msd-core/docs/ARCHITECTURE.md

GSD Core Architecture

System architecture for contributors and advanced users. For user-facing documentation, see Feature Reference or User Guide.

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Table of Contents

• System Overview
• Design Principles
• Component Architecture
• Agent Model
• Data Flow
• File System Layout
• Installer Architecture
• Hook System
• CLI Tools Layer
• Runtime Abstraction

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System Overview

GSD Core is a meta-prompting framework that sits between the user and AI coding agents (Claude Code, Kimi CLI, OpenCode, Kilo, Codex, Copilot, Antigravity, Trae, Cline, Augment Code). It provides:

1. Context engineering — Structured artifacts that give the AI everything it needs per task (see Context engineering)
2. Multi-agent orchestration — Thin orchestrators that spawn specialized agents with fresh context windows (see Multi-agent orchestration)
3. Spec-driven development — Requirements → research → plans → execution → verification pipeline
4. State management — Persistent project memory across sessions and context resets

┌──────────────────────────────────────────────────────┐
│                      USER                            │
│            /gsd-command [args]                        │
└─────────────────────┬────────────────────────────────┘
                      │
┌─────────────────────▼────────────────────────────────┐
│              COMMAND LAYER                            │
│   commands/gsd/*.md — Prompt-based command files      │
│   (Claude Code custom commands / Codex skills)        │
└─────────────────────┬────────────────────────────────┘
                      │
┌─────────────────────▼────────────────────────────────┐
│              WORKFLOW LAYER                           │
│   gsd-core/workflows/*.md — Orchestration logic  │
│   (Reads references, spawns agents, manages state)    │
└──────┬──────────────┬─────────────────┬──────────────┘
       │              │                 │
┌──────▼──────┐ ┌─────▼─────┐ ┌────────▼───────┐
│  AGENT      │ │  AGENT    │ │  AGENT         │
│  (fresh     │ │  (fresh   │ │  (fresh        │
│   context)  │ │   context)│ │   context)     │
└──────┬──────┘ └─────┬─────┘ └────────┬───────┘
       │              │                 │
┌──────▼──────────────▼─────────────────▼──────────────┐
│              CLI TOOLS LAYER                          │
│   gsd-tools.cjs command families + domain modules      │
│   command-routing-hub + observability seams            │
└──────────────────────┬───────────────────────────────┘
                       │
┌──────────────────────▼───────────────────────────────┐
│              FILE SYSTEM (.planning/)                 │
│   PROJECT.md | REQUIREMENTS.md | ROADMAP.md          │
│   STATE.md | config.json | phases/ | research/       │
└──────────────────────────────────────────────────────┘

---

Design Principles

1. Fresh Context Per Agent

Every agent spawned by an orchestrator gets a clean context window (up to 200K tokens). This eliminates context rot — the quality degradation that happens as an AI fills its context window with accumulated conversation.

2. Thin Orchestrators

Workflow files (gsd-core/workflows/*.md) never do heavy lifting. They:

• Load context via gsd-tools.cjs init <workflow>
• Spawn specialized agents with focused prompts
• Collect results and route to the next step
• Update state between steps

3. File-Based State

All state lives in .planning/ as human-readable Markdown and JSON. No database, no server, no external dependencies. This means:

• State survives context resets (/clear)
• State is inspectable by both humans and agents
• State can be committed to git for team visibility

4. Absent = Enabled

Workflow feature flags follow the absent = enabled pattern. If a key is missing from config.json, it defaults to true. Users explicitly disable features; they don't need to enable defaults.

5. Defense in Depth

Multiple layers prevent common failure modes:

• Plans are verified before execution (plan-checker agent)
• Execution produces atomic commits per task
• Post-execution verification checks against phase goals
• UAT provides human verification as final gate

---

Component Architecture

Commands (commands/gsd/*.md)

User-facing entry points. Each file contains YAML frontmatter (name, description, allowed-tools) and a prompt body that bootstraps the workflow. Commands are installed as:

• Claude Code: Custom slash commands (hyphen form, /gsd-command-name)
• OpenCode / Kilo: Slash commands (hyphen form, /gsd-command-name)
• Codex: Skills ($gsd-command-name)
• Copilot: Slash commands (hyphen form, /gsd-command-name)
• Kimi CLI: Agent Skills (/skill:gsd-command-name) plus an explicit custom agent launch with kimi --agent-file
• Antigravity: Skills

Total commands: see docs/INVENTORY.md for the authoritative count and full roster.

Two-stage hierarchical routing (v1.40, #2792)

To keep the eager skill-listing token cost low, v1.40 introduces six namespace meta-skills (gsd-workflow, gsd-project, gsd-quality, gsd-context, gsd-manage, gsd-ideate — sourced from commands/gsd/ns-*.md, but the invocable name: is the bare form shown here) layered above the concrete sub-skills. On runtimes with non-recursive skill loaders (cline, qwen, hermes, augment, trae) the installer now realizes this fully: it emits only the 6 namespace router bundles as top-level skills and nests the ~61 concrete skills under <router>/skills/<name>/SKILL.md, so the eager listing is ≈6 entries instead of ≈67. The model selects a namespace router, which instructs it to read the nested concrete skill file via a routing table embedded in the router body. On these runtimes concrete skills are not directly invocable by bare name via the Skill tool; they are reachable through the router. Slash commands (/gsd-*, via the separate commands surface) are unaffected where the runtime has one. On runtimes with recursive or unconfirmed skill loaders (claude global, cursor, codex, copilot, windsurf, codebuddy, opencode, kilo, antigravity) the layout remains flat — all skills emitted at the top level as before. Antigravity moved from nested to flat in #1614: agy scans only skills/<name>/SKILL.md, so nested sub-skills were unreachable. Claude was reverted to flat in #924: the Skill tool hard-errors on unknown names rather than re-routing via the router, so nested concrete skills were uninvokable.

The router descriptions use pipe-separated keyword tags (≤ 60 chars) per the Tool Attention research showing keyword-dense tags outperform prose for routing at ~40 % the token cost.

MCP token-budget interaction

The eager skill listing is one of two recurring per-turn token costs. The other is the MCP tool schema injected by every enabled MCP server in .claude/settings.json. Heavyweight MCP servers (browser/playwright, Mac-tools, Windows-tools) can each cost 20 k+ tokens per turn — often dwarfing what model_profile tuning saves. The toggle lives in the Claude Code harness (enabledMcpjsonServers / disabledMcpjsonServers in .claude/settings.json) and is not a GSD concern. Together, the two-stage routing layer (#2792) and disciplined MCP enablement are the largest cost levers per turn. See docs/USER-GUIDE.md and references/context-budget.md for the audit checklist.

Workflows (gsd-core/workflows/*.md)

Orchestration logic that commands reference. Contains the step-by-step process including:

• Context loading via gsd-tools.cjs init handlers
• Agent spawn instructions with model resolution
• Gate/checkpoint definitions
• State update patterns
• Error handling and recovery

Total workflows: see docs/INVENTORY.md for the authoritative count and full roster.

Progressive disclosure for workflows

Workflow files are loaded verbatim into Claude's context every time the corresponding /gsd-* command is invoked. The workflow size budget enforced by tests/workflow-size-budget.test.cjs keeps each file bounded, mirroring the the agent size-budget convention. The budget is measured in bytes (#717), not lines: line count over-penalizes prose and under-catches token-dense tables and code blocks, whereas bytes are deterministic and match the unit our vendors bound on — Codex truncates instruction docs past 32,768 bytes (project_doc_max_bytes). We adopt that unit, not that exact number: the XL/LARGE ceilings below sit above 32,768 because these are grandfathered top-level orchestrators loaded by Claude, not Codex AGENTS.md docs.

Tier	Per-file byte limit
XL	90,000 — top-level orchestrators (execute-phase, plan-phase, new-project)
LARGE	54,000 — multi-step planners and large feature workflows
DEFAULT	38,000 — focused single-purpose workflows (the target tier)

Ceilings are not fixed forever: under the tighten-only ratchet (#597) each one tracks its tier's current high-water mark within a small grace band, so budgets may only decrease over time.

Why the budget exists. With prompt caching the per-invocation cost of a large workflow is modest (cache reads run ~10% of input). The stronger, caching-independent reason is quality: as context grows, recall and reasoning degrade ("context rot" / attention budget), so leaner, higher-signal instructions produce better plans. The ceiling protects the agent's attention, not just the token bill.

Because the budget measures one file, it is a proxy for the real goal — bounded loaded context. Extraction only helps when the extracted content is loaded lazily (Read at the step that needs it). Moving prose into a file that is still eagerly @-imported shrinks the measured file without shrinking loaded context, which games the proxy rather than serving the goal.

workflows/discuss-phase.md is held to a stricter <30,000-byte ceiling per the discuss-phase byte budget (#717; the discuss-phase/modes split keeps it ≈32000 bytes). When a workflow grows beyond its tier, extract per-mode bodies into workflows/<workflow>/modes/<mode>.md, templates into workflows/<workflow>/templates/, and shared knowledge into gsd-core/references/. The parent file becomes a thin dispatcher that Reads only the mode and template files needed for the current invocation.

workflows/discuss-phase/ is the canonical example of this pattern — parent dispatches, modes/ holds per-flag behavior (power.md, all.md, auto.md, chain.md, text.md, batch.md, analyze.md, default.md, advisor.md), and templates/ holds CONTEXT.md, DISCUSSION-LOG.md, and checkpoint.json schemas that are read only when the corresponding output file is being written.

workflows/plan-phase.md, workflows/execute-phase.md, and the gsd-planner / gsd-executor agent definitions apply the same discipline to their MVP-only reference bodies — planner-mvp-mode.md, user-story-template.md, skeleton-template.md, and execute-mvp-tdd.md are referenced for the planner/executor to Read only on MVP, Walking-Skeleton, or MVP+TDD paths, rather than eagerly @-imported, so non-MVP runs do not pay their context cost (guards against the "@-import behind a conditional still loads eagerly" leak; see #720). The dedicated mvp-phase workflow keeps its eager imports, since it is always MVP.

Agents (agents/*.md)

Specialized agent definitions with frontmatter specifying:

• name — Agent identifier
• description — Role and purpose
• tools — Allowed tool access (Read, Write, Edit, Bash, Grep, Glob, WebSearch, etc.)
• color — Terminal output color for visual distinction

Total agents: 33

References (gsd-core/references/*.md)

Shared knowledge documents that workflows and agents @-reference (see docs/INVENTORY.md for the authoritative full roster):

Core references:

• checkpoints.md — Checkpoint type definitions and interaction patterns
• gates.md — 4 canonical gate types (Confirm, Quality, Safety, Transition) wired into plan-checker and verifier
• model-profiles.md — Per-agent model tier assignments
• model-profile-resolution.md — Model resolution algorithm documentation
• verification-patterns.md — How to verify different artifact types
• verification-overrides.md — Per-artifact verification override rules
• planning-config.md — Full config schema and behavior
• git-integration.md — Git commit, branching, and history patterns
• git-planning-commit.md — Planning directory commit conventions
• questioning.md — Dream extraction philosophy for project initialization
• tdd.md — Test-driven development integration patterns
• ui-brand.md — Visual output formatting patterns
• common-bug-patterns.md — Common bug patterns for code review and verification

Workflow references:

• agent-contracts.md — Formal interface between orchestrators and agents
• context-budget.md — Context window budget allocation rules
• continuation-format.md — Session continuation/resume format
• domain-probes.md — Domain-specific probing questions for discuss-phase
• gate-prompts.md — Gate/checkpoint prompt templates
• revision-loop.md — Plan revision iteration patterns
• universal-anti-patterns.md — Common anti-patterns to detect and avoid
• artifact-types.md — Planning artifact type definitions
• phase-argument-parsing.md — Phase argument parsing conventions
• decimal-phase-calculation.md — Decimal sub-phase numbering rules
• workstream-flag.md — Workstream active pointer conventions
• user-profiling.md — User behavioral profiling methodology
• thinking-partner.md — Conditional thinking partner activation at decision points

Thinking model references:

References for integrating thinking-class models (o3, o4-mini, Gemini 2.5 Pro) into GSD workflows:

• thinking-models-debug.md — Thinking model patterns for debugging workflows
• thinking-models-execution.md — Thinking model patterns for execution agents
• thinking-models-planning.md — Thinking model patterns for planning agents
• thinking-models-research.md — Thinking model patterns for research agents
• thinking-models-verification.md — Thinking model patterns for verification agents

Modular planner decomposition:

The planner agent (agents/gsd-planner.md) was decomposed from a single monolithic file into a core agent plus reference modules to stay under the 50K character limit imposed by some runtimes:

• planner-gap-closure.md — Gap closure mode behavior (reads VERIFICATION.md, targeted replanning)
• planner-reviews.md — Cross-AI review integration (reads REVIEWS.md from /gsd-review)
• planner-revision.md — Plan revision patterns for iterative refinement

Templates (gsd-core/templates/)

Markdown templates for all planning artifacts. Used by gsd-tools.cjs template fill / phase.scaffold (and top-level scaffold) to create pre-structured files:

• project.md, requirements.md, roadmap.md, state.md — Core project files
• phase-prompt.md — Phase execution prompt template
• summary.md (+ summary-minimal.md, summary-standard.md, summary-complex.md) — Granularity-aware summary templates
• DEBUG.md — Debug session tracking template
• UI-SPEC.md, UAT.md, VALIDATION.md — Specialized verification templates
• discussion-log.md — Discussion audit trail template
• codebase/ — Brownfield mapping templates (architecture, stack)
• research-project/ — Research output templates (SUMMARY, STACK, FEATURES, ARCHITECTURE, PITFALLS)

Hooks (hooks/)

Runtime hooks that integrate with the host AI agent:

Hook	Event	Purpose
gsd-statusline.js	statusLine	Displays model (long-context suffixes like (1M context) collapse to a compact (1M) badge), task, directory, and context usage bar
gsd-context-monitor.js	PostToolUse / AfterTool	Injects agent-facing context warnings at 35%/25% remaining by default (configurable — see CONFIGURATION.md)
gsd-check-update.js	SessionStart	Foreground trigger for the background update check
gsd-ensure-canonical-path.js	SessionStart	For Claude Code plugin installs, symlinks ~/.claude/gsd-core/{bin,contexts,references,templates,workflows} to the plugin's bundled tree so @~/.claude/gsd-core/... includes resolve; runs first in SessionStart, no-op in classic installs, self-heals after claude plugin update (#997)
gsd-check-update-worker.js	(helper)	Background worker spawned by gsd-check-update.js; no direct event registration
gsd-prompt-guard.js	PreToolUse	Scans .planning/ writes for prompt injection patterns (advisory)
gsd-read-injection-scanner.js	PostToolUse	Scans Read tool output for injected instructions in untrusted content
gsd-workflow-guard.js	PreToolUse	Detects file edits outside GSD workflow context (advisory, opt-in via hooks.workflow_guard)
gsd-secret-read-guard.js	PreToolUse	Hard-blocks Read / Grep / Bash reads of .env, .env.<suffix> (templates such as .env.example exempt) and .secrets; replaces the installer-written Read(.env*) permission deny rules, which made every cd DIR && grep … compound prompt for approval on Claude Code ≥ 2.1.259 (#4221)
gsd-read-guard.js	PreToolUse	Advisory guard preventing Edit/Write on files not yet read in the session
gsd-session-state.sh	SessionStart	Session state tracking for shell-based runtimes
gsd-validate-commit.sh	PreToolUse	Commit validation for conventional commit enforcement
gsd-phase-boundary.sh	PostToolUse	Phase boundary detection for workflow transitions

See docs/INVENTORY.md for the authoritative hook roster.

Crash policy (ADR-3889 Phase 7, #3911). Every enforcement hook terminates through hooks/lib/hook-exit.js's allow(payload) (exit 0), deny(payload, stderrPayload?) (exit 2), or crash(onCrash, payload) — the last dispatching per a HOOK_ON_CRASH policy the hook must declare explicitly (ALLOW or DENY, no default), so a hook's fail-open/fail-closed stance is a visible declaration rather than an inference from a bare process.exit(N). Two hooks are deliberate exceptions — gsd-read-injection-scanner.js (PostToolUse) and gsd-cursor-subagent-start.js (Cursor) — whose harnesses read the block decision from the JSON response body at exit 0, not from the exit code, so they never call deny(). See Declare a hook's crash policy.

Command Routing Hub (gsd-core/bin/lib/command-routing-hub.cjs)

CJS command family routers dispatch through CommandRoutingHub. The hub owns the no-throw pure-result contract (hub.dispatch() catches internal exceptions and returns { ok: false, kind, ...typedPayload }) and the closed runtime error taxonomy (UnknownCommand, InvalidArgs, HandlerRefusal, HandlerFailure). Router adapters remain thin CLI translators — they build the hub, call dispatch, then map the Result to output()/error() calls. The runtime is single-path (no dual-runtime mode selection). See docs/adr/0174-retire-gsd-sdk-package-boundary.md.

Planned (ADR-2346 / epic #2345): the runCommand 73-case switch is being dissolved into a two-layer dispatch — families via the commandFamilies registry (ADR-959 mechanism, completed) and single-purpose leaf verbs via a table filling the prepared _dispatchNonFamily seam — collapsing runCommand to a ~15-line dispatcher. Behavior-preserving; tracked phase-by-phase under epic #2345. The current-state description above holds until each phase lands.

Capability Command Dispatch (gsd-core/bin/gsd-tools.cjs, ADR-1244 D7)

Command families declared by capabilities (commands: [{ family, module, router }]) are dispatched from the registry rather than a hardcoded switch. The runCommand default arm tries, in order:

1. First-party — dispatchCapabilityCommand against the frozen capability-registry.cjs commandFamilies, loading the router from bin/lib/. The in-tree families (graphify, intel, audit) reach their routers this way (the legacy hardcoded switch is retired).
2. Third-party (installed overlay) — dispatchOverlayCapabilityCommand calls loadRegistry({ includeInstalled }) and dispatches a family only when its capId appears in _overlay.commandRoots. The loader lists a command root only for an accepted overlay capability with a committed ledger entry (consent gate), and the router module is require()'d from that capability's install root, confined by basename validation + realpath containment (rejecting .. traversal and symlink escape). This is the one point where third-party capability code executes; see the capability trust model for the consent + confinement + project-scope trust boundary.

Both paths share the same guards: prototype-pollution-safe command keys, an own-property router check, and synchronous-only routers (an async router is a fail-fast error).

Reviewer-Lane Capability Trait (#4209, ADR-2782)

/gsd-code-review optionally corroborates its internal review with external reviewer lanes (--codex, --agy, ...), gated by the reusable supportsReviewerLanes capability-step trait and dispatched through the single dispatchReviewerLanes interpreter — see gsd-core/references/loop-hook-dispatch.md for the trait and src/reviewer-step-dispatch.cts for the interpreter's fail-closed contract. gsd-code-reviewer is the sole consolidator: it independently re-verifies every external claim against the actual source before writing anything to REVIEW.md, so a lane's evidence is corroborating input, never a second output schema.

Research Module (src/research-{store,provider}.cts, src/package-legitimacy.cts)

The Research Module implements an L2-hybrid seam: code owns the cache, provider policy, and package legitimacy verdicts; MCP owns the actual network fetch.

Three compiled modules (generated to gsd-core/bin/lib/*.cjs per ADR-457) are reachable via gsd-tools query research-plan | research-store | package-legitimacy:

• Research Store — content-addressed cache (sha256(ecosystem+library+version+query+kind)) with per-source TTL (curated-doc: 30 d, medium: 7 d, web/synthesis: 1 d) and two storage tiers: ~/.gsd/research-cache for cross-project curated-doc hits, .planning/research/.cache for project-local web/synthesis results.
• Research Provider — single PROVIDER_WATERFALL (Context7→Ref→Jina→websearch for docs; Exa→Tavily→Perplexity→Brave→websearch for web; Firecrawl→Jina for scrape-only). planResearch() returns cache hits plus a fetch plan; classifyConfidence() stamps HIGH|MEDIUM|LOW by provider tier.
• Package Legitimacy — registry-API verdicts (npm/PyPI/crates.io injectable adapters) producing OK|SUS|SLOP per package. slopcheck is an optional escalate-only adapter; absence leaves registry verdicts intact rather than downgrading everything to [ASSUMED].

Data flow:

agent
  │
  ▼
gsd-tools query research-plan          ← Research Provider: check cache, build fetch plan
  │
  ├── [cache hits] ──────────────────► RESEARCH.md (digest only, no raw content)
  │
  └── [fetch plan] ──────────────────► MCP fetch (agent calls MCP tools with the plan)
                                          │
                                          ▼
                                    gsd-tools query research-store (put)
                                          │
                                          ▼
                                    RESEARCH.md path returned to orchestrator

Agents always return a RESEARCH.md path, never raw fetched content. Context discipline is enforced through subagent isolation, compact provider output, and fetch-to-disk. See ADR-0656.

Context Predicate Fact-Store (src/context-predicates.cts, ADR-1671)

The CONTEXT.md predicate fact-store — every backtick-wrapped CLASS.subkey=value declaration in the repo-root CONTEXT.md — has a compiled parser/selector seam (generated to gsd-core/bin/lib/context-predicates.cjs per ADR-457) reachable live via gsd-tools query context-predicates --class|--prefix|--contains. Fence-aware line skipping mirrors markdown-sectionizer.cts's exported scanFencedBlocks delimiter-matching rule exactly (proven by a fence-skip parity test suite), but is scanned by a LOCAL, interleaved single pass rather than a call into that seam directly: fences and HTML comments must mutually suppress each other's open/close detection while either is active (a fence delimiter inside a real comment, or a comment token inside a real fence, must not falsely toggle the other construct), and that precedence cannot be resolved by two independent passes over scanFencedBlocks's comment-blind output — see src/context-predicates.cts's module doc comment.

scripts/gen-context-index.cjs --check is the CI drift-guard for the committed docs/CONTEXT-INDEX.json artifact: it fails on staleness between a fresh parse of CONTEXT.md and the committed file, and on any duplicate predicate ID. It is wired into lint:generated-sync (so lint:ci, so CI). docs/CONTEXT-INDEX.json is generated — never hand-edit it; regenerate with gen-context-index.cjs --write (also wired into build, after build:lib, and into regen:derived). The generator require()s the compiled context-predicates.cjs, so it must run after build:lib in any pipeline; .github/workflows/test.yml does this.

The committed index intentionally carries no line field for any predicate (ADR-1671 open question 4, resolved by #2928) — committed-but-uncompared metadata goes silently stale, the same defect class the drift-guard exists to catch, with the alarm removed. The live gsd-tools query context-predicates parse still returns line/section for callers that want to cite a source location. See ADR-1671 and CLI Tools Reference.

Workflow Fragmentization and Emission (src/workflow-fragments.cts, ADR-1671)

Workflow markdown under gsd-core/workflows/*.md can mark one or more sections with an in-file <!-- gsd:section id="<id>" when="<when>" --> / <!-- /gsd:section --> pair. A compiled parser/composer seam (generated to gsd-core/bin/lib/workflow-fragments.cjs per ADR-457) partitions a marked document into fragments and recomposes them through the shared context-composer.cjs budget seam (ADR-1671, #2929) before any per-runtime converter sees the text — so a marker attribute can never be corrupted by a .claude/ → .windsurf/-style path-rewrite regex. bin/install.js's copyWithPathReplacement calls composeWorkflow on every workflow file at emit time; an unmarked file (88 of the 89 shipped workflows today) parses to a single implicit fragment and round-trips byte-identical, so this is a no-op for every workflow that hasn't opted in yet.

Every fragment in this phase carries the verbatim strategy, so composition is structurally non-lossy — nothing is trimmed regardless of budget. Fence and HTML-comment interleaving reuses the same LOCAL, single-pass, mutually-suppressing scan discipline as context-predicates.cts (see above), so a marker-shaped line inside a fenced code block or an unrelated comment is never misread as structural. Markers are stripped at emit — the installed artifact carries no build metadata and is smaller than the source by exactly the stripped marker bytes.

See Reference: Workflow fragments for the full marker grammar, the frozen when= vocabulary, and fail-closed authoring rules, and ADR-1671 (open questions 1 and 2) for why in-file markers were chosen over separate fragment files or a sidecar manifest.

Section Manifest (src/section-manifest.cts, ADR-1671 Phases 5 and 6.1)

Two seams turn a workflow's gsd:section markers into per-invocation applicability data. scripts/gen-section-manifest.cjs --write (wired into build after build:lib, and into lint:generated-sync) scans gsd-core/workflows/*.md and writes the committed gsd-core/workflows/section-manifest.json, keyed per workflow — {workflows: {"<name>": [{id, when, read}]}} — where read is the path of the step file the section's body was extracted to. A workflow with no marked sections contributes no key at all: an absent key means degraded/unknown (the caller reads every section, the safe superset), while a key present with an empty array means "computed, nothing applies". The generator reuses parseWorkflowSections unchanged rather than re-implementing marker parsing, and fails closed (--check) on a marker naming a step file that does not exist, a step file no marker references, or a committed artifact still carrying the pre-6.1 flat {sections: [...]} shape.

A separate pure evaluator, src/section-manifest.cts (compiled to gsd-core/bin/lib/section-manifest.cjs per ADR-457), maps one invocation's facts — {flags, phaseNumber, hasPriorPhases} plus the optional needsCodebaseMap, phaseMvpMode and worktreesEnabled booleans — to an included/excluded partition of section ids via selectSections. flags is a ReadonlySet<string> of flag tokens; because parseNamedArgs always materializes a boolean flag key (false when the token was absent, never undefined), presence is truthiness, and the init router folds a boolean flag's own false into the absent sentinel before the facts are built. Per Greenspun's Tenth Rule, the evaluator is a total lookup over the frozen 14-atom when= vocabulary, never a parser: WHEN_PREDICATES is a hand-written literal map that never derives a predicate from its atom string, and an unrecognized value fails closed rather than being silently excluded. An atom is admitted only when it has both a real consuming section and a fact the init seam actually computes — an atom without the latter would evaluate false forever and silently disable its own section.

execute-phase.md's partial-wave and gap-closure-artifacts sections — previously inlined directly per #2930's pilot — now delegate to dedicated step files under gsd-core/workflows/execute-phase/steps/, the same pattern the pre-existing regression-gate section already used.

CLI Tools (gsd-core/bin/)

Node.js CLI utility (gsd-tools.cjs) with domain modules split across gsd-core/bin/lib/ (see docs/INVENTORY.md for the authoritative roster):

Module	Responsibility
config-loader.cjs	Project config loading — defaults merge, legacy-key migration, workstream overlay, unknown-key/profile-override validation, and federated config overlay (ADR-857 phase 3b) (extracted from core.cjs, ADR-857)
federated-config.cjs	Defensive merge of capability-declared config slices (ADR-857 phase 3b); exports mergeFederatedConfig; live for migrated Capability keys that are absent from the central config schema
core-utils.cjs	Shared low-level utility primitives — POSIX path normalization, sub-repo/subdirectory scanning, phase file stats, slug/one-liner/plan-id helpers, time-ago (extracted from core.cjs, ADR-857)
core.cjs	Shared utilities; compatibility re-exports for planning, I/O (io.cjs), and phase-id helpers
io.cjs	CLI I/O primitives — output/error emission, JSON-error mode, large-payload temp-file spillover
phase-id.cjs	Pure phase-id parsing/matching helpers — normalize, token match, regex builders (extracted from core.cjs, ADR-857)
phase-locator.cjs	Phase-directory search and location — active-phase discovery (searchPhaseInDir, findPhaseInternal) and archived-phase-dir enumeration (getArchivedPhaseDirs), matching phase ids/tokens against the filesystem (extracted from core.cjs, ADR-857)
roadmap-parser.cjs	ROADMAP.md parsing — milestone slicing, current-milestone extraction, phase/milestone lookups, milestone-phase filter (extracted from core.cjs, ADR-857)
planning-workspace.cjs	Planning seam (planningDir, planningPaths, active workstream routing, .planning/.lock)
state.cjs	STATE.md parsing, updating, progression, metrics
phase.cjs	Phase directory operations, decimal numbering, plan indexing
roadmap.cjs	ROADMAP.md parsing, phase extraction, plan progress
config.cjs	config.json read/write, section initialization
verify.cjs	Plan structure, phase completeness, reference, commit validation
template.cjs	Template selection and filling with variable substitution
frontmatter.cjs	YAML frontmatter CRUD operations
init.cjs	Compound context loading for each workflow type
milestone.cjs	Milestone archival, requirements marking
commands.cjs	Misc commands (slug, timestamp, todos, scaffolding, stats)
model-profiles.cjs	Model profile resolution table
model-resolver.cjs	Model and effort resolution policy — resolves model, tier, granularity, effort, and fast-mode for a given agent from project config and model profiles/catalog (extracted from core.cjs, ADR-857)
security.cjs	Path traversal prevention, prompt injection detection, safe JSON parsing, shell argument validation
uat.cjs	UAT file parsing, verification debt tracking, audit-uat support
docs.cjs	Docs-update workflow init, Markdown scanning, monorepo detection
workstream.cjs	Workstream CRUD, migration, session-scoped active pointer
schema-detect.cjs	Schema-drift detection for ORM patterns (Prisma, Drizzle, etc.)
profile-pipeline.cjs	User behavioral profiling data pipeline, session file scanning
profile-output.cjs	Profile rendering, USER-PROFILE.md and dev-preferences.md generation
context-predicates.cjs	CONTEXT.md predicate fact-store parser/selector (ADR-1671, #2928); backs query context-predicates and scripts/gen-context-index.cjs's docs/CONTEXT-INDEX.json drift guard; compiled from src/context-predicates.cts
loop-host-contract.cjs	Generated Loop Host Contract — 12 loop points, per-step agent roles, and core artifacts; emitted by scripts/gen-loop-host-contract.cjs from workflow markers (ADR-894 §3); consumed by gen-capability-registry.cjs
capability-loader.cjs	Runtime registry overlay loader (ADR-1244 D2) — loadRegistry({ includeInstalled }) composes the frozen first-party registry with a validated installed overlay of third-party capability manifests read from global $GSD_HOME/.gsd/capabilities/ and project <projectRoot>/.gsd/capabilities/; first-party always wins; load-time engines.gsd re-gate skips incompatible overlays with a warning; gate-kind hooks on skipped capabilities fail OPEN — no gate is injected; a loud warning (stderr + envelope warnings) names the load failure and the gsd capability remove <id> remediation (#2009)
capability-registry.cjs	Generated central Capability Registry — role-partitioned index of all co-located capability declarations; emitted by scripts/gen-capability-registry.cjs (ADR-894 §5)
loop-resolver.cjs	Loop Extension Point resolver — ADR-857 phase 3c registry-consuming query; consumes resolved Capability State, filters byLoopPoint by capability enablement plus config activation, renders active hooks as markdown, emits { point, activeHooks, rendered } envelope; gsd-tools loop render-hooks <point> [--config-dir <path>]
capability-state.cjs	Unified capability-state resolver — ADR-857 phase 4b/6; composes install profile, runtime surface, and config activation into one per-capability view consumed by workflow hook rendering; pure resolveCapabilityState, reusable resolveCapabilityRuntimeState, I/O cmdCapabilityState, and convenience predicate isCapabilityActive(capId, cwd); gsd-tools capability state [--config-dir <path>] emits { runtimeConfigDir, capabilities[] } where each entry carries enabled (installed && surfaced) and active (enabled && configActivation via the capability's activationKey; absent key → active===enabled)
capability-validator.cjs	Shared capability conformance validator (ADR-1244 D2) — extracted from scripts/gen-capability-registry.cjs so the build-time generator and the runtime overlay loader share one validateCapability(manifest) implementation; generative-parity is CI-guarded
graphify-command-router.cjs	ADR-959 capability command router — first real capability command cutover (phase 4d-impl-2); extracted from the case 'graphify': arm in gsd-tools.cjs; dispatches build/query/status/diff subcommands; discovered via commandFamilies in the capability registry
audit-command-router.cjs	ADR-959 capability command router (phase 4d-impl-3); extracted from the case 'audit-uat': and case 'audit-open': arms in gsd-tools.cjs; routeAuditUat → uat.cjs:cmdAuditUat, routeAuditOpen → audit.cjs:{auditOpenArtifacts,formatAuditReport}; discovered via commandFamilies in the capability registry
intel-command-router.cjs	ADR-959 capability command router (phase 4d-impl-4, last first-party cutover); extracted from the case 'intel': arm in gsd-tools.cjs; routeIntelCommand → all 9 intel subcommands via lazy require('./intel.cjs'); preserves non-raw timeAgo transform on status.files[*].updated_at; discovered via commandFamilies in the capability registry
runtime-hooks-surface.cjs	Hook-surface writer and configured-entrypoint validation module (ADR-857 phase 5f-1); owns Cline rules/agents-md/pre-tool-use hook generation, Cursor/Windsurf hooks.json, Kimi hook TOML, Copilot session-hook config, Codex hook-block management, and construction-time records for paths emitted into runtime configuration. Installer success requires those records to pass non-executing file-type and interpreter-resolution checks.

---

Agent Model

Orchestrator → Agent Pattern

Orchestrator (workflow .md)
    │
    ├── Load context: gsd-tools.cjs init <workflow> <phase>
    │   Returns JSON with: project info, config, state, phase details
    │
    ├── Resolve model: gsd-tools.cjs resolve-model <agent-name>
    │   Returns: opus | sonnet | haiku | inherit
    │
    ├── Spawn Agent (Task/SubAgent call)
    │   ├── Agent prompt (agents/*.md)
    │   ├── Context payload (init JSON)
    │   ├── Model assignment
    │   └── Tool permissions
    │
    ├── Collect result
    │
    └── Update state: gsd-tools.cjs state update / state patch / state advance-plan

Primary Agent Spawn Categories

Conceptual spawn-pattern taxonomy for the primary agents. For the authoritative agent roster (including the advanced/specialized agents such as gsd-pattern-mapper, gsd-code-reviewer, gsd-code-fixer, gsd-ai-researcher, gsd-domain-researcher, gsd-eval-planner, gsd-eval-auditor, gsd-framework-selector, gsd-debug-session-manager, gsd-intel-updater), see docs/INVENTORY.md.

Category	Agents	Parallelism
Researchers	gsd-project-researcher, gsd-phase-researcher, gsd-ui-researcher, gsd-advisor-researcher	4 parallel (stack, features, architecture, pitfalls); advisor spawns during discuss-phase
Synthesizers	gsd-research-synthesizer	Sequential (after researchers complete)
Planners	gsd-planner, gsd-roadmapper	Sequential
Checkers	gsd-plan-checker, gsd-integration-checker, gsd-ui-checker, gsd-nyquist-auditor	Sequential (verification loop, max 3 iterations)
Executors	gsd-executor	Parallel within waves, sequential across waves
Verifiers	gsd-verifier	Sequential (after all executors complete)
Mappers	gsd-codebase-mapper	4 parallel (tech, arch, quality, concerns)
Debuggers	gsd-debugger	Sequential (interactive)
Auditors	gsd-ui-auditor, gsd-security-auditor	Sequential
Doc Writers	gsd-doc-writer, gsd-doc-verifier	Sequential (writer then verifier)
Profilers	gsd-user-profiler	Sequential
Analyzers	gsd-assumptions-analyzer	Sequential (during discuss-phase)

Wave Execution Model

During execute-phase, plans are grouped into dependency waves:

Wave Analysis:
  Plan 01 (no deps)      ─┐
  Plan 02 (no deps)      ─┤── Wave 1 (parallel)
  Plan 03 (depends: 01)  ─┤── Wave 2 (waits for Wave 1)
  Plan 04 (depends: 02)  ─┘
  Plan 05 (depends: 03,04) ── Wave 3 (waits for Wave 2)

Each executor gets:

• Fresh 200K context window (or up to 1M for models that support it)
• The specific PLAN.md to execute
• Project context (PROJECT.md, STATE.md)
• Phase context (CONTEXT.md, RESEARCH.md if available)

Adaptive Context Enrichment (1M Models)

When the context window is 500K+ tokens (1M-class models like Opus 4.6, Sonnet 4.6), subagent prompts are automatically enriched with additional context that would not fit in standard 200K windows:

• Executor agents receive prior wave SUMMARY.md files and the phase CONTEXT.md/RESEARCH.md, enabling cross-plan awareness within a phase
• Verifier agents receive all PLAN.md, SUMMARY.md, CONTEXT.md files plus REQUIREMENTS.md, enabling history-aware verification

The orchestrator reads context_window from config (gsd-tools.cjs config-get context_window) and conditionally includes richer context when the value is >= 500,000. For standard 200K windows, prompts use truncated versions with cache-friendly ordering to maximize context efficiency.

Parallel Commit Safety

When multiple executors run within the same wave, two mechanisms prevent conflicts:

1. --no-verify commits — Parallel agents skip pre-commit hooks (which can cause build lock contention, e.g., cargo lock fights in Rust projects). The orchestrator runs git hook run pre-commit once after each wave completes.
2. STATE.md file locking — All writeStateMd() calls use lockfile-based mutual exclusion (STATE.md.lock with O_EXCL atomic creation). This prevents the read-modify-write race condition where two agents read STATE.md, modify different fields, and the last writer overwrites the other's changes. Includes stale lock detection (10s timeout) and spin-wait with jitter.

The STATE.md Write Path

Locking decides who writes. A separate contract decides what survives the write.

STATE.md carries the same fact in two places — YAML frontmatter and the document body — and the body is authoritative. Every write therefore re-derives frontmatter from the body, which raises the question the write path exists to answer: when a re-derived value disagrees with the one already in frontmatter, which wins?

FIELD_CLASSIFICATION (src/state-transition.cts) answers it per field, declaring a preservation policy — preserve-when-unchanged, preserve-always, preserve-if-placeholder, derive — that applyStatePreservation executes after syncStateFrontmatter re-derives. (A fifth policy, clear, was listed here until ADR-3408 §8.6's amendment removed it: no row used it and no executor existed for it.)

The pipeline's precondition is a type, not a convention (ADR-3473 §8.6). A policy row can only be honored if the pre-write frontmatter snapshot it compares against is actually present. That snapshot now travels as a StateTransaction, built by openStateTransaction() — preservation applies — or rebuildStateTransaction() — it does not. Both carry the snapshot, and a transaction cannot be constructed without one: an absent snapshot is a construction failure, not a runtime skip. That distinction is the whole point. Previously the snapshot was nulled to signal "re-derive from disk", so a declared preserve-always row and a silently-skipped one were indistinguishable at runtime, which is how a curated progress: block was erased by verbs that had nothing to do with progress.

rebuildStateTransaction() is the typed form of ADR-3408 §8.3's closed exception list: state sync, which exists to let the body win, and /gsd-health --repair's factory reset. Both are deliberate and permanent, not debt — and because the type names them, the write-path drift guard no longer has to track them as strings in a ratcheted baseline.

What a command reports it wrote is the same snapshot, read back (ADR-3473 §8.7). Every state.* command returns an updated array. That array is now derived by comparing what was actually persisted against the transaction's pre-write snapshot: a field appears if, and only if, its persisted value changed. One comparison answers both of the questions that used to need separate machinery — a field the caller asked for that the pipeline then discarded is persisted-equals-snapshot and drops out, and a field nobody asked for that the write moved anyway is different and appears. Nothing is filtered by its preservation policy.

Reporting is at leaf granularity: when a single counter moves you are told progress.total_plans, not progress. The leaves are the ones the field-classification table already declares, so the report is bounded by a schema rather than by walking the document.

One field is excluded, and it is excluded for its provenance rather than its policy: last_updated is stamped on every save regardless of what you changed, so admitting it would make state patch's success signal — which is simply whether updated is non-empty — permanently true, and a patch in which every field failed would report success. state_head is deliberately not excluded: it is recomputed on every save but only changes when the commit it records actually moved, so reporting it tells you something true.

A practical consequence worth knowing: these arrays are now longer than they used to be, because they used to under-report. If you compare one exactly, expect more entries — and expect them to be the ones that really changed.

ADR-3408 is the normative contract for that path: one executor per declared policy, one write seam, and reports computed from what was actually persisted rather than from what the caller intended to write. Where the contract and the code disagree, the code is the defect. It is the write-side counterpart of ADR-3180, which gave each read-side derivation a single owner.

ADR-3473 owns the invariants that sit outside that contract. ADR-3408 governs what survives a write; it does not govern the pipeline's precondition, what a command reports it wrote, or where the set of STATE.md keys, types and enums is declared. ADR-3473 owns those, alongside document parsing, enumeration, and the return contract of every routine that can fail. It is the third application of ADR-3180's mechanism and the first whose success metric requires the guard surface to shrink as each seam lands.

---

Data Flow

New Project Flow

User input (idea description)
    │
    ▼
Questions (questioning.md philosophy)
    │
    ▼
4x Project Researchers (parallel)
    ├── Stack → STACK.md
    ├── Features → FEATURES.md
    ├── Architecture → ARCHITECTURE.md
    └── Pitfalls → PITFALLS.md
    │
    ▼
Research Synthesizer → SUMMARY.md
    │
    ▼
Requirements extraction → REQUIREMENTS.md
    │
    ▼
Roadmapper → ROADMAP.md
    │
    ▼
User approval → STATE.md initialized

Phase Execution Flow

discuss-phase → CONTEXT.md (user preferences)
    │
    ▼
ui-phase → UI-SPEC.md (design contract, optional)
    │
    ▼
plan-phase
    ├── Research gate (blocks if RESEARCH.md has unresolved open questions)
    ├── Phase Researcher → RESEARCH.md
    │       └── Package Legitimacy Gate: registry-API verdict on every package; [SLOP] removed,
    │           [SUS]/[ASSUMED] flagged; Audit table written to RESEARCH.md
    ├── Planner (with reachability check) → PLAN.md files
    │       └── checkpoint:human-verify injected before [ASSUMED]/[SUS] installs;
    │           T-{phase}-SC STRIDE row added for install-bearing plans
    ├── Plan Checker → Verify loop (max 3x)
    ├── Requirements coverage gate (REQ-IDs → plans)
    └── Decision coverage gate (CONTEXT.md `<decisions>` → plans, BLOCKING — #2492)
    │
    ▼
state planned-phase → STATE.md (Planned/Ready to execute)
    │
    ▼
execute-phase (context reduction: truncated prompts, cache-friendly ordering)
    ├── Wave analysis (dependency grouping)
    ├── Executor per plan → code + atomic commits
    ├── SUMMARY.md per plan
    └── Verifier → VERIFICATION.md
        └── Decision coverage gate (CONTEXT.md decisions → shipped artifacts, NON-BLOCKING — #2492)
    │
    ▼
verify-work → UAT.md (user acceptance testing)
    │
    ▼
ui-review → UI-REVIEW.md (visual audit, optional)

Context Propagation

Each workflow stage produces artifacts that feed into subsequent stages:

PROJECT.md ────────────────────────────────────────────► All agents
REQUIREMENTS.md ───────────────────────────────────────► Planner, Verifier, Auditor
ROADMAP.md ────────────────────────────────────────────► Orchestrators
STATE.md ──────────────────────────────────────────────► All agents (decisions, blockers)
CONTEXT.md (per phase) ────────────────────────────────► Researcher, Planner, Executor
RESEARCH.md (per phase) ───────────────────────────────► Planner, Plan Checker
PLAN.md (per plan) ────────────────────────────────────► Executor, Plan Checker
SUMMARY.md (per plan) ─────────────────────────────────► Verifier, State tracking
UI-SPEC.md (per phase) ────────────────────────────────► Executor, UI Auditor

---

File System Layout

Installation Files

~/.claude/                          # Claude Code (global install)
├── skills/gsd-ns-*/SKILL.md        # Global skills — nesting runtimes: 6 namespace routers (authoritative roster: docs/INVENTORY.md)
│   └── skills/<name>/SKILL.md     #   concrete skills nested under each router
│   (flat runtimes: skills/gsd-*/SKILL.md — all ~67 skills at top level)
├── commands/gsd/*.md               # Local Claude installs use slash commands instead of global skills
├── gsd-core/
│   ├── bin/gsd-tools.cjs           # CLI utility
│   ├── bin/lib/*.cjs               # Domain modules (authoritative roster: docs/INVENTORY.md)
│   ├── workflows/*.md              # Workflow definitions (authoritative roster: docs/INVENTORY.md)
│   ├── references/*.md             # Shared reference docs (authoritative roster: docs/INVENTORY.md)
│   └── templates/                  # Planning artifact templates
├── agents/*.md                     # Agent definitions (authoritative roster: docs/INVENTORY.md)
├── hooks/*.js                      # Node.js hooks (statusline, guards, monitors, update check)
├── hooks/*.sh                      # Shell hooks (session state, commit validation, phase boundary)
├── settings.json                   # Hook registrations
└── VERSION                         # Installed version number

Equivalent paths for other runtimes:

• OpenCode: ~/.config/opencode/ global or ./.opencode/ local
• Kilo: ~/.config/kilo/ global or ./.kilo/ local
• Kimi CLI: first-existing generic global root (~/.config/agents/ recommended, then ~/.agents/ if its skills/ directory already exists); local install is deferred and guarded
• Codex: ~/.codex/ global or ./.codex/ local
• Copilot: ~/.copilot/ global or ./.github/ local
• Antigravity: auto-detected global root (~/.gemini/antigravity/, ~/.gemini/antigravity-ide/, or ~/.gemini/antigravity-cli/) for settings and runtime files; global skills/agents under ~/.gemini/config/ (the machine-local discovery dir, #3738) or ./.agent/ local
• Cursor: ~/.cursor/ global or ./.cursor/ local
• Windsurf/Devin Desktop: ~/.codeium/windsurf/ global config or ./.windsurf/ local workflows
• Augment Code: ~/.augment/ global or ./.augment/ local
• Trae: ~/.trae/ global or ./.trae/ local
• Qwen Code: ~/.qwen/ global or ./.qwen/ local
• Hermes Agent: ~/.hermes/ global or ./.hermes/ local
• CodeBuddy: ~/.codebuddy/ global or ./.codebuddy/ local
• Cline: ~/.cline/ global or project-root .clinerules local

Project Files (.planning/)

.planning/
├── PROJECT.md              # Project vision, constraints, decisions, evolution rules
├── REQUIREMENTS.md         # Scoped requirements (v1/v2/out-of-scope)
├── ROADMAP.md              # Phase breakdown with status tracking
├── STATE.md                # Living memory: position, decisions, blockers, metrics
├── config.json             # Workflow configuration
├── MILESTONES.md           # Completed milestone archive
├── research/               # Domain research from /gsd-new-project
│   ├── SUMMARY.md
│   ├── STACK.md
│   ├── FEATURES.md
│   ├── ARCHITECTURE.md
│   └── PITFALLS.md
├── codebase/               # Brownfield mapping (from /gsd-map-codebase or /gsd-onboard)
├── onboarding/             # Brownfield onboarding summary (from /gsd-onboard)
│   ├── STACK.md            # YAML frontmatter carries `last_mapped_commit`
│   ├── ARCHITECTURE.md     # for the post-execute drift gate (#2003)
│   ├── CONVENTIONS.md
│   ├── CONCERNS.md
│   ├── STRUCTURE.md
│   ├── TESTING.md
│   └── INTEGRATIONS.md
├── phases/
│   └── XX-phase-name/
│       ├── XX-CONTEXT.md       # User preferences (from discuss-phase)
│       ├── XX-RESEARCH.md      # Ecosystem research (from plan-phase)
│       ├── XX-YY-PLAN.md       # Execution plans
│       ├── XX-YY-SUMMARY.md    # Execution outcomes
│       ├── XX-VERIFICATION.md  # Post-execution verification
│       ├── XX-VALIDATION.md    # Nyquist test coverage mapping
│       ├── XX-UI-SPEC.md       # UI design contract (from ui-phase)
│       ├── XX-UI-REVIEW.md     # Visual audit scores (from ui-review)
│       └── XX-UAT.md           # User acceptance test results
├── quick/                  # Quick task tracking
│   └── YYMMDD-xxx-slug/
│       ├── PLAN.md
│       └── SUMMARY.md
├── todos/
│   ├── pending/            # Captured ideas
│   └── completed/          # Completed todos
├── threads/               # Persistent context threads (from /gsd-thread)
├── seeds/                 # Forward-looking ideas (from /gsd-capture --seed)
├── debug/                  # Active debug sessions
│   ├── *.md                # Active sessions
│   ├── resolved/           # Archived sessions
│   └── knowledge-base.md   # Persistent debug learnings
├── ui-reviews/             # Screenshots from /gsd-ui-review (gitignored)
└── continue-here.md        # Context handoff (from pause-work)

Post-Execute Codebase Drift Gate (#2003)

After the last wave of /gsd-execute-phase commits, the workflow runs a non-blocking codebase_drift_gate step (between schema_drift_gate and verify_phase_goal). It compares the diff last_mapped_commit..HEAD against .planning/codebase/STRUCTURE.md and counts four kinds of structural elements:

1. New directories outside mapped paths
2. New barrel exports at (packages|apps)/<name>/src/index.*
3. New migration files
4. New route modules under routes/ or api/

If the count meets workflow.drift_threshold (default 3), the gate either warns (default) with the suggested /gsd-map-codebase --paths … command, or auto-remaps (workflow.drift_action = auto-remap) by spawning gsd-codebase-mapper scoped to the affected paths. Any error in detection or remap is logged and the phase continues — drift detection cannot fail verification.

last_mapped_commit lives in YAML frontmatter at the top of each .planning/codebase/*.md file; bin/lib/drift.cjs provides readMappedCommit and writeMappedCommit round-trip helpers.

The baseline is written by gsd-tools stamp-codebase-map, a shell step in the map-codebase workflow, not by the mapper agent. The mapper's own freshness markers (**Analysis Date:**, <!-- refreshed: ... -->) are restamped unconditionally on an Update run, so an agent that rewrites only the dates still looks current to a reader; the machine-readable stamp is the one marker that cannot be satisfied by a date-only rewrite, which is exactly why it is not the agent's to write. --files a.md,b.md narrows the stamp to the documents a caller actually refreshed, as the auto-remap path does.

An absent or unresolvable baseline is reported as skipped with reason no-mapped-commit or unresolvable-mapped-commit, never as drift. Diffing HEAD against the empty tree would report every tracked file as newly added, which makes a stale map indistinguishable from a fresh one. Files under .planning/ are excluded from the diff: the map's own commit is a planning artifact, not codebase structure.

---

Installer Architecture

The installer (bin/install.js, ~10,700 lines) handles:

1. Runtime detection — Interactive prompt or CLI flags (--claude, --opencode, --kimi, --kilo, --codex, --copilot, --antigravity, --cursor, --windsurf, --augment, --trae, --qwen, --hermes, --codebuddy, --cline, --all)
2. Location selection — Global (--global) or local (--local)
3. File deployment — Copies commands, skills, workflows, references, templates, agents, and hooks
4. Runtime adaptation — Transforms file content per runtime:

• Claude Code: Uses as-is
• OpenCode: Converts commands/agents to OpenCode-compatible flat command + subagent format
• Kilo: Reuses the OpenCode conversion pipeline with Kilo config paths
• Codex: Generates TOML config + skills from commands
• Kimi CLI: Generates Agent Skills under skills/gsd-*/SKILL.md, custom agent YAML/prompt files, and explicit kimi_cli.tools.* module paths
• Copilot: Maps tool names (Read→read, Bash→execute, etc.)
• Antigravity: Skills-first with Google model equivalents; adjusts hook event names (AfterTool instead of PostToolUse)
• Cursor: Skills-first with Cursor rule references
• Windsurf: Skills-first with Windsurf rule references
• Trae: Skills-first install to ~/.trae / ./.trae with no settings.json or hook integration
• Qwen Code: Skills-first with Qwen-branded path and prompt rewrites
• Hermes Agent: Category-based skills under skills/gsd/
• CodeBuddy: Skills-first with CodeBuddy path and prompt rewrites
• Cline: Writes .clinerules for rule-based integration
• Augment Code: Skills-first with full skill conversion and config management

5. Path normalization — Replaces ~/.claude/ paths with runtime-specific paths
6. Settings integration — Registers hooks in runtime's settings.json
7. Patch backup — Since v1.17, backs up locally modified files to gsd-local-patches/ for /gsd-update --reapply
8. Manifest tracking — Writes gsd-file-manifest.json for clean uninstall. The manifest also records which runtime and which scope (global/local) wrote it, under a manifestVersion schema field, so a reader can answer "which surfaces are installed, at which scopes" without inferring it from the directory the file sits in (ADR 2866, #2872). Manifests written before that carry no such fields and are read without error — no reinstall is required. See Installer Migrations → File Manifest
9. Uninstall mode — --uninstall removes all GSD files, hooks, and settings

installRuntimeArtifacts (install-engine.cjs) returns the executed plan it ran — per kind, per scope, including on the combined OpenCode/Kilo family path, which previously early-returned void — rather than being observable only by re-reading disk afterward. Its destination-writing IO (copies, removals, snapshot/restore, best-effort cleanup) now routes through an injectable fs seam, install-fs-adapter.cjs, so a full install can be exercised against a fake adapter with zero real destination IO; locating this package's own source tree remains real by design (a destination-fake is never seeded with the repo's own paths). Writes stay byte-identical and existing void-ignoring callers are unaffected. This completes ADR 58's registry → adapter → helpers → cleanup rollout — the cleanup step had not previously landed (#2874, epic #2866 Phase 5).

Install-time file moves, stale-artifact cleanup, config rewrites, and user-data preservation are governed by the Installer Migration Module. See Installer Migrations and ADR 0008. The migration module also owns the gated first-time baseline scan for legacy installs, classifying known runtime install surfaces before later migrations remove or rewrite anything.

The plan drift guard (plan_review.source_grounding) — which verifies symbol references in generated plans against live source before execution — is specified in ADR 22.

The same switch gates a second, cross-artifact axis: a fact-drift pass that compares the same fact as stated in ROADMAP.md, PLAN.md, STATE.md and CONTEXT.md and reports contradictions (a phase status, a success criterion, a requirement ID, a glossary term) with both locations and the authoritative side named. Where the source-grounding axis grounds a plan against code, this one grounds the planning artifacts against each other. It keys on contradicting knowledge rather than similar-looking text, and is advisory only — it never sets hardBlock and never contributes to the convergence counts.

Platform Handling

• Windows: windowsHide on child processes, EPERM/EACCES protection on protected directories, path separator normalization
• WSL: Detects Windows Node.js running on WSL and warns about path mismatches
• Docker/CI: Supports CLAUDE_CONFIG_DIR env var for custom config directory locations

---

Hook System

Architecture

Runtime Engine (Claude Code / Antigravity CLI)
    │
    ├── statusLine event ──► gsd-statusline.js
    │   Reads: stdin (session JSON)
    │   Writes: stdout (formatted status), /tmp/claude-ctx-{session}.json (bridge)
    │
    ├── PostToolUse/AfterTool event ──► gsd-context-monitor.js
    │   Reads: stdin (tool event JSON), /tmp/claude-ctx-{session}.json (bridge)
    │   Writes: stdout (hookSpecificOutput with additionalContext warning)
    │
    └── SessionStart event
        ├──► gsd-ensure-canonical-path.js   (runs first)
        │    Reads:  ${CLAUDE_PLUGIN_ROOT}/gsd-core/ (plugin installs only)
        │    Writes: ~/.claude/gsd-core/{bin,contexts,references,templates,workflows} symlinks
        │            (no-op in classic installs; preserves user files; self-heals)
        └──► gsd-check-update.js
             Reads:  VERSION file
             Writes: ~/.claude/cache/gsd-update-check.json (spawns background process)

Context Monitor Thresholds

Remaining Context	Level	Agent Behavior
> 35%	Normal	No warning injected
≤ 35%	WARNING	"Avoid starting new complex work"
≤ 25%	CRITICAL	"Context nearly exhausted, inform user"

The two fire-points are defaults. hooks.context_warning_threshold and hooks.context_critical_threshold in .planning/config.json move them per project; see context-monitor.md for the resolution and fallback rules.

Debounce: 5 tool uses between repeated warnings. Severity escalation (WARNING→CRITICAL) bypasses debounce.

Safety Properties

• All hooks wrap in try/catch, exit silently on error
• stdin timeout guard (3s) prevents hanging on pipe issues
• Stale metrics (>60s old) are ignored
• Missing bridge files handled gracefully (subagents, fresh sessions)
• Context monitor is advisory — never issues imperative commands that override user preferences

Package Legitimacy Gate (v1.42.1)

The researcher → planner → executor pipeline includes a supply-chain gate against slopsquatting (AI-hallucinated package names pre-registered with malicious post-install scripts).

Threat model: GSD automates the full path from "researcher names a package" to "executor runs npm install". A hallucinated name that passes npm view (proving only registration, not legitimacy) would previously flow through undetected. ~20% of AI-generated package references are hallucinated; ~43% of those names recur consistently across prompts, making pre-registration economically viable for attackers.

Gate layers:

Layer	Component	Action
Research	gsd-phase-researcher	Runs gsd-tools query package-legitimacy check --ecosystem <npm|pypi|crates> <pkgs>; writes ## Package Legitimacy Audit table to RESEARCH.md; strips [SLOP] packages before RESEARCH.md is written
Planning	gsd-planner	Reads Audit table; inserts checkpoint:human-verify before any [ASSUMED] or [SUS] install task; adds T-{phase}-SC STRIDE supply-chain row to <threat_model>
Execution	gsd-executor	RULE 3 excludes package installation from auto-fix scope; failed installs surface as checkpoints, never silent substitutions

Claim provenance integration: Package names discovered via WebSearch are tagged [ASSUMED] (not [VERIFIED]) regardless of the registry-API verdict. This extends the existing [ASSUMED] / [VERIFIED] / [CITED] provenance system by enforcing the provenance tag as a hard gate at the install boundary — [ASSUMED] always generates a checkpoint:human-verify in PLAN.md.

Ecosystem coverage: The gate resolves signals directly from each ecosystem's registry API rather than a single generic check — registry.npmjs.org + api.npmjs.org/downloads (Node), pypi.org/pypi/<pkg>/json (Python), the crates.io API (Rust). This catches cross-ecosystem hallucination (~9% rate documented in 2025 USENIX research).

Graceful degradation: Each registry adapter degrades to null signals (never throws) on a failed lookup; missing signals push a package to [SUS], which is gated behind the same checkpoint:human-verify checkpoint as [ASSUMED]. Research and planning proceed; the system never hard-fails on a network or tool outage. slopcheck is an optional escalate-only adapter — it can only raise a verdict, never lower it, and is not the install-or-degrade gate. No shipped configuration wires it.

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Security Hooks (v1.27)

For a conceptual overview of how the hook and guard layers fit into the broader security approach, see Security model.

Prompt Guard (gsd-prompt-guard.js):

• Triggers on Write/Edit to .planning/ files
• Scans content for prompt injection patterns (role override, instruction bypass, system tag injection)
• Advisory-only — logs detection, does not block
• Patterns are inlined (subset of security.cjs) for hook independence
• Output contract: hookSpecificOutput carries both additionalContext and findings — an array of { ruleId, match } records (INJECTION-PATTERN or INVISIBLE-UNICODE), module-local to this hook (not shared with gsd-read-injection-scanner.js's own RULE_IDS). The advisory is rendered from findings via a single mapper, so the two cannot disagree. Consumers should read findings rather than parsing the advisory text.

Read Injection Scanner (gsd-read-injection-scanner.js):

• Triggers on Read / WebFetch / WebSearch PostToolUse events
• Advisory by default; blocks only HIGH severity, and only when security.injection_blocking is true
• Severity is LOW for 1-2 matched patterns, HIGH for 3 or more
• Skips content shorter than 20 characters, and skips excluded paths (.planning/, REVIEW.md, CHECKPOINT*, security/injection docs, and GSD's own staged hook bundle)
• Rule ids: the MD-LINK-* markdown-link rules mirrored from security.cjs's MARKDOWN_LINK_PATTERNS, plus INJECTION-PATTERN, INVISIBLE-UNICODE, and UNICODE-TAG-BLOCK
• Patterns are shared with gsd-prompt-guard.js via hooks/lib/injection-patterns.js (#3504); the markdown-link list is inlined for hook independence
• Output contract: hookSpecificOutput carries additionalContext (the human-readable advisory sentence), findings — an array of { ruleId, match } records naming each rule that fired — plus severity (LOW for 1-2 matches, HIGH for 3+) and source (the scanned file path, URL, or search: <query> string). findings and severity are the structured surface; the advisory is rendered from them, so the three cannot disagree. match is null for rules with no captured text (INVISIBLE-UNICODE, UNICODE-TAG-BLOCK). Consumers should read findings/severity/source rather than parsing the advisory text.

Workflow Guard (gsd-workflow-guard.js):

• Triggers on Write/Edit to non-.planning/ files
• Detects edits outside GSD workflow context (no active /gsd- command or Task subagent)
• Advises using /gsd-quick or /gsd-fast for state-tracked changes
• Opt-in via hooks.workflow_guard: true (default: false)
• Output contract: the advisory leg's hookSpecificOutput carries code: 'WORKFLOW_ADVISORY' alongside additionalContext. This is distinct from the hook's separate force-add block leg (code: 'WORKTREE_AGENT_FORCE_ADD_FORBIDDEN', decision: 'block') — the two are disambiguated by code, never by presence.

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Runtime Abstraction

GSD supports multiple AI coding runtimes through a unified command/workflow architecture:

Runtime Install Contract Matrix

This matrix describes the runtime surfaces the installer materializes today. The migration-specific ownership and source snapshots live in Installer Migrations.

Runtime	Global root	Local root	Invocation surface	Agent surface	Config and hooks
Claude Code	~/.claude	./.claude	Global skills/gsd-*/SKILL.md (flat, #924); local commands/gsd/*.md	agents/gsd-*.md	settings.json hook and statusLine entries
OpenCode	~/.config/opencode	./.opencode	commands/gsd-*.md	agents/gsd-*.md	opencode.json or opencode.jsonc; no GSD hooks
Kilo	~/.config/kilo	./.kilo	command/gsd-*.md	agents/gsd-*.md	kilo.json or kilo.jsonc; no GSD hooks
Kimi CLI	First-existing generic root: ~/.config/agents recommended, then ~/.agents when ~/.agents/skills exists and ~/.config/agents/skills does not	Deferred and guarded	skills/gsd-*/SKILL.md (flat) invoked as /skill:gsd-*	agents/gsd.yaml, agents/gsd.md, and agents/subagents/gsd-* YAML/prompt pairs	Explicit kimi --agent-file <configRoot>/agents/gsd.yaml; no GSD hooks or statusline
Codex	~/.codex	./.codex	skills/gsd-*/SKILL.md (flat)	agents/ source markdown plus per-agent TOML (Codex auto-discovers each agents/gsd-*.toml; this is the sole canonical role registration, #2406)	config.toml bare [agents] dispatch-tuning scalar (max_depth, no per-role [agents.gsd-*] tables), [features].hooks (canonical; legacy alias codex_hooks is recognized and migrated forward on reinstall, #3566), and hook tables
GitHub Copilot	~/.copilot	./.github	skills/gsd-*/SKILL.md (flat), copilot-instructions.md, and AGENTS.md (repo root, local)	.agent.md files	Self-contained sessionStart hook (hooks/gsd-session.json, inline command type); no statusline
Antigravity	auto-detected: ~/.gemini/antigravity, ~/.gemini/antigravity-ide, or ~/.gemini/antigravity-cli	./.agent	~/.gemini/config/skills/gsd-*/SKILL.md (flat, #1614; global home override #3738)	~/.gemini/config/agents/gsd-*.md (#3738)	Gemini-style settings.json hook entries when installed by GSD
Cursor	~/.cursor	./.cursor	skills/gsd-*/SKILL.md (flat)	agents/gsd-*.md	Rule references under rules/; hooks.json with sessionStart context injection and postToolUse STATE.md monitor (#777)
Windsurf	~/.codeium/windsurf config	./.windsurf	workflows/gsd-*.md slash-command workflows	No custom-agent artifact surface	No GSD hooks
Augment Code	~/.augment	./.augment	skills/gsd-ns-*/SKILL.md (6 routers) + skills/gsd-ns-*/skills/<name>/SKILL.md (nested concretes)	agents/gsd-*.md	No GSD hooks or statusline
Trae	~/.trae	./.trae	skills/gsd-ns-*/SKILL.md (6 routers) + skills/gsd-ns-*/skills/<name>/SKILL.md (nested concretes)	agents/gsd-*.md	Rule references under rules/; no GSD hooks
Qwen Code	~/.qwen	./.qwen	skills/gsd-ns-*/SKILL.md (6 routers) + skills/gsd-ns-*/skills/<name>/SKILL.md (nested concretes)	agents/gsd-*.md	Common GSD settings and hook entries where supported
Hermes Agent	~/.hermes	./.hermes	skills/gsd/ns-*/SKILL.md (6 routers, prefix='') + skills/gsd/ns-*/skills/<name>/SKILL.md (nested concretes)	agents/gsd-*.md	Common GSD settings and hook entries where supported
CodeBuddy	~/.codebuddy	./.codebuddy	skills/gsd-*/SKILL.md (flat, user-invocable: false)	agents/gsd-*.md	/gsd-* slash commands under commands/; common GSD settings and hook entries where supported
Cline	~/.cline	project root	skills/gsd-ns-*/SKILL.md (6 routers) + skills/gsd-ns-*/skills/<name>/SKILL.md (nested concretes) + .clinerules	Rules only	No GSD hooks or statusline

Upstream Contract Sources

Runtime install expectations are checked against primary documentation where available. The current source snapshot is 2026-05-11, with Kimi CLI rechecked on 2026-06-07:

• Claude Code: Anthropic slash commands, settings, hooks, and subagents docs.
• OpenCode and Kilo: OpenCode config docs and Kilo custom subagent docs.
• Qwen Code: command/config docs; Qwen command docs were last updated 2026-05-06.
• Kimi CLI: Agent Skills docs for user-level brand roots and first-existing generic roots (~/.config/agents/skills/ recommended, then ~/.agents/skills/), plus Agents docs for YAML files, system_prompt_path, kimi_cli.tools.* module paths, and explicit kimi --agent-file launch.
• Codex: OpenAI Codex docs and config-schema.json; the installer also carries Codex 0.124.0 compatibility for agent table shape.
• Copilot, Cursor, Cline, Augment, Hermes, and CodeBuddy: vendor docs for custom instructions, rules, skills, or config.
• Antigravity, Windsurf, and Trae: source-limited rows. The installer documents current compatibility shims, and migrations must refresh those sources before rewriting their config.

Abstraction Points

1. Tool name mapping — Each runtime has its own tool names (e.g., Claude's Bash → Copilot's execute)
2. Hook event names — Claude uses PostToolUse, Antigravity uses AfterTool
3. Agent frontmatter — Each runtime has its own agent definition format
4. Path conventions — Each runtime stores config in different directories
5. Model references — inherit profile lets GSD defer to runtime's model selection

The installer handles all translation at install time. Workflows and agents are written in Claude Code's native format and transformed during deployment.

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Related

• Multi-agent orchestration
• Security model
• CLI tools
• docs index