msd-core/docs/CLI-TOOLS.md

GSD CLI Tools Reference

Reference for the gsd-tools CLI (gsd-core/bin/gsd-tools.cjs). For slash commands and user flows, see Command Reference. Return to docs index.

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Overview

gsd-tools.cjs centralizes config parsing, model resolution, phase lookup, git commits, summary verification, state management, and template operations across GSD commands, workflows, and agents.

Shipped path	gsd-core/bin/gsd-tools.cjs
Implementation	20 domain modules under gsd-core/bin/lib/ (the directory is authoritative)
Status	Primary runtime command surface for orchestration, workflows, and automation.

Usage (CJS):

node gsd-tools.cjs <command> [args] [--raw] [--cwd <path>]

Global flags (CJS):

Flag	Description
--raw	Machine-readable output (JSON or plain text, no formatting)
--cwd <path>	Override working directory (for sandboxed subagents)
--ws <name>	Workstream context for .planning/workstreams/<name> paths

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State Commands

Manage .planning/STATE.md — the project's living memory.

# Load full project config + state as JSON
node gsd-tools.cjs state load

# Output STATE.md frontmatter as JSON
node gsd-tools.cjs state json

# Update a single field
node gsd-tools.cjs state update <field> <value>

# Get STATE.md content or a specific section
node gsd-tools.cjs state get [section]

# Batch update multiple fields
node gsd-tools.cjs state patch --field1 val1 --field2 val2

# Increment plan counter
node gsd-tools.cjs state advance-plan

# Record execution metrics
node gsd-tools.cjs state record-metric --phase N --plan M --duration Xmin [--tasks N] [--files N]

# Recalculate progress bar
node gsd-tools.cjs state update-progress

# Add a decision
node gsd-tools.cjs state add-decision --summary "..." [--phase N] [--rationale "..."]
# Or from files:
node gsd-tools.cjs state add-decision --summary-file path [--rationale-file path]

# Add/resolve blockers
node gsd-tools.cjs state add-blocker --text "..."
node gsd-tools.cjs state resolve-blocker --text "..."

# Record session continuity
node gsd-tools.cjs state record-session --stopped-at "..." [--resume-file path]

# Phase start — update STATE.md Status/Last activity for a new phase
node gsd-tools.cjs state begin-phase --phase N --name SLUG --plans COUNT

# Agent-discoverable blocker signalling (used by discuss-phase / UI flows)
node gsd-tools.cjs state signal-waiting --type TYPE --question "..." --options "A|B" --phase P
node gsd-tools.cjs state signal-resume

State Snapshot

Structured parse of the full STATE.md:

node gsd-tools.cjs state-snapshot

Returns JSON with: current position, phase, plan, status, decisions, blockers, metrics, last activity.

Smart Entry

Read-only situation classifier used by /gsd-next.

node gsd-tools.cjs smart-entry          # Human summary + recommended route
node gsd-tools.cjs smart-entry --json   # Machine-readable result for workflows

The JSON result contains situation, recommended, summary, signals, and ordered actions[]. Detection reads .planning/STATE.md, ROADMAP.md, latest verification/summary artifacts, and git status; it does not write files or dispatch commands.

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Phase Commands

Manage phases — directories, numbering, and roadmap sync.

# Find phase directory by number
node gsd-tools.cjs find-phase <phase>

# Calculate next decimal phase number for insertions
node gsd-tools.cjs phase next-decimal <phase>

# Append new phase to roadmap + create directory
node gsd-tools.cjs phase add <description>

# Insert decimal phase after existing
node gsd-tools.cjs phase insert <after> <description>

# Remove phase, renumber subsequent
node gsd-tools.cjs phase remove <phase> [--force]

# Mark phase complete, update state + roadmap
# Also emits advisory `warnings[]` when a phase SUMMARY references a file that
# is not on disk — see "Phase SUMMARY artifact check" below.
node gsd-tools.cjs phase complete <phase>

# Evaluate HUMAN-UAT results for a phase (markdown-aware; ignores false-positive contexts)
# Returns JSON: { passed, uat_files[], verification_files[], checks[], blockers[], policy }
node gsd-tools.cjs phase uat-passed <phase> [--require-verification]

# Index plans with waves and status
node gsd-tools.cjs phase-plan-index <phase>

# List phases with filtering
node gsd-tools.cjs phases list [--type planned|executed|all] [--phase N] [--include-archived]

Phase SUMMARY artifact check

A phase SUMMARY.md asserts which files the phase created or modified. On phase complete, each SUMMARY in the phase is scanned for referenced file paths and any path that is not on disk is reported in the command's existing warnings[] array — the case where a summary reports work that never landed.

Advisory only. Findings never block completion; the completion gate is the phase's VERIFICATION.md status, which this does not touch. /gsd-execute-phase surfaces the warnings before advancing.

Scope and limits, so the output is not read as more than it is:

• Paths are recovered heuristically from the SUMMARY body — backticked paths and Created:/Modified:-style lines. Globs, URLs, bare hostnames, and paths resolving outside the project are skipped rather than reported.
• The key-files: frontmatter block is not read. Its YAML flow-sequence form (created: [a.ts, b.ts]) is not matched by the prose scan, so a summary whose only file claims live there produces no findings.
• Commit hashes in the SUMMARY are not resolved here. The pattern matches any hex-shaped token in prose, which is too loose to surface.

Every path the scan does recover is checked — there is no cap. The standalone verify-summary verb keeps its historical default of checking the first two.

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Roadmap Commands

Parse and update ROADMAP.md.

# Extract phase section from ROADMAP.md
node gsd-tools.cjs roadmap get-phase <phase>

# Full roadmap parse with disk status
node gsd-tools.cjs roadmap analyze

# Update progress table row from disk
node gsd-tools.cjs roadmap update-plan-progress <N>

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Config Commands

Read and write .planning/config.json.

# Initialize config.json with defaults
node gsd-tools.cjs config-ensure-section

# Set a config value (dot notation)
node gsd-tools.cjs config-set <key> <value>

# Get a config value
node gsd-tools.cjs config-get <key>

# Set model profile
node gsd-tools.cjs config-set-model-profile <profile>

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Capability Commands

The capability command family resolves and mutates capability state (ADR-857). One resolved state composes three substrates: the install profile (.gsd-profile), the runtime surface (.gsd-surface.json), and config gates (.planning/config.json workflow.*). enabled = installed && surfaced; a hook is active only when its capability is enabled and its config gate is on.

capability state

node gsd-tools.cjs capability state [--config-dir <path>] [--raw]

Resolves and prints every capability's installed, surfaced, enabled, and per-hook active state. Read-only. --config-dir selects the runtime config directory (defaults to the resolved Claude home). --raw emits JSON.

capability set

node gsd-tools.cjs capability set <id> [--on | --off] [--gate <key>=<true|false>]... [--config-dir <path>] [--runtime <name>] [--scope <global|project>] [--raw]

Mutates one capability, re-resolves, and reports the result. Two axes:

• --on / --off (aliases --enable / --disable): the capability on/off switch, applied through the runtime surface. --off unsurfaces the capability; the change is reversible and reclaims the surface budget. A capability that owns no skills has no surface footprint — use --gate for those.
• --gate <key>=<true|false> (repeatable): toggles one of the capability's own config keys (a hook gate) within an enabled capability.
• --runtime / --scope: materialise the surface change for that runtime's artifact layout.

After writing, the command re-resolves and prints two message classes to stderr: errors (non-zero exit) — unknown capability id, a --gate key the capability does not own, a non-boolean gate value, or --on for a capability whose skills are not in the install profile; warnings (exit 0) — --on/--off on a skill-less capability, or a capability left surfaced while every hook is gated off ("present but dead"). Exit status is non-zero only when a requested change could not be applied.

Examples:

# Turn the UI capability off
node gsd-tools.cjs capability set ui --off --config-dir ~/.claude

# Keep the capability on, gate one hook off
node gsd-tools.cjs capability set code-review --gate workflow.code_review=false

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Teams Status

query teams-status

node gsd-tools.cjs query teams-status [--active]

Read-only detector for claude-code's experimental agent-teams feature (issue #1355). Resolves the runtime via the canonical GSD_RUNTIME → config.runtime → 'claude' precedence, then checks CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS.

Default (no flags): prints a JSON object and exits 0:

{
  "active": false,
  "runtime": "claude",
  "env_present": false,
  "source": "off: flag absent"
}

Fields:

Field	Type	Description
active	boolean	true only when CLAUDE_CODE_EXPERIMENTAL_AGENT_TEAMS is strictly truthy ("1" or "true", case-insensitive) and the resolved runtime is "claude"
runtime	string	The resolved runtime name (e.g. "claude", "codex")
env_present	boolean	true when the env flag is set to a strictly-truthy value
source	string	One of: "on: env", "off: flag absent", "off: non-claude"

--active flag: exits 0 if active is true, exits 1 otherwise. Prints nothing. Useful in bash conditionals:

if gsd_run query teams-status --active >/dev/null 2>&1; then
  echo "agent-teams is on"
fi

This command is strictly read-only — no config writes, no disk mutation.

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query eval.score

node gsd-tools.cjs query eval.score --covered <N> --total <N> --infra <tooling>,<dataset>,<cicd>,<guardrails>,<tracing>

Deterministic scorer for eval-auditor results. Computes coverage, infrastructure, and overall scores from audited inputs. Called by gsd-eval-auditor in its calculate_scores step — agents must not recompute these values by hand.

Inputs:

Flag	Type	Description
--covered	integer	Number of eval dimensions scored COVERED
--total	integer	Total planned eval dimensions
--infra	string	Comma-separated list of 5 infra component statuses (order: tooling, dataset, cicd, guardrails, tracing); each value is ok, partial, or missing

Output JSON:

Field	Type	Description
coverage_score	number	covered / total × 100
infra_score	number	(sum of component weights) / 5 × 100 (ok=1, partial=0.5, missing=0)
overall_score	number	(coverage_score × 0.6) + (infra_score × 0.4)
verdict	string	PRODUCTION READY (80–100) / NEEDS WORK (60–<80) / SIGNIFICANT GAPS (40–<60) / NOT IMPLEMENTED (0–<40)

Example:

node gsd-tools.cjs query eval.score --covered 3 --total 5 --infra ok,partial,missing,ok,ok
# → {"coverage_score":60,"infra_score":70,"overall_score":64,"verdict":"NEEDS WORK"}

This command is strictly read-only — no config writes, no disk mutation.

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query context-predicates

node gsd-tools.cjs query context-predicates --class <CLASS> | --prefix <dotted.prefix> | --contains <text>

Selector surface for the CONTEXT.md predicate fact-store (ADR-1671, #2928). Parses the repo-root CONTEXT.md live on every call via the compiled context-predicates.cjs — it never reads the committed docs/CONTEXT-INDEX.json (that artifact is a CI drift-guard byproduct, not a query source, so it can never go stale relative to the live predicates it answers about).

Selectors (at least one required; when more than one is given they are ANDed together):

Flag	Type	Description
--class <CLASS>	string	Exact match on the predicate's class (the segment before the first .)
--prefix <dotted.prefix>	string	Match predicate ids starting with this dotted prefix
--contains <text>	string	Case-insensitive substring match against id + ' ' + value

Each flag also accepts the inline-assignment form (--contains=<text>), which is the escape hatch for a flag-shaped value the space-separated form cannot express — e.g. --contains=--dry-run to search for the literal substring --dry-run. The space-separated form (--contains --dry-run) always reads a following --... token as a missing value, by design.

Output JSON:

{
  "matched": 2,
  "predicates": [
    { "id": "RULESET.EXAMPLE", "klass": "RULESET", "value": "…", "line": 42, "section": "Glossary" }
  ]
}

Field	Type	Description
matched	number	Count of predicates satisfying all given selectors
predicates	array	Each entry is a live Predicate — id, klass, value, line (1-based source line), section (nearest enclosing heading)

This command is strictly read-only — no config writes, no disk mutation. See ADR-1671 and Architecture — CLI Tools.

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Model Resolution

# Get model for agent based on current profile
node gsd-tools.cjs resolve-model <agent-name>
# Raw output returns the selected model ID/tier.
# JSON output also includes profile and, when the active runtime supports it,
# reasoning_effort.

Agent names: gsd-planner, gsd-executor, gsd-phase-researcher, gsd-project-researcher, gsd-research-synthesizer, gsd-verifier, gsd-plan-checker, gsd-integration-checker, gsd-roadmapper, gsd-debugger, gsd-codebase-mapper, gsd-nyquist-auditor

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Verification Commands

Validate plans, phases, references, and commits.

# Verify SUMMARY.md file
node gsd-tools.cjs verify-summary <path> [--check-count N]

# Check PLAN.md structure + tasks
node gsd-tools.cjs verify plan-structure <file>

# Check all plans have summaries
node gsd-tools.cjs verify phase-completeness <phase>

# Check @-refs + paths resolve
node gsd-tools.cjs verify references <file>

# Batch verify commit hashes
node gsd-tools.cjs verify commits <hash1> [hash2] ...

# Check must_haves.artifacts
node gsd-tools.cjs verify artifacts <plan-file>

# Check must_haves.key_links
node gsd-tools.cjs verify key-links <plan-file>

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Validation Commands

Check project integrity.

# Check phase numbering, disk/roadmap sync
node gsd-tools.cjs validate consistency

# Check .planning/ integrity, optionally repair
node gsd-tools.cjs validate health [--repair]

# Probe context-window utilization for status-line / hook callers (v1.40.0)
node gsd-tools.cjs validate context

# Context utilization as typed JSON surface (#455)
node gsd-tools.cjs validate context --json

validate context emits a structured envelope with utilization, status (ok / warn / critical at the 60 % / 70 % thresholds), and a suggestion string. The same data backs /gsd-health --context. Pass --json to receive the typed IR directly (useful in scripts and test assertions).

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Template Commands

Template selection and filling.

# Select summary template based on granularity
node gsd-tools.cjs template select <type>

# Fill template with variables
node gsd-tools.cjs template fill <type> --phase N [--plan M] [--name "..."] [--type execute|tdd] [--wave N] [--fields '{json}']

Template types for fill: summary, plan, verification

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Frontmatter Commands

YAML frontmatter CRUD operations on any Markdown file.

# Extract frontmatter as JSON
node gsd-tools.cjs frontmatter get <file> [--field key]

# Update single field
node gsd-tools.cjs frontmatter set <file> --field key --value jsonVal

# Merge JSON into frontmatter
node gsd-tools.cjs frontmatter merge <file> --data '{json}'

# Validate required fields
node gsd-tools.cjs frontmatter validate <file> --schema plan|summary|verification

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Scaffold Commands

Create pre-structured files and directories.

# Create CONTEXT.md template
node gsd-tools.cjs scaffold context --phase N

# Create UAT.md template
node gsd-tools.cjs scaffold uat --phase N

# Create VERIFICATION.md template
node gsd-tools.cjs scaffold verification --phase N

# Create phase directory
node gsd-tools.cjs scaffold phase-dir --phase N --name "phase name"

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Init Commands (Compound Context Loading)

Load all context needed for a specific workflow in one call. Returns JSON with project info, config, state, and workflow-specific data. init onboard [--fast] [--text] reports brownfield signals, planning-doc candidates, codebase-map completeness, fast-map readiness, text-mode routing, partial planning state, and onboarding summary status for /gsd-onboard.

node gsd-tools.cjs init execute-phase <phase>
node gsd-tools.cjs init plan-phase <phase>
node gsd-tools.cjs init new-project
node gsd-tools.cjs init new-milestone
node gsd-tools.cjs init onboard [--fast] [--text]
node gsd-tools.cjs init quick <description>
node gsd-tools.cjs init resume
node gsd-tools.cjs init verify-work <phase>
node gsd-tools.cjs init phase-op <phase>
node gsd-tools.cjs init code-review <phase> [--fix]
node gsd-tools.cjs init review <phase>
node gsd-tools.cjs init discuss-phase-assumptions <phase> [--auto]
node gsd-tools.cjs init todos [area]
node gsd-tools.cjs init milestone-op
node gsd-tools.cjs init map-codebase
node gsd-tools.cjs init progress
node gsd-tools.cjs init manager
node gsd-tools.cjs init complete-milestone
node gsd-tools.cjs init autonomous [--converge] [--cross-ai]
node gsd-tools.cjs init docs-update
node gsd-tools.cjs init update [--next] [--rc]
node gsd-tools.cjs init transition

# Workstream-scoped init (`--ws` flag)
node gsd-tools.cjs init execute-phase <phase> --ws <name>
node gsd-tools.cjs init plan-phase <phase> --ws <name>

Large payload handling: When output exceeds ~50KB, the CLI writes to a temp file and returns @file:/tmp/gsd-init-XXXXX.json. Workflows check for the @file: prefix and read from disk:

INIT=$(node gsd-tools.cjs init execute-phase "1")
if [[ "$INIT" == @file:* ]]; then INIT=$(cat "${INIT#@file:}"); fi

---

Milestone Commands

# Archive milestone
node gsd-tools.cjs milestone complete <version> [--name <name>] [--no-archive-phases]

# Mark requirements as complete
node gsd-tools.cjs requirements mark-complete <ids>
# Accepts: REQ-01,REQ-02 or REQ-01 REQ-02 or [REQ-01, REQ-02]

---

Agent Skills

Emit the skill block for a given agent type.

# Emit raw XML skill block (default — safe for shell expansion)
node gsd-tools.cjs agent-skills <agent-type>

# Emit typed JSON surface (#455) — { agent_type, block, skills_count, warnings, configured, reason, source, degraded }
node gsd-tools.cjs agent-skills <agent-type> --json

The --json flag returns a typed IR object suitable for structured consumption and test assertions, while the default (no flag) preserves the raw XML output that workflow shell expansions rely on.

--json field reference (as of #1415, Resolution Provenance P2):

Field	Type	Description
agent_type	string	The agent type that was queried.
block	string	The <agent_skills> XML block, or "" when empty.
skills_count	number	Number of skill paths configured for this agent type.
warnings	string[]	Per-path warnings for skills that were skipped (missing SKILL.md, unsafe path, etc.). Empty when all configured paths resolved.
configured	boolean	true when the agent type appears in agent_skills in the config; false when the key is absent entirely.
reason	string	Resolution reason: "resolved" (block non-empty), "not_configured" (agent not in agent_skills — silent), "configured_empty" (configured but paths list is empty — emits stderr WARNING), "configured_unresolved" (configured with paths but all failed to resolve — emits stderr WARNING).
source	string	Config provenance: "root" (.planning/config.json), "workstream" (workstream-scoped config), "global-defaults" (~/.gsd/defaults.json), "builtin-defaults" (no project config).
degraded	boolean	true when a workstream was requested but its config.json was absent and the command fell back to root config; false otherwise.

The command anchors to the project root via findProjectRoot before loading config, so invoking it from a descendant subdirectory resolves the same config as the project root.

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Skill Manifest

Pre-compute and cache skill discovery for faster command loading.

# Generate skill manifest (writes to .claude/skill-manifest.json)
node gsd-tools.cjs skill-manifest

# Generate with custom output path
node gsd-tools.cjs skill-manifest --output <path>

Returns JSON mapping of all available GSD skills with their metadata (name, description, file path, argument hints). Used by the installer and session-start hooks to avoid repeated filesystem scans.

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Utility Commands

# Convert text to URL-safe slug
node gsd-tools.cjs generate-slug "Some Text Here"
# → some-text-here

# Get timestamp
node gsd-tools.cjs current-timestamp [full|date|filename]

# Count and list pending todos
node gsd-tools.cjs list-todos [area]

# List captured seeds (optionally filter by status: dormant|active|triggered)
node gsd-tools.cjs list-seeds [status]

# Check file/directory existence
node gsd-tools.cjs verify-path-exists <path>

# Append a row to STATE.md's "Quick Tasks Completed" table (schema-backed; #2133)
node gsd-tools.cjs quick-tasks-append --task "<description>"

# Aggregate all SUMMARY.md data
node gsd-tools.cjs history-digest

# Extract structured data from SUMMARY.md
node gsd-tools.cjs summary-extract <path> [--fields field1,field2]

# Project statistics
node gsd-tools.cjs stats [json|table]

# Progress rendering (human-readable)
node gsd-tools.cjs progress [json|table|bar]

# Progress as typed JSON surface (#455)
node gsd-tools.cjs progress --json

# Complete a todo
node gsd-tools.cjs todo complete <filename>

# UAT audit — scan all phases for unresolved items
node gsd-tools.cjs audit-uat

# Cross-artifact audit queue — scan `.planning/` for unresolved audit items
node gsd-tools.cjs audit-open [--json]

# Reverse-migrate a GSD-2 project into the current structure (backs `/gsd-import --from-gsd2`)
node gsd-tools.cjs from-gsd2 [--path <dir>] [--force] [--dry-run]

# Git commit with config checks
node gsd-tools.cjs commit <message> [--files f1 f2] [--amend] [--no-verify] [--respect-staged]

--no-verify: Skips pre-commit hooks. Used by parallel executor agents during wave-based execution to avoid build lock contention (e.g., cargo lock fights in Rust projects). The orchestrator runs hooks once after each wave completes. Do not use --no-verify during sequential execution — let hooks run normally. --files <paths> staging behaviour: by default, --files runs git add -- <path> for each named file before committing. This overwrites any per-hunk staging set up via git add -p. Pass --respect-staged to skip the git add step and commit only what is already in the index within the requested pathspec. If nothing is staged within that scope, the command returns { committed: false, reason: 'nothing staged' } without error. The trailing -- <paths> pathspec on the commit is applied under both modes, so files staged outside the --files scope are never included (#3061 invariant).

# Web search (requires Brave API key)
node gsd-tools.cjs websearch <query> [--limit N] [--freshness day|week|month]

---

Update Backup and Restore

The two halves of /gsd-update's user-added-file protection. detect-custom-files lists files that exist inside GSD-managed directories but are absent from gsd-file-manifest.json — the update workflow copies those into gsd-user-files-backup/ before the clean-install wipe. restore-custom-files puts them back afterwards.

# List user-added files the installer would destroy (JSON)
node gsd-tools.cjs detect-custom-files --config-dir <config-dir>

# Plan a restore — reports what would be restored, writes nothing
node gsd-tools.cjs restore-custom-files --config-dir <config-dir>

# Restore the eligible entries
node gsd-tools.cjs restore-custom-files --config-dir <config-dir> --apply

restore-custom-files emits one entry per backed-up file:

Field	Meaning
path	Path relative to the config dir — where the file came from and goes back to
outcome	eligible (plan mode) · restored · skipped_destination_managed · skipped_destination_exists · skipped_copy_failed · skipped_unsafe_path
warnings	Advisory {code, detail} findings from the compatibility pass; never blocks a restore

Warning codes: destination_managed, destination_exists, missing_referenced_path, missing_referenced_command, frontmatter_missing_field, write_failed.

The compatibility pass runs against the newly installed release, so it catches a backed-up skill that @-references a workflow the new version retired, invokes a /gsd: command that no longer exists, or is missing the name / description frontmatter its runtime needs.

Three things the restore never does: it never deletes the backup, it never overwrites a path the new release ships (skipped_destination_managed), and it never overwrites a different file already on disk (skipped_destination_exists). Symlinked backup entries are skipped outright rather than followed (skipped_unsafe_path). A single unwritable entry is reported and the remaining entries still restore.

---

Worktree Commands

Diagnose and configure the worktree fork base used by Claude Code's isolation="worktree" executor dispatch. These commands address the branch-divergence condition described in Fix the worktree base-mismatch (exit 42) error.

# Check whether the current HEAD has diverged from the worktree fork base.
# Returns JSON: { shouldDegrade, reason, message, headSha, forkRef, forkSha }
node gsd-tools.cjs worktree base-check

# Write worktree.baseRef:"head" into .claude/settings.local.json (no-clobber).
# Returns JSON: { changed, skipped, previous, baseRef, file }
node gsd-tools.cjs worktree set-baseref

worktree base-check reads worktree.baseRef from a three-layer cascade — .claude/settings.local.json, then .claude/settings.json, then the user/global settings.json under CLAUDE_CONFIG_DIR (or ~/.claude) — and compares the current HEAD SHA against origin/HEAD. Project-level settings take precedence over the user/global layer, so a machine-wide worktree.baseRef:"head" set via /config is honored when no project override exists. The shouldDegrade field is true when the execute-phase orchestrator will fall back to sequential execution. Possible reason values:

reason	shouldDegrade	Meaning
baseref-head	false	worktree.baseRef:"head" is set; no mismatch possible
head-matches-fork	false	HEAD and origin/HEAD are the same commit
head-diverged-from-fork	true	Branch is ahead of or diverged from origin/HEAD
fork-ref-unknown	true	origin/HEAD could not be resolved
no-head	false	Not in a git repo (no HEAD)

worktree set-baseref applies a no-clobber write of worktree.baseRef:"head" to .claude/settings.local.json. If the file already contains an explicit baseRef value other than "head", the existing value is preserved and skipped:"explicit-other" is returned. Malformed JSON causes an error rather than a silent overwrite. Both fresh installs and upgrades of GSD Core run this automatically when workflow.use_worktrees is enabled (the default); the command is also available for manual use — for example, to apply the setting when worktrees were toggled on after installation, or to re-apply it after a settings change.

Wave-manifest recording

The execute-phase orchestrator records each spawned executor's worktree identity into a wave cleanup manifest so the matching cleanup-wave reader can later merge and remove exactly those worktrees.

# Append a validated per-agent entry to the wave cleanup manifest.
# Returns JSON: { ok, reason, entry, manifest_path } (exit 0), or
#   { ok:false, reason, hint } with a non-zero exit on a rejected entry.
node gsd-tools.cjs worktree record-agent \
  --manifest <path> --agent-id <id> --path <worktree> --branch <branch> --base <sha>

worktree record-agent appends one {agent_id, worktree_path, branch, expected_base} entry to an already-initialized manifest, validating every field at write time using the same rules the cleanup-wave reader enforces — --branch must match the disposable ^(worktree-)?agent-[A-Za-z0-9._/-]+$ namespace (accepts both agent-<id> and legacy worktree-agent-<id>), and --path/--branch/--base must be non-empty. --agent-id is required (write-strict), even though the reader treats it as optional. A missing or garbled field — or a duplicate (worktree_path, branch) the reader would dedup away — fails loudly with a recovery hint and a non-zero exit without writing, instead of appending an under-populated or silently-dropped entry. Whitespace-only --path/--base are rejected (values are trimmed). The on-disk manifest shape is unchanged (the reader re-derives allowed_bases); the orchestrator still initializes the empty {orchestrator_root, worktrees: []} shell inline before any agent is recorded.

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Graphify

Build, query, and inspect the project knowledge graph in .planning/graphs/. Requires graphify.enabled: true in config.json (see Configuration Reference).

# Build or rebuild the knowledge graph
node gsd-tools.cjs graphify build

# Search the graph for a term
node gsd-tools.cjs graphify query <term>

# Show graph freshness and statistics
node gsd-tools.cjs graphify status

# Show changes since the last build
node gsd-tools.cjs graphify diff

# Write a named snapshot of the current graph
node gsd-tools.cjs graphify snapshot [name]

User-facing entry point: /gsd-graphify (see Command Reference).

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Module Architecture

Module	File	Exports
Core	lib/core.cjs	error(), output(), parseArgs(), shared utilities, compatibility re-exports
State	lib/state.cjs	All state subcommands, state-snapshot
Phase	lib/phase.cjs	Phase CRUD, find-phase, phase-plan-index, phases list
Planning Workspace	lib/planning-workspace.cjs	Planning seam: planningDir, planningPaths, active workstream routing, .planning/.lock
Roadmap	lib/roadmap.cjs	Roadmap parsing, phase extraction, progress updates
Config	lib/config.cjs	Config read/write, section initialization
Verify	lib/verify.cjs	All verification and validation commands
Template	lib/template.cjs	Template selection and variable filling
Frontmatter	lib/frontmatter.cjs	YAML frontmatter CRUD
Init	lib/init.cjs	Compound context loading for all workflows
Milestone	lib/milestone.cjs	Milestone archival, requirements marking
Commands	lib/commands.cjs	Misc: slug, timestamp, todos, scaffold, stats, websearch
Model Profiles	lib/model-profiles.cjs	Profile resolution table
UAT	lib/uat.cjs	Cross-phase UAT/verification audit
Profile Output	lib/profile-output.cjs	Developer profile formatting
Profile Pipeline	lib/profile-pipeline.cjs	Session analysis pipeline
Graphify	lib/graphify.cjs	Knowledge graph build/query/status/diff/snapshot (backs /gsd-graphify)
Learnings	lib/learnings.cjs	Extract learnings from phases/SUMMARY artifacts (backs /gsd-extract-learnings)
Audit	lib/audit.cjs	Phase/milestone audit queue handlers; audit-open helper
GSD2 Import	lib/gsd2-import.cjs	Reverse-migration importer from GSD-2 projects (backs /gsd-import --from-gsd2)
Intel	lib/intel.cjs	Queryable codebase intelligence index (backs /gsd-map-codebase --query)
Context Predicates	lib/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
Capability State	lib/capability-state.cjs	Capability-state resolver — composes install profile, surface, and config into per-capability enabled/active view
Capability Writer	lib/capability-writer.cjs	Capability-state writer (ADR-1213) — write-side inverse; projects --on/--off/--gate onto surface + config substrates then re-resolves
Worktree Base Ref	lib/worktree-base-ref.cjs	Worktree fork-base detection and worktree base-check / set-baseref commands (#683)

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Reviewer CLI Routing

review.models.<cli> maps a reviewer flavor to a bare model id injected into the CLI's --model (or -m) flag by the code-review workflow. Set via /gsd-config --integrations or directly:

node gsd-tools.cjs config-set review.models.codex    "gpt-5"
node gsd-tools.cjs config-set review.models.gemini   "gemini-2.5-pro"
node gsd-tools.cjs config-set review.models.opencode "claude-sonnet-4"
node gsd-tools.cjs config-set review.models.claude   ""   # clear — fall back to session model

Slugs are validated against [a-zA-Z0-9_-]+; empty or path-containing slugs are rejected. See docs/CONFIGURATION.md for the full field reference.

Secret Handling

API keys configured via /gsd-settings (brave_search, firecrawl, exa_search) are written plaintext to .planning/config.json but are masked (****<last-4>) in every config-set / config-get output, confirmation table, and interactive prompt. See gsd-core/bin/lib/secrets.cjs for the masking implementation. The config.json file itself is the security boundary — protect it with filesystem permissions and keep it out of git (.planning/ is gitignored by default).

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Related

• Commands
• Configuration
• Architecture
• Fix the worktree base-mismatch (exit 42) error
• docs index