 62-column box drawn with `╔`, `║` and `╚`. Those
runs are ordinary text to whatever renders GSD's output. In a pane narrower than
the run, the rule wraps and the leftover glyphs land on a second line — so the
border comes apart from the heading it was framing, and the output looks broken
rather than merely narrow. Reported against the Codex desktop interface in
[#3028](https://github.com/open-gsd/gsd-core/issues/3028).

A Markdown heading and a thematic break carry the same structure without
committing to a width, so they read correctly in a narrow pane and a wide one.

This is unconditional: every runtime gets the same output. The alternative — a
capability flag that kept line-art for terminal-oriented runtimes — was weighed
and rejected, because it leaves two output conventions to keep in sync forever
for a gain that is aesthetic rather than structural. What a terminal loses is the
drawn frame; what it keeps is the title, the hierarchy and the break, none of
which depended on the frame. The reasoning is recorded in
`gsd-core/references/ui-brand.md § Why this is unconditional, not per-runtime`.
If you run GSD in a host where the heading form reads worse than the old boxes
did, that is worth reporting — it is the evidence that would justify the flag.

Single-cell tokens are unaffected and unchanged: the status symbols
(`✓ ✗ ◆ ○ ⚠`), the `GSD ►` prefix, and the ten-cell progress gauge
(`Progress: ████████░░ 80%`) are not runs and do not wrap.

The convention is specified in `gsd-core/references/ui-brand.md` and enforced
against all shipped content by `tests/responsive-separators.test.cjs`.

---

## Project lifecycle overview

The core GSD loop is: **discuss → plan → execute → verify → ship**, repeated per phase. The full step-by-step walkthrough — including example outputs, what files get created, and all the flags in play — is in the dedicated tutorial.

See [Your first project](tutorials/your-first-project.md).

For onboarding an existing codebase before starting a new milestone, run `/gsd-onboard` or see [Onboarding an existing codebase](tutorials/onboarding-an-existing-codebase.md).

**Relevant flags at a glance:**

| Flag | Command | When to use |
| ---- | ------- | ----------- |
| `--auto` | `/gsd-new-project` | Skip interactive questions, ingest from a PRD file |
| `--research` | `/gsd-quick` | Add a research agent to an ad-hoc task |
| `--validate` | `/gsd-quick` | Add plan-checking and post-execution verification |
| `--chain` | `/gsd-discuss-phase` | Auto-chain discuss → plan → execute without stopping |
| `--skip-research` | `/gsd-plan-phase` | Skip research agents when the domain is already familiar |
| `--draft` | `/gsd-ship` | Create a draft PR instead of a ready-for-review one |

For the full command reference with all flags, see [`docs/COMMANDS.md`](COMMANDS.md). For configuration options (model profiles, workflow agents, git branching), see [`docs/CONFIGURATION.md`](CONFIGURATION.md).

---

## Workflow Diagrams

### Full Project Lifecycle

```text
  ┌──────────────────────────────────────────────────┐
  │                   NEW PROJECT                    │
  │  /gsd-new-project                                │
  │  Questions -> Research -> Requirements -> Roadmap│
  └─────────────────────────┬────────────────────────┘
                            │
             ┌──────────────▼─────────────┐
             │      FOR EACH PHASE:       │
             │                            │
             │  ┌────────────────────┐    │
             │  │ /gsd-discuss-phase │    │  <- Lock in preferences
             │  └──────────┬─────────┘    │
             │             │              │
             │  ┌──────────▼─────────┐    │
             │  │ /gsd-ui-phase      │    │  <- Design contract (frontend)
             │  └──────────┬─────────┘    │
             │             │              │
             │  ┌──────────▼─────────┐    │
             │  │ /gsd-plan-phase    │    │  <- Research + Plan + Verify
             │  └──────────┬─────────┘    │
             │             │              │
             │  ┌──────────▼─────────┐    │
             │  │ /gsd-execute-phase │    │  <- Parallel execution
             │  └──────────┬─────────┘    │
             │             │              │
             │  ┌──────────▼─────────┐    │
             │  │ /gsd-verify-work   │    │  <- Manual UAT
             │  └──────────┬─────────┘    │
             │             │              │
             │  ┌──────────▼─────────┐    │
             │  │ /gsd-ship          │    │  <- Create PR (optional)
             │  └──────────┬─────────┘    │
             │             │              │
             │     Next Phase?────────────┘
             │             │ No
             └─────────────┼──────────────┘
                            │
            ┌───────────────▼──────────────┐
            │  /gsd-audit-milestone        │
            │  /gsd-complete-milestone     │
            └───────────────┬──────────────┘
                            │
                   Another milestone?
                       │          │
                      Yes         No -> Done!
                       │
               ┌───────▼──────────────┐
               │  /gsd-new-milestone  │
               └──────────────────────┘
```

### Planning Agent Coordination

```text
  /gsd-plan-phase N
         │
         ├── Phase Researcher (x4 parallel)
         │     ├── Stack researcher
         │     ├── Features researcher
         │     ├── Architecture researcher
         │     └── Pitfalls researcher
         │           │
         │     ┌──────▼──────┐
         │     │ RESEARCH.md │
         │     └──────┬──────┘
         │            │
         │     ┌──────▼──────┐
         │     │   Planner   │  <- Reads PROJECT.md, REQUIREMENTS.md,
         │     │             │     CONTEXT.md, RESEARCH.md
         │     └──────┬──────┘
         │            │
         │     ┌──────▼───────────┐     ┌────────┐
         │     │   Plan Checker   │────>│ PASS?  │
         │     └──────────────────┘     └───┬────┘
         │                                  │
         │                             Yes  │  No
         │                              │   │   │
         │                              │   └───┘  (loop, up to 3x)
         │                              │
         │                        ┌─────▼──────┐
         │                        │ PLAN files │
         │                        └────────────┘
         └── Done
```

### Validation Architecture (Nyquist Layer)

During plan-phase research, GSD maps automated test coverage to each phase requirement before any code is written. The researcher detects your existing test infrastructure, maps each requirement to a specific test command, and identifies any test scaffolding that must be created before implementation begins (Wave 0 tasks). The plan-checker enforces this as an 8th verification dimension: plans where tasks lack automated verify commands will not be approved.

**Output:** `{phase}-VALIDATION.md` — the feedback contract for the phase.

**Disable:** Set `workflow.nyquist_validation: false` in `/gsd-settings` for rapid prototyping phases where test infrastructure isn't the focus.

### Retroactive Validation (`/gsd-validate-phase`)

For phases executed before Nyquist validation existed, or for existing codebases with only traditional test suites, retroactively audit and fill coverage gaps:

```text
  /gsd-validate-phase N
         |
         +-- Detect state (VALIDATION.md exists? SUMMARY.md exists?)
         |
         +-- Discover: scan implementation, map requirements to tests
         |
         +-- Analyze gaps: which requirements lack automated verification?
         |
         +-- Present gap plan for approval
         |
         +-- Spawn auditor: generate tests, run, debug (max 3 attempts)
         |
         +-- Update VALIDATION.md
               |
               +-- COMPLIANT -> all requirements have automated checks
               +-- PARTIAL -> some gaps escalated to manual-only
```

The auditor never modifies implementation code — only test files and VALIDATION.md. If a test reveals an implementation bug, it's flagged as an escalation for you to address.

### Assumptions Discussion Mode

By default, `/gsd-discuss-phase` asks open-ended questions about your implementation preferences. Assumptions mode inverts this: GSD reads your codebase first, surfaces structured assumptions about how it would build the phase, and asks only for corrections.

**Enable:** Set `workflow.discuss_mode` to `'assumptions'` via `/gsd-settings`.

See [docs/workflow-discuss-mode.md](workflow-discuss-mode.md) for the full discuss-mode reference.

### Decision Coverage Gates

The discuss-phase captures implementation decisions in CONTEXT.md under a `<decisions>` block as numbered bullets (`- **D-01:** …`). Two gates ensure those decisions survive into plans and shipped code.

**Plan-phase translation gate (blocking).** After planning, GSD refuses to mark the phase planned until every trackable decision appears in at least one plan's scanned surfaces: front-matter `must_haves`/`truths`/`objective`, a `## must_haves`/`truths`/`tasks`/`objective` heading, or an `<objective>`/`<tasks>`/`<task>`/`<action>`/`<read_first>`/`<behavior>`/`<verify>`/`<acceptance_criteria>`/`<done>` tag body.

**Verify-phase validation gate (non-blocking).** During verification, GSD searches plans, SUMMARY.md, modified files, and recent commit messages for each trackable decision. Misses are logged to VERIFICATION.md as a warning section; verification status is unchanged.

**Opting a decision out.** Move it under the `### Claude's Discretion` heading inside `<decisions>`, or tag it: `- **D-08 [informational]:** …`, `- **D-09 [folded]:** …`, `- **D-10 [deferred]:** …`.

**Disabling the gates.** Set `workflow.context_coverage_gate: false` in `.planning/config.json` (or via `/gsd-settings`). Default is `true`.

### Execution Wave Coordination

```text
  /gsd-execute-phase N
         │
         ├── Analyze plan dependencies
         │
         ├── Wave 1 (independent plans):
         │     ├── Executor A (fresh 200K context) -> commit
         │     └── Executor B (fresh 200K context) -> commit
         │
         ├── Wave 2 (depends on Wave 1):
         │     └── Executor C (fresh 200K context) -> commit
         │
         └── Verifier
               ├── Check codebase against phase goals
               ├── Test quality audit (disabled tests, circular patterns, assertion strength)
               │
               ├── PASS -> VERIFICATION.md (success)
               └── FAIL -> Issues logged for /gsd-verify-work
```

### Isolated-run Recovery (fail-safe)

When a worktree-isolated run is rejected — the user declines to merge it, or the run over-reached the requested scope, or the orchestrator surfaces recovery guidance for a blocked plan — GSD halts safely and offers two options: (a) re-attempt in a fresh, narrowly-scoped worktree, or (b) inspect or discard the rejected worktree without merging. GSD never defaults recovery to editing the primary checkout (`main`). Any path that edits the primary checkout requires explicit, clearly-labeled confirmation from the user first. This behavior is unconditional and applies to both `/gsd-execute-phase` (worktree executor waves) and `/gsd-quick` (quick-mode isolated runs).

---

## UI Design Contract

AI-generated frontends are visually inconsistent not because Claude Code is bad at UI but because no design contract existed before execution. `/gsd-ui-phase` locks the design contract before planning; `/gsd-ui-review` audits the result after execution.

For the full workflow, configuration, shadcn initialisation, and the registry safety gate, see [Design a UI phase](how-to/design-a-ui-phase.md).

**Quick reference:**

| Command              | Description                                              |
| -------------------- | -------------------------------------------------------- |
| `/gsd-ui-phase [N]`  | Generate UI-SPEC.md design contract for a frontend phase |
| `/gsd-ui-review [N]` | Retroactive 6-pillar visual audit of implemented UI      |

| Setting                   | Default | Description                                                 |
| ------------------------- | ------- | ----------------------------------------------------------- |
| `workflow.ui_phase`       | `true`  | Generate UI design contracts for frontend phases            |
| `workflow.ui_safety_gate` | `true`  | plan-phase prompts to run /gsd-ui-phase for frontend phases |

---

## Spiking & Sketching

Use `/gsd-spike` to validate technical feasibility before planning, and `/gsd-sketch` to explore visual direction before designing. Both store artifacts in `.planning/` and integrate with the project-skills system via their wrap-up companions.

For the full workflow and flow diagram, see [Spike and sketch](how-to/spike-and-sketch.md).

**Typical flow:**

```bash
/gsd-spike "SSE vs WebSocket"     # Validate the approach
/gsd-spike --wrap-up              # Package learnings

/gsd-sketch "real-time feed UI"   # Explore the design
/gsd-sketch --wrap-up             # Package decisions

/gsd-discuss-phase N              # Lock in preferences (now informed by spike + sketch)
/gsd-plan-phase N                 # Plan with confidence
```

---

## Backlog & Threads

### Backlog Parking Lot

Ideas that aren't ready for active planning go into the backlog using 999.x numbering, keeping them outside the active phase sequence.

```bash
/gsd-capture --backlog "GraphQL API layer"     # Creates 999.1-graphql-api-layer/
/gsd-capture --backlog "Mobile responsive"     # Creates 999.2-mobile-responsive/
```

Backlog items get full phase directories, so you can use `/gsd-discuss-phase 999.1` to explore an idea further or `/gsd-plan-phase 999.1` when it's ready. Backlog directories (and the `0-*` pre-milestone directory some projects carry) are excluded from `/gsd-progress`, `/gsd-stats`, and phase listings for the current milestone — they stay out of the active phase sequence for counting purposes too, not just for planning.

**Review and promote** with `/gsd-review-backlog` — it shows all backlog items and lets you promote (move to active sequence), keep (leave in backlog), or remove (delete).

### Seeds

Seeds are forward-looking ideas with trigger conditions. Unlike backlog items, seeds surface automatically when the right milestone arrives.

```bash
/gsd-capture --seed "Add real-time collab when WebSocket infra is in place"
```

`/gsd-new-milestone` scans all seeds and presents matches. **Storage:** `.planning/seeds/SEED-NNN-slug.md`

Once you've parked a few, audit them on demand instead of waiting for the next milestone to surface them:

```bash
/gsd-capture --list-seeds            # Review every parked seed
/gsd-capture --list-seeds dormant    # Narrow to one status
```

This is read-only — it renders an audit table (ID, status, scope, trigger, title) and a per-status summary, and never modifies a seed. Filter by `dormant`, `active`, or `triggered` when you only want to see seeds in one state.

### Persistent Context Threads

Threads are lightweight cross-session knowledge stores for work that spans multiple sessions but doesn't belong to any specific phase.

```bash
/gsd-thread                              # List all threads
/gsd-thread fix-deploy-key-auth          # Resume existing thread
/gsd-thread "Investigate TCP timeout"    # Create new thread
```

Threads can be promoted to phases (`/gsd-phase`) or backlog items (`/gsd-capture --backlog`) when they mature. **Storage:** `.planning/threads/{slug}.md`

---

## Workstreams & Workspaces

Workstreams and workspaces both provide isolation, but at different levels.

**Workstreams** share the same codebase and git history but isolate planning artifacts — lighter weight, good for working on multiple milestone areas concurrently. See [Work in parallel with workstreams](how-to/work-in-parallel-with-workstreams.md).

**Workspaces** create separate repo worktrees with their own `.planning/` — heavier, for feature-branch or multi-repo isolation. See [Isolate work with workspaces](how-to/isolate-work-with-workspaces.md).

| Command                            | Purpose                                              |
| ---------------------------------- | ---------------------------------------------------- |
| `/gsd-workstreams create <name>`   | Create a new workstream with isolated planning state |
| `/gsd-workstreams switch <name>`   | Switch active context to a different workstream      |
| `/gsd-workstreams list`            | Show all workstreams and which is active             |
| `/gsd-workstreams complete <name>` | Mark a workstream as done and archive its state      |

```bash
# Workspace example — feature branch isolation
/gsd-workspace --new --name feature-b --repos .
cd ~/gsd-workspaces/feature-b
/gsd-new-project

/gsd-workspace --list
/gsd-workspace --remove feature-b
```

---

## Security

### Defense-in-Depth (v1.27)

GSD generates markdown files that become LLM system prompts. This means any user-controlled text flowing into planning artifacts is a potential indirect prompt injection vector. v1.27 introduced centralised security hardening:

**Path Traversal Prevention:** All user-supplied file paths (`--text-file`, `--prd`) are validated to resolve within the project directory. macOS `/var` → `/private/var` symlink resolution is handled.

**Prompt Injection Detection:** The `security.cjs` module scans for known injection patterns in user-supplied text before it enters planning artifacts.

**Runtime Hooks:**

- `gsd-prompt-guard.js` — Scans Write/Edit calls to `.planning/` for injection patterns (always active, advisory-only)
- `gsd-workflow-guard.js` — Warns on file edits outside GSD workflow context (opt-in via `hooks.workflow_guard`)
- `gsd-write-guard.js` — Hard-blocks a whole-file `Write` that catastrophically shrinks a curated `.planning/` artifact (`ROADMAP.md`, milestone roadmaps, `STATE.md`) below 40% of its on-disk line count; files under 40 lines are exempt. The check is stateless per Write, comparing each payload against the file's *current* on-disk size — a single-shot collapse (the #973 shape) is blocked, but a sequence of individually-tolerated shrinks that erodes the file across several Writes is not detected. For a legitimate milestone reset or large deletion, bypass once with the single-use sentinel — write the target's path into `.planning/.gsd-allow-shrink` (fresh within 15 minutes; consumed by the allowed write) — or, interactively, with `GSD_ALLOW_PLANNING_SHRINK=1` in the runtime's environment. Scope the guarantee accordingly: this stops accidental and single-shot collapse, and is not a defense against a determined agent — the sentinel is a plain file, so anything with shell access can arm one; what it buys is that the bypass becomes a deliberate, path-bound, single-use and auditable action rather than a sentence to reason past (always active, blocking; #2255, fix 3 of #973)
- `gsd-secret-read-guard.js` — Hard-blocks reads of secret files — `.env`, `.env.<suffix>` and `.secrets`, matched case-insensitively (`.ENV`, `.Secrets`) — through Read (`file_path`), Grep (an explicit `path`, or a `glob` that selects them, judged per brace alternative) and Bash (operands, input redirects, `$( )` / backtick / `<( )` bodies, and `git show <ref>:<path>` shapes). A shell interpreter (`bash`/`sh`/`zsh`/`dash`/`ksh`) has its script scanned however it arrives — `-c '…'`, a `<( )` file operand, a heredoc / here-string, or a pipe from a knowable `echo`/`printf` source (`echo cat .env | bash`) — as do `eval`'s joined operands, a `source`/`.` process-substitution operand, and `find … | xargs cat` pipelines (upstream literal names become the sub-command's read operands). A name is exempt when its **final extension** is `example`, `sample`, `template` or `dist`, so `.env.example` and equally `.env.local.example` / `.env.production.sample` stay readable (they are the templates GSD's own phase prompt reads). Stated cost: the exempt set is that unbounded family, not four fixed names — a real secret is not protected if it is named to end in one of those four extensions. Order matters, and only the last segment counts: `.env.example.local` is a secret and stays blocked. Trailing dots and spaces are stripped before the name is judged, because Windows resolves `.env.`, `.env ` and `.secrets.` to the protected file itself. Existence checks (`[ -f .env ]`, `ls .env*`, `test`, `stat`, `rm`, `touch`, `echo`, …) pass. Not covered, by construction: `$VAR` indirection (`bash -c "$CMD"`), shell globs (`cat .e*`), interpreter one-liners, a piped script from a non-`echo`/`printf` source (`cat gen.sh | bash`, `curl … | sh`), reads inside scripts the agent runs, and a Grep `glob: '*'` reaching a `.env` that is not gitignored — none are statically resolvable by a hook. This replaces the `Read(.env)` / `Read(.env.*)` / `Read(.secrets)` permission deny rules the installer used to write: on Claude Code ≥ 2.1.259 any `Read()` deny rule makes every `cd DIR && grep …` compound prompt for approval even in `auto` mode, while a hook denial is not a permission rule and applies in `auto` and `bypassPermissions` alike (always active, blocking; #4221)

**CI Scanner:** `prompt-injection-scan.security.test.cjs` scans all agent, workflow, and command files for embedded injection vectors.

---

### Package Legitimacy Gate (v1.42.1)

AI coding tools hallucinate package names. Attackers pre-register those names on npm, PyPI, and crates.io with malicious post-install scripts — a technique called *slopsquatting*. v1.42.1 adds a three-layer gate that stops this before it reaches your shell.

**In RESEARCH.md** — every phase that recommends external packages includes a `## Package Legitimacy Audit` table:

```markdown
## Package Legitimacy Audit

| Package | Registry | Age | Downloads | Source Repo | Verdict | Disposition |
|---------|----------|-----|-----------|-------------|---------|-------------|
| express | npm | 13 yrs | 100M+/wk | github.com/expressjs/express | [OK] | Approved |
| some-new-util | npm | 3 days | 47 | none | [SLOP] | REMOVED |
| api-bridge | npm | 6 mo | 1.2k/wk | github.com/user/api-bridge | [SUS] | Flagged |
```

`[SLOP]` packages are removed from RESEARCH.md entirely and never reach the planner.

**In PLAN.md** — `[SUS]` or `[ASSUMED]` packages trigger a `checkpoint:human-verify` task before the install.

**During execution** — if an install fails, the executor surfaces a checkpoint and stops rather than silently trying an alternative.

**Legitimacy verdicts:**

| Verdict | Meaning | GSD action |
|---------|---------|------------|
| `[OK]` | Passes all legitimacy checks | Proceeds — no checkpoint added |
| `[SUS]` | Suspicious signals | Flagged; planner adds `checkpoint:human-verify` |
| `[SLOP]` | High-confidence hallucination | Removed from RESEARCH.md; never reaches planner |

Verdicts are computed from live registry APIs (npm, PyPI, crates.io) — there
is no separate tool to install. `slopcheck` is an optional escalate-only
adapter (it can raise a verdict but never lower one); no shipped
configuration wires it, and its absence does not change the gate's behavior.

---

## Code Review Workflow

After executing a phase, run a structured code review before UAT. See [Set up cross-AI review](how-to/set-up-cross-ai-review.md) for the full workflow.

```bash
/gsd-code-review 3               # Review all changed files in phase 3
/gsd-code-review 3 --depth=deep  # Deep cross-file review
/gsd-code-review 3 --fix         # Fix Critical + Warning findings atomically
/gsd-code-review 3 --fix --auto  # Fix and re-review until clean (max 3 iterations)
/gsd-audit-fix                   # Audit + classify + fix (medium+ severity, max 5)
```

The review step slots in after execution and before UAT:

```text
/gsd-execute-phase N  ->  /gsd-code-review N  ->  /gsd-code-review N --fix  ->  /gsd-verify-work N
```

**Optional external source-review lanes (#4209):** `/gsd-code-review` accepts the same reviewer-lane flags as `/gsd-review` (run `gsd_run review-lane flags` to list the flags your installation's roster declares, e.g. `--codex`, `--agy`). Adding one asks that lane to independently review the *same* file scope alongside the internal `gsd-code-reviewer` agent; its findings are unverified corroborating evidence that `gsd-code-reviewer` re-checks against the actual source before writing anything to `REVIEW.md` — there is still exactly one `REVIEW.md`. No reviewer-lane flag is the default and reviews with only the internal agent, unchanged from before #4209. This is separate from `/gsd-review`, which reviews `PLAN.md` files *before* execution, not source code — see [Set up cross-AI review](how-to/set-up-cross-ai-review.md).

```bash
/gsd-code-review 3 --codex       # Corroborate the internal review with the codex reviewer lane
```

---

## Coverage-Aware UAT Routing

Historically, `/gsd-verify-work` turned every `## Accomplishments` bullet in a SUMMARY into a manual checkpoint — even deliverables already covered one-to-one by a passing unit test. With a green test suite you were still asked to re-confirm things the tests had already proven, every phase.

GSD now lets the executor record, at authoring time, *how each deliverable was verified*. When a SUMMARY.md carries a `coverage:` frontmatter block (see [the `coverage:` block reference](COMMANDS.md#summary-coverage-block)), `/gsd-verify-work` routes deterministically:

- **Auto-passed** — a deliverable marked `human_judgment: false` whose `verification` list is non-empty and entirely `pass` is recorded as passed (`source: automated`) and never prompted.
- **Presented** — everything else is shown to you for sign-off: anything flagged `human_judgment: true` (visual adequacy, multi-device behaviour, subjective quality), anything with no verification, anything not fully passing, and any malformed entry.

The asymmetry is deliberate. The worst outcome is auto-passing something broken that UAT existed to catch, so auto-pass is the narrow, fully-proven case and *uncertainty always routes back to you*. Flipping the flag alone cannot skip a prompt — a passing test reference is also required. SUMMARYs without a `coverage:` block behave exactly as before (prose-based checkpoints), so nothing changes for existing or un-migrated phases.

---

## Command And Configuration Reference

- **Command Reference:** see [`docs/COMMANDS.md`](COMMANDS.md) for every stable command's flags, subcommands, and examples.
- **Configuration Reference:** see [`docs/CONFIGURATION.md`](CONFIGURATION.md) for the full `config.json` schema, model-profile table, git branching strategies, and security settings.
- **Discuss Mode:** see [`docs/workflow-discuss-mode.md`](workflow-discuss-mode.md) for interview vs assumptions mode.

### Graphify capability gate (tri-state, v1.43+)

Graphify commands (`graphify status`, `graphify build`, `graphify query`, `graphify diff`) now respect the **full tri-state capability gate**:

1. **Installed** — the `gsd-graphify-*` skills are present in the active install profile.
2. **Surfaced** — those skills appear on the current runtime surface (e.g., in `~/.claude/commands/gsd/`).
3. **Config-enabled** — `graphify.enabled: true` is set in `.planning/config.json`.

All three conditions must be true. Setting `graphify.enabled: true` alone is no longer sufficient if graphify has not been installed and surfaced. If graphify commands return `{ disabled: true }` after upgrading, verify that the install profile includes graphify skills (`gsd-tools capability state`) and re-run the installer to surface them.

### Intel capability gate (tri-state, v1.44+)

Intel commands (`intel status`, `intel query`, `intel diff`, `intel snapshot`, `intel validate`, `intel api-surface`) now respect the **full tri-state capability gate** (same resolver as graphify above):

1. **Installed** — the intel capability is present in the active install profile (intel has no skill files, so this is vacuously true for all profiles).
2. **Surfaced** — the intel capability is on the current runtime surface (vacuously true for all surfaces since intel registers no skill stems).
3. **Config-enabled** — `intel.enabled: true` is set in `.planning/config.json`.

For intel, conditions 1 and 2 are always satisfied (intel has no skill files). The effective gate is `intel.enabled` in config — the same behaviour as before, but now enforced through the shared `isCapabilityActive('intel', cwd)` resolver rather than a direct config read. This means intel honours the full capability-state pipeline, including any future install-profile or surface restrictions. If intel commands return `{ disabled: true }`, ensure `intel.enabled: true` is set in `.planning/config.json` and verify `gsd-tools capability state` shows intel as active.

### Compact content mode (`workflow.compact_content`, v4139+)

GSD's own workflow instructions, planning-artifact templates, and (for non-Claude runtimes)
agent personas are prose — and a large eagerly-loaded instruction body is context the model
spends on GSD's own orchestration rather than on your code. `workflow.compact_content` (default
`false`) opts a project into token-minimized variants of that content wherever one has been
authored, without changing what GSD actually does.

**Why turn it on: finite attention, not price.** The point of this key is not a cheaper
invocation — with prompt caching, the per-request cost of re-sending a large instruction file
is already small. The point is what a large always-loaded instruction body costs in *attention*:
every byte of GSD's own prose sitting in context is a byte not spent reasoning about your
codebase. That cost is paid whether or not the tokens were cheap to transport. Turn it on when
you're running long sessions, working in a large codebase that already competes for context, or
on a runtime with a small context window; leave it off (the default) if you'd rather have every
elaboration and worked example available up front, or you're evaluating GSD for the first time
and want full detail while you learn how it thinks.

**What actually changes.** Nothing is compressed at runtime. Every compact variant is a
hand-authored, reviewed file sitting beside its canonical sibling — the key only chooses which
one GSD reads. Guardrails, output-format contracts, few-shot examples, and security language are
never shortened or dropped in a compact variant; only rarely-needed elaboration and restatement
are. With the key off, behavior is unchanged from before this feature existed.

**How to turn it on:** answer "Yes" to the Compact Content question during `/gsd-new-project`,
or run `/gsd-settings` (or `/gsd-config` with no flag) on an existing project and toggle
Compact Content. See [`docs/CONFIGURATION.md`](CONFIGURATION.md#workflow-toggles) for the
mechanics and [ADR-4139](adr/4139-compact-content-seam.md) for the full design rationale.

---

## Usage Examples

### New Project (Full Cycle)

```bash
claude --dangerously-skip-permissions
/gsd-new-project            # Answer questions, configure, approve roadmap
/clear
/gsd-discuss-phase 1        # Lock in your preferences
/gsd-ui-phase 1             # Design contract (frontend phases)
/gsd-plan-phase 1           # Research + plan + verify
/gsd-execute-phase 1        # Parallel execution
/gsd-verify-work 1          # Manual UAT
/gsd-ship 1                 # Create PR from verified work
/gsd-ui-review 1            # Visual audit (frontend phases)
/clear
/gsd-progress --next                   # Auto-detect and run next step
...
/gsd-audit-milestone        # Check everything shipped
/gsd-complete-milestone     # Archive, tag, done
/gsd-pause-work --report         # Generate session summary
```

> [!CAUTION]
> **The permissions flag is optional.** It skips per-file confirmation while
> GSD's sub-agents read and write files. Use it only in low-stakes or
> throwaway contexts. To keep confirmations enabled, start with `claude` instead.
> For real work, read the [security model](../explanation/security-model.md) first.


### New Project from Existing Document

```bash
/gsd-new-project --auto @prd.md   # Auto-runs research/requirements/roadmap from your doc
/clear
/gsd-discuss-phase 1               # Normal flow from here
```

### Existing Codebase

```bash
/gsd-onboard                # Safely map, ingest docs, and initialize planning
# Follow the printed top-level handoff commands, then rerun /gsd-onboard
# (normal phase workflow from here)
```

`/gsd-onboard` routes through `/gsd-map-codebase`, `/gsd-ingest-docs`, and `/gsd-new-project` without nesting interactive workflows or overwriting existing planning files silently.

**Post-execute drift detection (#2003).** After every `/gsd-execute-phase`, GSD checks whether the phase introduced enough structural change to make `.planning/codebase/STRUCTURE.md` stale. Flip the behavior with:

```bash
/gsd-settings workflow.drift_action auto-remap       # remap automatically
/gsd-settings workflow.drift_threshold 5             # tune sensitivity
```

### Plan Drift Guard

**Default-on.** The plan drift guard (`plan_review.source_grounding: true`) runs during plan review and verifies that every symbol your plans cite — decorators, classes, functions, CLI flags — actually exists in your source tree at review time. This catches hallucinated names before any execution agent runs.

**Two axes, one switch.** The same guard also runs a cross-artifact fact-drift pass: when ROADMAP.md, PLAN.md, STATE.md and CONTEXT.md state the *same* fact in contradictory ways — a phase marked complete in one and in progress in the other, a success criterion the plan restates with a different outcome, a term used against its CONTEXT.md definition — you get an advisory finding in REVIEWS.md naming both locations and which one is authoritative. It keys on contradicting *knowledge*, not on similar-looking text, so a plan that simply restates a criterion in its own words is not flagged. The findings never block convergence.

**What it catches:**

- Functions referenced in a PLAN.md step that don't exist in source
- Class or decorator names that were renamed or removed since the plan was written
- CLI flags documented in a plan that are not defined in the argument parser
- Module paths cited in implementation steps that resolve to no files

**Needs-acknowledgement behavior.** When the guard finds a missing symbol, it emits a `needs-acknowledgement` notice in the plan review output rather than hard-blocking. You can acknowledge and proceed (the symbol may be intentionally new) or request a plan revision. The guard does not auto-reject plans — it surfaces signal for human decision.

**Works without intel.** By default the guard uses `grep`/`ripgrep` to search source files — no pre-indexing required. If you have run `/gsd-map-codebase` with `intel.enabled: true`, set `plan_review.source_grounding_authority: intel` to use the faster pre-built `api-map.json` index instead.

```bash
# Enable/disable (default: on)
/gsd-settings plan_review.source_grounding true
/gsd-settings plan_review.source_grounding false

# Switch resolver authority
/gsd-settings plan_review.source_grounding_authority grep   # live grep (default)
/gsd-settings plan_review.source_grounding_authority intel  # pre-indexed api-map.json
```

Toggle at project setup (`/gsd-new-project` asks during workflow preferences) or any time via `/gsd-settings` (Planning section → Drift Guard).

### Quick Bug Fix

```bash
/gsd-quick
> "Fix the login button not responding on mobile Safari"
```

### Resuming After a Break

```bash
/gsd-progress               # See where you left off and what's next
# or
/gsd-resume-work            # Full context restoration from last session
```

### Preparing for Release

```bash
/gsd-audit-milestone        # Check requirements coverage, detect stubs
/gsd-complete-milestone     # Archive, tag, done
```

### Speed vs Quality Presets

| Scenario    | Mode          | Granularity | Profile    | Research | Plan Check | Verifier |
| ----------- | ------------- | ----------- | ---------- | -------- | ---------- | -------- |
| Prototyping | `yolo`        | `coarse`    | `budget`   | off      | off        | off      |
| Normal dev  | `interactive` | `standard`  | `balanced` | on       | on         | on       |
| Production  | `interactive` | `fine`      | `quality`  | on       | on         | on       |

**Skipping discuss-phase in autonomous mode:** When running in `yolo` mode, set `workflow.skip_discuss: true` via `/gsd-settings`.

### Mid-Milestone Scope Changes

```bash
/gsd-phase                  # Append a new phase to the roadmap (default mode)
/gsd-phase --insert 3       # Insert urgent work between phases 3 and 4
/gsd-phase --remove 7       # Descope phase 7 and renumber
/gsd-phase --edit 4         # Edit any field of phase 4 in place
```

---

## Troubleshooting

For a comprehensive troubleshooting guide, see [Recover and troubleshoot](how-to/recover-and-troubleshoot.md). The most common issues are summarised below.

### Programmatic CLI (`gsd-tools query` vs `gsd-tools.cjs`)

For automation, prefer **`gsd-tools query`** with a registered subcommand (see [CLI-TOOLS.md — SDK and programmatic access](CLI-TOOLS.md#sdk-and-programmatic-access) and QUERY-HANDLERS.md). The legacy `node $HOME/.claude/gsd-core/bin/gsd-tools.cjs` CLI remains supported.

### STATE.md Out of Sync

```bash
node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" state validate          # Detect drift
node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" state sync --verify     # Preview changes
node "$HOME/.claude/gsd-core/bin/gsd-tools.cjs" state sync              # Reconstruct STATE.md
```

`state validate`'s report carries a `scope` field alongside `valid` — `valid:true` means no drift was found, but `scope` says whether the check could actually run at all (a phase that could not be resolved, or an unreadable frontmatter/phases directory, reports `valid:true` too, because there was nothing to flag). See [Interpret `state validate` results](how-to/interpret-state-validate-results.md) before treating a passing `state validate` as "clean."

### A Command Looks Frozen After "Spawning..."

GSD subagents run in a separate context window — their work is invisible to the parent session while in progress. Do not interrupt the session. Wait for the result; research and planning agents routinely take 1–5 minutes.

### Context Degradation During Long Sessions

Clear your context window between major commands: `/clear` in Claude Code. GSD is designed around fresh contexts — every subagent gets a clean 200K window. Use `/gsd-resume-work` or `/gsd-progress` to restore state after clearing.

### Plans Seem Wrong or Misaligned

Run `/gsd-discuss-phase [N]` before planning. Most plan quality issues come from Claude making assumptions that `CONTEXT.md` would have prevented.

### Execution Fails or Produces Stubs

Check that the plan was not too ambitious. Plans should have 2–3 tasks maximum. Re-plan with smaller scope.

### Lost Track of Where You Are

Run `/gsd-progress`. It reads all state files and tells you exactly where you are and what to do next.

### Model Costs Too High

Switch to budget profile: `/gsd-config --profile budget`. Disable research and plan-check agents via `/gsd-settings` if the domain is familiar.

### Tuning model cost by phase (`models`) — added in v1.40

Add a `models` block to `.planning/config.json`:

```json
{
  "model_profile": "balanced",
  "models": {
    "planning": "opus",
    "discuss": "opus",
    "research": "sonnet",
    "execution": "opus",
    "verification": "sonnet",
    "completion": "sonnet"
  }
}
```

Need a per-agent exception? Add `model_overrides` alongside — it wins over `models`:

```json
{
  "models": { "research": "sonnet" },
  "model_overrides": {
    "gsd-codebase-mapper": "haiku"
  }
}
```

For the full mapping table and resolution-precedence rules, see [Per-Phase-Type Models](CONFIGURATION.md#per-phase-type-models-models--added-in-v140).

### Cheap-by-default with `dynamic_routing` — added in v1.40

```json
{
  "dynamic_routing": {
    "enabled": true,
    "tier_models": {
      "light":    "haiku",
      "standard": "sonnet",
      "heavy":    "opus"
    },
    "escalate_on_failure": true,
    "max_escalations": 1
  }
}
```

For the full agent → tier mapping, see [Dynamic Routing](CONFIGURATION.md#dynamic-routing-with-failure-tier-escalation-dynamic_routing--added-in-v140).

### Trim MCP servers to reduce per-turn cost

Before tuning `model_profile` or `models.<phase_type>`, audit which **MCP servers** your harness has enabled. Every enabled MCP server injects its tool schema into every turn — heavyweight servers can cost 20k+ tokens each.

This is a **harness setting**, not a GSD setting. The toggle lives in `.claude/settings.json`:

```json
{
  "enabledMcpjsonServers": ["context7"],
  "disabledMcpjsonServers": ["playwright", "mac-tools"]
}
```

Quick audit before a long phase:

- Are any browser / playwright tools enabled when this phase has no UI work?
- Are any platform-specific tools enabled when not needed?
- Are any project-specific MCPs from a different project still enabled here?

Each disabled server removes its schema from every subsequent turn. Trimming MCPs **compounds** with `model_profile` tuning — both levers are additive, and MCP savings show up immediately across every subagent the orchestrator spawns.

For the full audit, harness reference, and the composition note with `model_profile`, see [MCP Tool Schema Cost](../gsd-core/references/context-budget.md#mcp-tool-schema-cost-harness-concern) in the bundled `context-budget.md` reference.

### Using Non-Claude Runtimes (Codex, OpenCode, Antigravity CLI, Kilo)

> **Codex CLI minimum supported version: `0.130.0`** (issue [#3562](https://github.com/open-gsd/gsd-core/issues/3562)).

If you installed GSD for a non-Claude runtime, the installer already configured model resolution. No manual setup is needed — `resolve_model_ids: "omit"` is set automatically, which tells GSD to skip Anthropic model ID resolution and let the runtime choose its own default model.

To assign different models on a non-Claude runtime:

```json
{
  "resolve_model_ids": "omit",
  "model_overrides": {
    "gsd-planner": "o3",
    "gsd-executor": "o4-mini",
    "gsd-debugger": "o3"
  }
}
```

#### Codex skill picker and agent scheduling (#774)

GSD enriches each Codex install with an additional artifact:

- **Flex-tier scheduling** — light-tier agents (haiku-equivalent) emit `service_tier = "flex"` and `model_verbosity = "low"` in their agent TOML. The Codex scheduler routes these agents to the flex tier (lower cost, background processing) and suppresses verbose token output.

GSD skills appear in the Codex `/skills` picker via their `SKILL.md` file, which Codex discovers automatically. No `agents/openai.yaml` sidecar is emitted — doing so caused duplicate autocomplete entries (#1326).

This enrichment is written automatically at install time and requires no manual configuration. Requires Codex CLI ≥ 0.130.0.

#### Switching from Claude to Codex with one config change (#2517)

```json
{
  "runtime": "codex",
  "model_profile": "balanced"
}
```

See [Runtime-Aware Profiles](CONFIGURATION.md#runtime-aware-profiles-2517).

#### Per-runtime command enrichment

When generating artifacts, the installer adapts GSD commands to each runtime's native command schema:

- **Qwen Code** — main-loop skills carry Qwen's numeric `priority` field so the most-used workflows (e.g. `new-project`, `plan-phase`, `execute-phase`) sort first in the `/skills` list; utility skills are left unset. Higher values sort earlier; the field affects only the `/skills` list order.

See [How to install GSD Core on your runtime](how-to/install-on-your-runtime.md) for the full per-runtime details.

### Manual install / no-Node.js setup

If you cannot run the GSD installer, you cannot use the source files in `agents/` directly — they are in Claude Code's native frontmatter format. For OpenCode, two transformations are required:

| Field | GSD source format | OpenCode-valid format | Action |
|---|---|---|---|
| `tools:` | `Read, Bash, Grep` (comma-string) | Not a frontmatter field | Remove the `tools:` line entirely |
| `color:` | Plain CSS color name | Hex or OpenCode semantic name | Convert to hex or remove |

**Alternative:** run the installer on any machine with Node.js:

```bash
npx @opengsd/gsd-core@latest --opencode --global
```

### Installing for Cline

```bash
npx @opengsd/gsd-core --cline --global   # applies to all projects
npx @opengsd/gsd-core --cline --local    # this project only
```

### Installing for CodeBuddy

```bash
npx @opengsd/gsd-core --codebuddy --global
```

GSD installs four surfaces for CodeBuddy: `/gsd-*` slash commands in `~/.codebuddy/commands/`, subagents in `~/.codebuddy/agents/`, model-invocable skills in `~/.codebuddy/skills/`, and `settings.json` hooks. The skills are emitted with `user-invocable: false` so the slash commands are the single `/` menu surface (no duplicate entries).

### Installing for Qwen Code

```bash
npx @opengsd/gsd-core --qwen --global
```

### Installing for Prerelease Editions

Set the runtime's `*_CONFIG_DIR` env var to the prerelease directory before running the installer:

```bash
WINDSURF_CONFIG_DIR=~/.codeium/windsurf-next npx @opengsd/gsd-core@latest --windsurf --global
```

**Env-var reference for supported runtimes:**

| Runtime | Stable default | Override env var |
|---|---|---|
| Claude Code | `~/.claude` | `CLAUDE_CONFIG_DIR` |
| OpenCode | `XDG_CONFIG_HOME/opencode` | `OPENCODE_CONFIG_DIR` |
| Codex | (per Codex CLI) | `--config-dir` flag |
| Copilot | `~/.copilot` | `COPILOT_CONFIG_DIR` (or `COPILOT_HOME`) |
| Cursor | `~/.cursor` | `CURSOR_CONFIG_DIR` |
| Windsurf / Devin Desktop | `~/.codeium/windsurf` | `WINDSURF_CONFIG_DIR` |
| Antigravity | auto-detected | `ANTIGRAVITY_CONFIG_DIR` |
| Augment | `~/.augment` | `AUGMENT_CONFIG_DIR` |
| Trae | `~/.trae` | `TRAE_CONFIG_DIR` |
| Qwen Code | `~/.qwen` | `QWEN_CONFIG_DIR` |
| Kilo | `~/.config/kilo` | `KILO_CONFIG_DIR` |
| CodeBuddy | `~/.codebuddy` | `CODEBUDDY_CONFIG_DIR` |
| Cline | `~/.cline` | `CLINE_CONFIG_DIR` |

### Using Claude Code with Non-Anthropic Providers

Switch to the `inherit` profile: `/gsd-config --profile inherit`. This makes all agents use your current session model.

### Working on a Sensitive/Private Project

Set `commit_docs: false` during `/gsd-new-project` or via `/gsd-settings`. Add `.planning/` to your `.gitignore`.

### GSD Update Overwrote My Local Changes

Which recovery you need depends on whether you *modified a GSD file* or *added your own*:

- **You edited a file GSD ships** (an agent prompt, a workflow). Since v1.17 the installer backs it up to `gsd-local-patches/`. Run `/gsd-update --reapply` to merge your changes back.
- **You added your own file inside a GSD-managed directory** (a custom skill under `skills/`, an extra file in `commands/gsd/`). The installer saves it to `gsd-user-files-backup/`, and the update offers to restore it once the new version is installed. If you declined, or the backup is left over from an older update, restore it any time:

  ```bash
  node <config-dir>/gsd-core/bin/gsd-tools.cjs restore-custom-files --config-dir <config-dir> --apply
  ```

  Run it without `--apply` first to see what would be restored. The backup is never deleted, and the restore skips any file that would overwrite something the new release ships.

### Install or Refresh a Release Candidate

To install or refresh GSD from the `@next` RC dist-tag (the pre-release channel established by ADR #660), run:

```bash
/gsd-update --next
# or equivalently:
/gsd-update --rc
```

The same scope/runtime detection, changelog preview, custom-file backup, and cache clearing apply. Omitting `--next`/`--rc` keeps targeting `@latest` (stable channel, no change). Only the `@latest` and `@next` channels are supported — no arbitrary dist-tag can be passed.

### Cannot Update via npm

See [docs/manual-update.md](manual-update.md) for a step-by-step manual update procedure.

### Workflow Diagnostics (`/gsd-forensics`)

When a workflow fails in a non-obvious way, run `/gsd-forensics` to generate a diagnostic report covering git history anomalies, artifact integrity, and state inconsistencies. Output goes to `.planning/forensics/`.

### Pre-populated Permissions (Claude Code)

Since v1.3.1, the installer pre-populates `~/.claude/settings.json` (or
`settings.local.json` for local installs) with the core permissions GSD needs:

```json
{
  "permissions": {
    "allow": [
      "Bash(npx gsd-core *)",
      "Read(.planning/*)",
      "Edit(.planning/*)",
      "Read(STATE.md)",
      "Edit(STATE.md)"
    ]
  }
}
```

These entries eliminate first-run approval prompts for GSD's own tool calls. The
merge is non-destructive — your existing permissions are preserved and GSD entries
are only appended. Uninstalling GSD removes exactly these entries and preserves
any others.

**Secret-file protection moved from deny rules to a hook (#4221).** Earlier
versions also wrote three `permissions.deny` rules — `Read(.env)`,
`Read(.env.*)` and `Read(.secrets)`. Claude Code 2.1.259 hardened the
Bash-side enforcement of `Read()` deny rules so that *any* such rule makes every
`cd DIR && grep …` / `cd DIR && cat …` compound prompt for approval, even in
`auto` mode — and GSD's subagents emit hundreds of those per session. The same
protection now ships as the always-on `gsd-secret-read-guard.js` PreToolUse hook
(Read, Grep and Bash; see Runtime Hooks above for what it covers and its
documented gaps). A hook denial is not a permission rule, so it never arms that
check, and it applies in `auto` and `bypassPermissions` modes alike. On install
and uninstall the three retired strings are removed from `permissions.deny`
(and an emptied `deny` array is dropped). Note the removal is byte-exact: a
rule you wrote by hand that is identical to one of the three is indistinguishable
from the installer's and is removed as well — re-add it if you want both layers.

### Executor Subagent Gets "Permission denied" on Bash Commands

Add the required patterns to `~/.claude/settings.json`. Core patterns needed for all stacks:

```json
"Bash(git add:*)",
"Bash(git commit:*)",
"Bash(git merge:*)",
"Bash(git worktree:*)",
"Bash(git rebase:*)",
"Bash(git reset:*)",
"Bash(git checkout:*)",
"Bash(git switch:*)",
"Bash(git restore:*)",
"Bash(git stash:*)",
"Bash(git rm:*)",
"Bash(git mv:*)",
"Bash(git fetch:*)",
"Bash(git cherry-pick:*)",
"Bash(git apply:*)",
"Bash(gh:*)"
```

**Per-project permissions:** add the same `permissions.allow` block to `.claude/settings.local.json` in your project root instead of `~/.claude/settings.json`.

### Parallel Execution Causes Build Lock Errors

GSD handles this automatically since v1.26. If you're on an older version, add to your project's `CLAUDE.md`:

```markdown
## Git Commit Rules for Agents
All subagent/executor commits MUST use `--no-verify`.
```

To disable parallel execution entirely: `/gsd-settings` → set `parallelization.enabled` to `false`.

---

## Recovery Quick Reference

| Problem                              | Solution                                                                 |
| ------------------------------------ | ------------------------------------------------------------------------ |
| Lost context / new session           | `/gsd-resume-work` or `/gsd-progress`                                    |
| Phase went wrong                     | `git revert` the phase commits, then re-plan                             |
| Need to change scope                 | `/gsd-phase` (default), `/gsd-phase --insert`, or `/gsd-phase --remove`  |
| Something broke                      | `/gsd-debug "description"` (add `--diagnose` for analysis without fixes) |
| STATE.md out of sync                 | `state validate` then `state sync` — check the report's `scope` field, not just `valid` ([interpret results](how-to/interpret-state-validate-results.md)) |
| Workflow state seems corrupted       | `/gsd-forensics`                                                         |
| Quick targeted fix                   | `/gsd-quick`                                                             |
| Plan doesn't match your vision       | `/gsd-discuss-phase [N]` then re-plan                                    |
| Costs running high                   | `/gsd-config --profile budget` and `/gsd-settings` to toggle agents off  |
| Update broke local changes           | `/gsd-update --reapply`                                                  |
| Custom file gone after an update     | `gsd-tools restore-custom-files --config-dir <dir> --apply`              |
| Want session summary for stakeholder | `/gsd-pause-work --report`                                               |
| Don't know what step is next         | `/gsd-progress --next`                                                   |
| Parallel execution build errors      | Update GSD or set `parallelization.enabled: false`                       |

---

## Project File Structure

```text
.planning/
  PROJECT.md              # Project vision and context (always loaded)
  REQUIREMENTS.md         # Scoped v1/v2 requirements with IDs
  ROADMAP.md              # Phase breakdown with status tracking
  STATE.md                # Decisions, blockers, session memory
  config.json             # Workflow configuration
  MILESTONES.md           # Completed milestone archive
  HANDOFF.json            # Structured session handoff (from /gsd-pause-work)
  research/               # Domain research from /gsd-new-project
  reports/                # Session reports (from /gsd-pause-work --report)
  todos/
    pending/              # Captured ideas awaiting work
    completed/             # Completed todos
  debug/                  # Active debug sessions
    resolved/             # Archived debug sessions
  spikes/                 # Feasibility experiments (from /gsd-spike)
    NNN-name/             # Experiment code + README with verdict
    MANIFEST.md           # Index of all spikes
  sketches/               # HTML mockups (from /gsd-sketch)
    NNN-name/             # index.html (2-3 variants) + README
    themes/
      default.css         # Shared CSS variables for all sketches
    MANIFEST.md           # Index of all sketches with winners
  codebase/               # Brownfield codebase mapping (from /gsd-map-codebase or /gsd-onboard)
  onboarding/             # Brownfield onboarding summary (from /gsd-onboard)
  phases/
    XX-phase-name/
      XX-YY-PLAN.md       # Atomic execution plans
      XX-YY-SUMMARY.md    # Execution outcomes and decisions
      CONTEXT.md          # Your implementation preferences
      RESEARCH.md         # Ecosystem research findings
      VERIFICATION.md     # Post-execution verification results
      XX-UI-SPEC.md       # UI design contract (from /gsd-ui-phase)
      XX-UI-REVIEW.md     # Visual audit scores (from /gsd-ui-review)
  ui-reviews/             # Screenshots from /gsd-ui-review (gitignored)
```

---

## Related

- [Docs index](README.md)
- [Commands](COMMANDS.md)
- [Configuration](CONFIGURATION.md)
- [The phase loop](explanation/the-phase-loop.md)
- [Community Capability Registry & EoS Registry](registries/README.md) — discover third-party Capabilities and EoS host integrations