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
--pick <field>	Extract one field from a command's JSON output — see --pick <field> contract below

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--pick <field> contract

--pick <field> runs <command> as normal, parses its stdout as JSON, and extracts one field by name (dotted paths and [N] array indices are supported, e.g. a.b.c, directories[-1]). As of ADR-3473 §8.4 / #3884, the three possible outcomes are distinguished by exit code, never by an ambiguous empty string:

Outcome	stdout	stderr	Exit code
Field present	The field's value, coerced to a string	(none)	0
Field absent (missing key, out-of-range index, dotted path partially missing, or a non-object JSON root)	empty	Diagnostic naming the field and the available top-level keys (or the actual JSON root type)	1 (pick_field_absent)
Command output is not JSON (including --raw output, which is plain text/human-readable, not JSON)	empty	Diagnostic saying the output was not JSON	1 (pick_output_not_json)

A null or empty-string ('') field value is a real answer, not an absence — it still prints (an empty line) at exit 0. Only the absence of the field itself is a failure. This is why --raw and --pick are, in practice, mutually exclusive: --raw output is not JSON, so combining them always hits pick_output_not_json.

This replaces the previous behavior. Before #3884, an absent field (or non-JSON output) silently printed an empty string at exit 0 — indistinguishable from a field that genuinely held null or ''. That coercion is gone. The common shell idiom

X=$(gsd_run query some.command --pick some_field 2>/dev/null) || X=default

now works as written: the || X=default arm fires exactly when the field could not be resolved, and never fires merely because the resolved value happens to be empty.

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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. Frontmatter keys are projections of body fields —
# write the body field (see COMMANDS.md#state-update-field-value).
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
# When no labeled plan position can be parsed (e.g. ## Current Position drifted
# to pure narrative prose), declines with reason "plan_position_unreadable" plus
# the disk-derived counts and the exact labeled lines to re-insert; STATE.md is
# left byte-identical.

# 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 (at least one of --stopped-at / --resume-file is required)
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> [--sibling]

# 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]

# Archive (or, with --force, permanently delete) every current phase directory —
# used by /gsd-new-milestone before roadmapping the next cycle
node gsd-tools.cjs phases clear [--confirm] [--force] [--archive-version <version>]

Milestone-scoped phase listing (phases list)

The bare phases list (no --phase, no --include-archived) is scoped to the current milestone's ROADMAP.md window and filtered through the canonical sentinel predicate: 999.* backlog directories and 0-* pre-milestone directories are not listed as current-milestone phases. --phase <N> (a direct lookup) and --include-archived (an archive listing) are deliberately not scoped or sentinel-filtered — they answer "does this phase exist" and "what has ever existed here," not "what belongs to this milestone," so they still see sentinel and out-of-window directories.

phases clear and sentinel directories

phases clear moves (or, with --force and no prior archive, permanently deletes) every phase directory under .planning/phases/ except sentinels. It now excludes both 999.* (backlog) and 0-* (pre-milestone) directories via the same canonical sentinel predicate phases list uses — previously its own regex excluded 999 but not 0, so a 0-* directory could be destroyed on this irreversible path.

find-phase plan/summary counts (live vs physical)

find-phase's JSON carries the existing plans[] / summaries[] arrays unchanged, plus three additive scalar fields:

Field	Set	Answers
plan_count	live — status: superseded plans excluded	"how much outstanding work is left in this phase?" (same set as plans[])
summary_count	live	same, for summaries[]
plan_count_all	physical — every canonically-named plan file on disk, superseded included	"what has the planner actually written to disk?"

Naming mirrors roadmap analyze's existing plan_count/summary_count, and the _all suffix echoes the underlying scanPhasePlans field it is drawn from. Pick by the question you're asking, not by which number looks bigger: a phase where every plan is status: superseded correctly reports plan_count: 0 — that is a real "nothing outstanding" answer, not a bug — while plan_count_all still reports the physical count, so a check for "did the planner produce anything at all" doesn't misread a fully-superseded phase as untouched.

When the phase can't be resolved, all three fields are null, not 0 — a fabricated 0 would read identically to a genuinely empty phase.

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.

phase-plan-index: unresolved depends_on tokens (ADR-3473 §8.5, #3427/#3885)

A plan's depends_on: token must resolve to another plan in the same phase (by exact id or by canonical id). When a token resolves to neither, the edge is dropped and the dependent plan becomes a DAG root — phase-plan-index now names this in warnings[] instead of silently discarding it:

Plan 03-02: depends_on token "typo-plan-id" does not resolve to any plan in this
phase — edge dropped, wave placement for this plan may be unreliable

The token is escaped (quoted, control characters and embedded newlines backslash-escaped) before it is embedded in the warning, so a depends_on value crafted to contain a newline or a quote cannot forge a second, fabricated warning entry when warnings[] is printed one-per-line.

The wave-mismatch warning is suppressed for an affected plan. Normally a plan whose declared wave: disagrees with the computed DAG wave gets its own warning ("declared wave: N but depends_on DAG places it in wave M"). When the disagreement is caused by a dropped edge on that same plan, that warning would blame the author for a mismatch the tool itself manufactured by losing an edge — so it does not fire for that plan; the unresolved-token warning above stands in its place. A plan with no dropped edges and a genuinely wrong wave: still gets the mismatch warning as before.

This does not repair waves / wave themselves — those fields stay computed from the DAG with the edge missing, since the edge cannot be invented. A consumer using wave for scheduling (WAVE_FILTER, the wave-safety check) is still working from the degraded assignment; only the diagnostic surfaces the loss.

The ROADMAP **Requirements**: line grammar

phase complete reads each phase's **Requirements**: line to decide which REQ-IDs to mark. The grammar is deliberately small, and it is documented here because the command now warns about it (#3697) — a warning about a rule that cannot be looked up is not actionable.

The canonical form is a comma-separated list of REQ-IDs. Square brackets are optional; a REQ-ID is PREFIX-N, where the prefix is a letter followed by letters or digits. Two tolerances are worth knowing because the warnings below do not fire on them: the line is split on commas and whitespace, so REQ-01 REQ-02 selects both; and the ID shape is matched case-insensitively, so req-01 is selected and marked. Write the comma list anyway — it is what every template and every example uses — but neither spelling is an error:

**Requirements**: REQ-01, REQ-02, REQ-03
**Requirements**: [REQ-01, REQ-02, REQ-03]

Ranges are not expanded — REQ-01 … REQ-05 selects the two endpoints and nothing between them, and REQ-01..REQ-05 selects nothing at all, because the whole token fails the ID shape. This is a deliberate non-feature, not an oversight: the line is a traceability record, and silently inventing IDs that appear nowhere in REQUIREMENTS.md is worse than declining to.

A deliberately empty line is written TBD or None. Those two words are the placeholder vocabulary, and they are matched as the line's leading token, so None (per ADR-7) and **None** are declared-empty too. Any other wording that selects no REQ-IDs warns — Deferred, N/A, Pending, TBA, a bare -, or free prose — because from the command's side an unrecognised word is indistinguishable from a line that was meant to cite requirements and failed to. A line whose only content is an HTML comment is not "other wording" and stays silent, so the shipped template's own <!-- ... --> does not warn.

Write each requirement as a bare ID, separated by a comma. The line is split on commas and whitespace only, and nothing else is stripped, so anything attached to an ID takes the ID with it. REQ-01; REQ-02 marks only REQ-02; so do REQ-01 ;REQ-02, **REQ-01;** REQ-02 and an ID carrying a stray invisible character. Those are the cases the warning names — it reports the dropped ID, because this is the quietest way to lose a requirement here (the command reports requirements_updated: true either way).

What the warning does NOT reach. Stated so its silence is not read as a clean bill, and enumerated rather than summarised, because each of these is a requirement that goes missing without a word. The check fires only when the thing touching the ID is a ;, a :, or an invisible character:

• Markdown styling on its own is silent. **REQ-01**, REQ-02 drops REQ-01 and says nothing at all. Styling is not evidence that a separator was meant. **REQ-01**; REQ-02 is silent for the same reason — the ** sits between the ID and the ;, so nothing is touching the ID.
• Any other attached punctuation is silent. REQ-01/ REQ-02, REQ-01| REQ-02, REQ-01. REQ-02, REQ-01+ REQ-02, REQ-01> REQ-02 and their full-width and non-ASCII equivalents (；, ，, ؛) each mark only REQ-02. A fully crossed sweep — 21 separators against bare, leading-space, trailing-space and both-spaces spellings, 84 combinations — found 34 silent under-selections, every one of them a separator glued to exactly one of the two IDs. Only ; and : are in the set. Widening it is a live option — say the word — but each past widening of this check first fired on a citation, so it is not done blind.
• A dropped ID whose prefix matches nothing selected is silent. REQ-01, REQ-02: login is reported; REQ-01, FOO-02: x is not. A citation is textually identical to a dropped requirement — REQ-01, see ADR-7: section 3 carries ADR-7: in exactly the shape REQ-01; has — and prefix agreement is the only thing that separates them without guessing at prose. Anything inside matched parentheses is left alone for the same reason: (see ADR-7: section 3) is a citation.

The prefix gate is not complete in the other direction either: a citation that shares a selected prefix — REQ-01, see REQ-7: sec 3 — does warn, naming REQ-7 as dropped. Nothing at the token level separates that from a real drop.

Dash spellings need a full ID on both sides. REQ-01-REQ-05 reads as a range; REQ-01-05 does not, and neither does any of its typographic variants (en dash, em dash, minus sign, and the rest). The reason is that PREFIX-<digits><dash><digits> is also a date (FY-2026-08) and a sub-numbered ID (API-2-01), so warning on it would be noise on lines that are perfectly correct. .., …, to, thru and through have no such reading and do accept a bare numeric endpoint (REQ-01..05). The cost is that REQ-01, REQ-02-05 is not reported; a bare REQ-02-05 still is, because it selects nothing.

What warns, and in which of the three voices. All go to warnings[] and none blocks completion:

• "could not be parsed as a comma-separated REQ-ID list" — the line did not yield the requirements it appears to name. That covers two cases, and the message says which one it is: ID-shaped text on the line was not selected, so something was demonstrably dropped; or the line selected nothing at all while not being a TBD/None placeholder, in which case there may be no ID-shaped text on it whatsoever (Deferred takes this voice). Either way nothing was marked and the line needs fixing.
• "contains what reads as a range between two cited REQ-IDs" — the separator is the only thing in question: a separator between two cited IDs could equally be a range or an annotation, and the command cannot tell them apart, so it states both readings rather than asserting a failure that may not have happened. It speaks about the separator, not about the whole line. It is also the weakest of the three claims, so it yields to the other two: a demonstrated drop elsewhere on the line makes it a misparse, and an unexamined over-cap token makes the line unverified — a voice whose claim is that nothing was dropped cannot speak over a token no rule read.

Each warning carries a machine-readable kind. The prose goes to warnings[] as before — that field is unchanged and is still an array of strings — and the kind is emitted beside it as requirements_line_warning, one of req-line-misparse, req-line-range-reading or req-line-unverified. The field is absent entirely when the line is clean. Key on the kind rather than on the wording; the wording is free to improve.

Either of those two voices may add a factual note naming ID-shaped text on the line that was not selected. Square brackets are stripped — [REQ-01, REQ-02] is the documented form — but parentheses are not, so (REQ-02) is not marked. The command cannot tell that from (ADR-7), which is a citation and correctly ignored, so it names what it skipped and leaves the judgement to you. Where the skipped text is PREFIX-<digits>-<digits> — the shape the dash rule above declines to adjudicate, because FY-2026-08 is a date and API-2-01 is a legal requirement id and no rule separates them — it is still named, with that ambiguity stated alongside it. Naming it and saying why it is ambiguous beats both alternatives: filtering it hides a real dropped requirement, and reporting it bare asks you to check whether a date is a requirement. The third voice is for input the command could not examine: "could not be checked ... the REQ-ID selection on this line is unverified". Range detection is bounded at 2,048 characters per token, so a longer token is not classified — and unclassified is reported, never treated as clean. Selection itself is not bounded, so a valid REQ-ID longer than that is still selected and marked normally; it only triggers this voice if something beside it could have formed a range with it, which is the case where the bound actually suppressed a check.

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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>

When the phase has no writable ROADMAP entry — no matching Progress-table row, no ### Phase N detail section, and no checklist bullet this command can update (the checklist-only form) — the command declines with updated: false and a missing_phase_details reason instead of claiming success, and leaves ROADMAP.md byte-identical.

Milestone window scope (roadmap analyze)

roadmap analyze scopes its phase list to the current milestone's section of ROADMAP.md. Its JSON output carries a scope field describing how much of the intended input that scoping actually saw:

scope	Meaning
complete	The window was computed over the whole intended input. phase_count: 0 here is a real answer — a freshly-declared milestone genuinely has no phases yet.
truncated	The milestone's heading was found, but its window closed before reaching the document's phase region — typically because a closed-milestone heading sits between the active milestone and its ### Phase N: sections. phase_count: 0 here is a non-answer.
unscoped	No milestone version could be resolved (or its section is absent) on a ROADMAP that does use versioned milestones, so the result is not milestone-scoped.
unreadable	ROADMAP.md could not be read.

Before this field existed, all four cases produced the same well-formed phase_count: 0 with no error, so a consumer could not tell a genuinely empty milestone from a scoping failure. Branch on scope, not on phase_count alone.

A ROADMAP with no versioned milestone headings at all (the free-form legacy shape) reports complete: the whole document is the milestone there. Note this answer is specific to windowing — see the next section for why milestone identity answers the same document differently.

A non-COMPLETE scope withholds the percentage entirely (#3217)

roadmap analyze --json's progress_percent, stats --raw's percent / plan_percent, query progress --raw's percent, and state json --raw's progress.percent are now nullable — a Tier-2 contract change. When the phase set a percentage would be computed from is not fully trustworthy (any scope other than complete), these surfaces render no percentage at all rather than a number computed from a truncated, unscoped, or unreadable set:

Surface	Non-complete behavior
roadmap analyze --json	progress_percent: null
stats --raw	percent: null, plan_percent: null
query progress --raw	percent: null
state json --raw	progress.percent is omitted from the progress object (not 0, not present as null)
state update-progress --raw	false — no write; STATE.md's Progress field is left untouched, and a [gsd-tools] WARNING: line is written to stderr naming the scope

0 is a legitimate, real answer under a complete scope (e.g. a freshly-declared milestone with zero phases, or a phase with zero plan files) and is never withheld — only a non-complete scope withholds.

roadmap analyze --json gates total_plans / total_summaries / phases / completed_phases on the top-level scope field described above (heading windowing identity), but progress_percent is governed by a separate progress_scope field — the scope of the phase-directory set the percentage was actually computed from. The two can legitimately disagree (e.g. scope: "complete" — the ROADMAP heading resolves fine — alongside progress_scope: "unreadable" when .planning/phases itself cannot be read), so a consumer must branch on progress_scope, not scope, to know why progress_percent is null.

Milestone identity (which milestone, and what it is called)

Milestone identity — the version and name behind STATE.md's milestone: field, roadmap analyze's milestones[] array, and the milestone shown by query progress, stats, init manager, validate health and workstream create — is resolved by one implementation:

• STATE.md's milestone: field selects the version when present. The ROADMAP heuristics are the fallback, not the primary.
• The heading is located by the same canonical locator that computes the milestone window, so a ### Phase N: … heading is never read as the milestone heading — even when it mentions a version. Previously a ROADMAP whose phase heading preceded its milestone heading could write a wrong milestone: to disk.
• The name is the heading text after that heading's own version token, with one leading delimiter (—, –, :, -) and any trailing ✅/📋/🚧 marker removed. Parentheses are ordinary characters: a milestone named v3.3 — Portability (Windows) keeps its full name rather than being cut at the (.
• When identity cannot be determined it is reported as absent rather than defaulted. A free-form legacy ROADMAP with no version anywhere is unscoped with no identity — unlike windowing above, there is no version token to report, and inventing one would be indistinguishable from a real answer.

Two consumers act on that distinction rather than just displaying it: state sync / state record-session write null instead of a fabricated milestone:/name, and phases clear falls back to its dated archive label (archived-<YYYYMMDD>) instead of filing phase history under a fabricated milestones/<version>-phases/ directory.

milestone complete refuses an untrustworthy window

milestone complete archives ROADMAP.md/REQUIREMENTS.md and moves phase directories — a one-way door. When the milestone window's scope is truncated — the milestone heading was found but its section closes before reaching any phase entries, even though the ROADMAP has phase entries elsewhere — phase scoping cannot be trusted, and the command now refuses rather than falling back to an over-inclusive filter that would archive every phase directory in the project. unreadable (no ROADMAP.md at all) and unscoped (no section for this version) are pre-existing, legitimately handled states and are not refused here. Pass --force --confirm to override, the same affordance the unstarted-phase guard uses (--confirm is required for any mutating run — #3726; --force alone does not imply it).

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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>

---

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

---

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 → per-install runtime marker → 'claude' precedence (#3897), 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.

---

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.

---

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.

---

Intel Commands

node gsd-tools.cjs intel query <term>

Searches every JSON intel file under .planning/intel/ (keys and values, including arch-decisions.json) for <term>. No-ops with { enabled: false } when the intel capability is not active (intel.enabled in config).

Output JSON:

{ "matches": [{ "source": "file-roles.json", "entries": [...] }], "term": "…", "total": 3, "truncated": false }

Field	Type	Description
total	number	Count of matched entries across every intel file
truncated	boolean	true when the recursive walk of at least one intel file hit the 48-level depth ceiling before finishing — see below

The 48-level recursion ceiling and truncated (ADR-3473 §8.5, #3885)

The search recurses into nested objects/arrays up to 48 levels deep (the bound is on depth, not breadth or total node count — a wide-but-shallow structure is unaffected). A match at or above the ceiling is not returned, and truncated is set to true on the result so a caller can tell "I stopped looking" apart from "there is no match here."

truncated: false means the walk reached the bottom of every branch it visited — it does not by itself mean anything was found; check total for that. Before this fix, a search past the ceiling threw an uncaught RangeError: Maximum call stack size exceeded instead of returning a diagnosable result; a shallower search (depth ≤ 48) is unaffected and its result is unchanged.

---

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

---

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>

verify key-links confines each link's from:/to: to the project directory (#3493): a path that resolves outside the project (via ../ traversal, an absolute path, or a symlink) is never read. That link's links[] entry reports path_rejected: "from" or path_rejected: "to" (whichever field was rejected) alongside verified: false, without echoing the underlying path-confinement error (which would embed an absolute host path). A rejected link fails independently — it does not abort evaluation of the other links in the same plan, and does not set path_rejected on links whose paths resolve inside the project.

---

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 consistency's warnings entries are coded diagnostics ({code, message, fix, repairable}), not bare strings. A phase declared in ROADMAP.md with no directory on disk, or a directory on disk with no ROADMAP.md entry, reports under W006/W007 — the same codes validate health uses for the identical check, since it's one enumeration with two callers, not a separate check. The four subjects unique to this command (numbering gaps in phases or plans, orphan *-SUMMARY.md files, plans missing wave frontmatter) use a new C0NN code range (C001-C004).

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).

---

Planning Snapshot Commands

planning inspect

Emits a read-only, schema-versioned snapshot of everything .planning/ knows, as one JSON document. It exists so a downstream tool — a harness UI, a mission-control view, a dashboard — can consume planning state without parsing ROADMAP.md / REQUIREMENTS.md / *-PLAN.md / *-SUMMARY.md a second time and drifting from gsd-core's own answers.

gsd-tools query planning inspect
gsd-tools query planning.inspect     # dotted canonical form — identical output

Takes no arguments. A stray positional or an unrecognized flag is a fail-loud usage error, not a silently-ignored one: a caller who believed --phase 3 was scoping the query would otherwise receive a whole-project snapshot presented as a scoped one.

planning inspect writes nothing, anywhere. It is safe to run against a project mid-workflow.

The schema contract

{ "schema_version": 1, "...": "..." }

schema_version is the contract. A consumer must reject any value other than the one it was written against rather than best-effort-parsing a shape it does not know. Every top-level key is always present; a key is never omitted to signal absence, because omission is itself something callers come to depend on.

Key	What it carries
schema_version	Always 1 today
generated_from	Resolved cwd and .planning/ root (null when there is no planning root)
milestone	version, name, and the scope of that answer
active	phase, plan, and status — three distinct STATE.md facts, each scoped separately
phases[]	Per phase: completion, verification, roadmap acceptance, UAT, plan and task rows
orphan_phase_dirs[]	Directories under phases/ that the current milestone window does not declare
requirements[]	Requirement rows with mapped-phase traceability
progress	accepted_phases and completed_plans, as independent fractions
diagnostics[]	Coded reasons for every non-answer above

Three kinds of evidence, never folded together

Each phase reports verification, roadmap_acceptance, and uat side by side. They are not combined into a single verdict, because they answer different questions and can legitimately disagree — a phase can pass verification while UAT items remain open.

roadmap_acceptance.checkbox is reported with authoritative: false. A ticked ROADMAP checkbox is a human annotation with no machine authority: completion is derived from disk state (a passing *-VERIFICATION.md), and a stale tick never overrides it. See Milestone window scope.

Unknown is a real answer; nothing is inferred

Where the evidence is absent, or where two sources disagree, the value is null or "unknown" and a coded entry in diagnostics[] says why. It is never reconciled, guessed, or filled from a plausible default.

The most common case is task-scoped file provenance. A <task> block declares the files it plans to touch, but SUMMARY.md's ## Files Created/Modified section describes the whole plan, not an individual task. Spreading that plan-level list across the plan's tasks would be inference, so instead:

provenance	Meaning
task_scoped	The summary attributed files to this specific task (via a deviation block naming Found during: Task N)
plan_scoped	A summary exists, but only carries a plan-level file list — this task's changed files are unknown
absent	No summary exists yet

When a task's planned and changed file sets both exist and disagree, agreement is "conflicting" and both lists are emitted verbatim.

Percentages are withheld rather than guessed

progress.accepted_phases and progress.completed_plans are independent fractions, each {completed, total, percent, scope}. percent is null whenever scope is anything other than complete — the same rule the roadmap and progress surfaces follow, for the same reason. See A non-COMPLETE scope withholds the percentage entirely.

0 is a real answer under a complete scope and is never withheld.

Large payloads

Output over ~50 KB is written to a temp file and returned as @file:<path>, which gsd-tools resolves transparently before writing to stdout — the same channel init uses. Callers see JSON either way.

---

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

---

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

---

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"

---

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> (--confirm | --dry-run) [--name <name>] [--no-archive-phases] [--force] [--archive-quick]

# Archive .planning/quick/* into milestones/<version>-quick/ WITHOUT the milestone complete close-out (#2142)
node gsd-tools.cjs milestone archive-quick <version> [--dry-run]

# 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]

milestone complete flags

Flag	Description
<version>	Milestone version label to archive (e.g. v1.0).
--confirm	Required to mutate (#3726). The archive is irreversible — ROADMAP.md/REQUIREMENTS.md archived, phase directories MOVED, STATE.md rewritten — so without this flag the command refuses and changes nothing (exit 1, with a message naming both --confirm and --dry-run). Not implied by --force, which only overrides the guards below.
--name <name>	Display name for the MILESTONES.md entry. Defaults to <version>.
--no-archive-phases	Leave phase directories in place instead of moving them into .planning/milestones/<version>-phases/.
--archive-quick	Opt-in (default OFF, #2142): also move every directory under .planning/quick/ into .planning/milestones/<version>-quick/, (re)write that archive directory's README.md index, and clear STATE.md's ### Quick Tasks Completed table rows. See "milestone archive-quick" below for the narrower standalone form and the full behavior.
--force	Override the unstarted-phase guard (see below).
--dry-run	Print the archive plan (roadmap, requirements, phases, and — when --archive-quick is also passed — quick-task dirs to move) without mutating anything.

Unstarted-phase guard. Before archiving, the command scans the ROADMAP scoped for <version> and refuses if any ### Phase N: heading in that slice has no matching phase directory on disk (disk_status: no_directory). Phase 0 (pre-milestone) and Phase 999 (backlog) sentinels are excluded. The guard runs whenever --force is absent, independent of STATE.md's milestone: field — if that field is present but does not match <version>, a WARNING naming both values is emitted to stderr and the scan still runs (#2946). Pass --force --confirm to override (--confirm is required for any mutating run — #3726; --force alone does not imply it).

Sentinel directories are never archived. The phase-directory move performed when --no-archive-phases is absent is now filtered through the same canonical sentinel predicate as phases list and phases clear: 999.* (backlog) and 0-* (pre-milestone) directories are left in place rather than moved into .planning/milestones/<version>-phases/. Previously this path was scoped only by the milestone window, with no sentinel filter, so a sentinel directory sitting inside the window could be archived along with the milestone's real phases.

milestone archive-quick (#2142 escalation)

A narrower sibling of milestone complete --archive-quick, for callers that need to sweep .planning/quick/* WITHOUT the full milestone close-out — chiefly gsd-core/workflows/cleanup.md, which runs against milestones that are typically already completed.

Flag	Description
<version>	Milestone version label to archive quick-task directories under (e.g. v1.0). Same validation as milestone complete's <version> — letters/digits/./-/_ only, no path separators or ...
--dry-run	List what would move (would_archive) without mutating anything.

It moves every directory under .planning/quick/ into .planning/milestones/<version>-quick/, (re)writes that archive directory's README.md index, and clears STATE.md's ### Quick Tasks Completed table rows — the same move/index/reset logic milestone complete --archive-quick uses. Unlike milestone complete, it never archives ROADMAP.md/REQUIREMENTS.md, never writes a MILESTONES.md entry, and runs neither the unstarted-phase guard nor the milestone-window refusal — so, unlike milestone complete --archive-quick, it can be safely re-run against an already-completed milestone. JSON result: { version, archived, entries, archive_dir, state_updated, warnings }.

milestone archive-quick is a second subcommand of milestone (alongside complete) — it is not a separate top-level command.

---

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.

---

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.

---

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>"
# Optional (#3356) — supply a real quick id and task directory to write the canonical row the
# `/gsd-quick` workflow itself renders, instead of a positional `#` and an em-dash `Directory`:
node gsd-tools.cjs quick-tasks-append --task "<description>" --quick-id <id> --slug <slug>
node gsd-tools.cjs quick-tasks-append --task "<description>" --directory "[<id>-<slug>](./quick/<id>-<slug>/)"
# All three flags are optional. Omit them (as `fast.md` does, having neither an id nor a task
# directory) and the emitted row is byte-identical to the pre-#3356 behavior. `--directory` wins
# outright when given; otherwise `--quick-id` + `--slug` together derive the permalink.
# This append touches only the body table — it no longer forces a re-derive of the disk-derived
# `progress.*` frontmatter, which previously overwrote curated values (#3356).
# See "Milestone Commands" below for `milestone archive-quick` (#2142) — sweeps .planning/quick/* into
# milestones/<version>-quick/ and clears this table, without a full `milestone complete`.

# 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

Both stats and progress are scoped to the current milestone's ROADMAP.md window and sentinel-filtered: 999.* backlog directories and 0-* pre-milestone directories are not counted as current-milestone phases, and the aggregate completion percentage no longer reads 100 while phases from the active window are still outstanding.

# Complete a todo
node gsd-tools.cjs todo complete <filename> [--dry-run]

--dry-run previews the completion (a dry_run/would_* JSON payload naming the source, the destination, and the frontmatter keys it would set) without moving the file or touching anything on disk. A real completion moves the todo from todos/pending/ to todos/completed/ and upserts completed: and status: completed inside the file's frontmatter block. Unknown flags are rejected loudly.

<filename> is a basename inside the todos root, not a path. A basename guard runs first, before <filename> is joined onto any directory: a value containing an embedded separator (either / or \, e.g. sub/name.md or sub\name.md), a value whose own basename differs from itself (e.g. a/../../b.md, ../sibling.md), a bare . or .., an absolute path (e.g. /etc/passwd), or a NUL byte is rejected as a usage error before any file is read or moved (#4327, #4652). A traversal that only escapes the pending/ completed subdirectory without leaving the todos root (../sibling.md) is caught by this same guard, not by containment. Containment against the todos root still runs afterward as defense-in-depth for the resolved source and target paths, so neither half of the move can land outside the root. The check covers both halves of the move, and --dry-run is rejected on the same terms rather than previewing a resolved outside path.

# 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]

# Suppress one open audit item — writes a self-invalidating `audit_acknowledged`
# marker; never overwrites the artifact's own `status:` (except `deferred_items`,
# where the marker IS the entry's `status:`). See docs/COMMANDS.md's
# `/gsd-complete-milestone` entry for the full per-category identifier flag table.
node gsd-tools.cjs audit-open acknowledge --category <category> --milestone <version> [--at <date>] <identifier flags…>

# 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] [--files-removed f3 dir/] [--amend] [--no-verify] [--respect-staged]

--files-removed <paths> (#4208): the caller-declared deletions. A --files entry that is missing on disk is skipped, never staged as a deletion (#2014) — so a moved file's old path cannot be recorded through --files at all, and the only form that recorded a move was a directory entry, which also commits any unrelated file sitting in that directory. Each --files-removed entry names a file, or a directory whose tracked-but-absent files are the removals; those paths are staged as deletions and join the commit pathspec. "Tracked" means in the index or in HEAD, so a deletion the caller already staged with git rm is committed too; "present" is the path itself (lstat), so a symlink counts as present even when its target is gone. A file entry that is still present on disk fails the commit closed (reason: 'staging_failed'); a path git never tracked is a no-op. Absence alone is not removal: an index entry that is absent from the worktree by design — a submodule gitlink, a skip-worktree (sparse-checkout) path, an assume-unchanged path, an unmerged entry, an intent-to-add (git add -N) entry — is never staged as a deletion; under a directory entry it is left alone like a present file, and named directly (by any spelling that resolves to it) it fails closed naming the state. On a staging failure the rollback puts back every index entry this call removed with its recorded mode and blob (update-index --cacheinfo), including on an unborn HEAD where git reset has nothing to restore from; like the addition-side reset it is best-effort — an index that cannot be written reports the staging error, not a clean rollback. --files keeps its skip-if-missing contract unchanged. A move is therefore --files new/path --files-removed old/path. GSD's own close_phase_todos step (execute-phase.md) uses exactly that form, naming each moved todo on both sides rather than passing the two directories: a directory entry would also commit an unrelated todo a concurrent session dropped into pending/ or completed/ while the phase was closing.

--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 · already_present · 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). A destination that is already byte-identical to its backup is reported as already_present and left untouched — it counts toward neither eligible_count nor restored_count, so a plan run after a successful restore no longer offers the same file again. 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. --mode declares who creates the isolated worktree (#3659): harness-worktree (the default — the runtime harness forks it and does not read project-settings baseRef, #48) or orchestrator-worktree (GSD itself runs git worktree add with an explicit start-point and honors "head"); invalid values fail closed with an error. Possible reason values:

reason	shouldDegrade	Meaning
baseref-head	false	worktree.baseRef:"head" is set and --mode orchestrator-worktree declares GSD-managed worktrees — the fork base is the orchestrator HEAD by construction
baseref-head-ignored-by-harness	true	worktree.baseRef:"head" is set but HEAD differs from origin/HEAD in harness (default) mode — the harness does not read the setting (#48), so the run degrades to sequential (#3659)
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) — git rev-parse HEAD exited 128 (definitive), or exited 0 with empty stdout
head-unresolvable	true	git rev-parse HEAD did not return a definitive answer (timed out, git missing, or any other non-128 failure) — fails closed rather than being treated as 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.

Worktree creation

# Create an agent worktree and atomically record it in 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/failed create.
node gsd-tools.cjs worktree create \
  --manifest <path> --agent-id <id> --path <worktree> --branch <branch> --base <sha> --root <dir> \
  [--files "<space-separated declared paths>"]

worktree create validates and records the manifest entry BEFORE running any git command, then runs git worktree add for the validated {path, branch, base}, and only on success finalizes the manifest write — a rejected entry or a failed git worktree add never leaves a partially-recorded manifest or an unmanifested worktree on disk. --root is mandatory (#3050): the fail-closed root-confinement check resolves --path and --root and rejects (reason:"path_outside_root") unless --path resolves strictly inside --root — this closes a prior gap where an unconfined --path (no --root check at all) could point a spawned executor's worktree anywhere on the filesystem. Omitting --root fails closed with reason:"root_required" rather than silently skipping confinement. All other flags share worktree record-agent's validation rules above (--branch namespace, non-empty/non-whitespace --path/--branch/--base, --agent-id required). It also accepts the same optional --files as record-agent (#2596).

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> \
  [--files "<space-separated declared paths>"]

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 unless --files is supplied (see below); the reader still re-derives allowed_bases, and the orchestrator still initializes the empty {orchestrator_root, worktrees: []} shell inline before any agent is recorded.

--files is optional (#2596). When supplied it records the plan's declared files_modified — the same whitespace-separated PLAN_FILES list the per-plan worktree gate already builds — as an extra files_modified array on the entry, and cleanup-wave then reports any path the branch committed outside it. A blank or omitted --files writes no field at all, leaving the 4-field on-disk shape untouched, and the scope check is simply skipped for that entry: an unrecorded scope means unknown, never declares nothing. Values are compared against a diff, never opened as paths and never passed to a shell.

--deletions is optional (#3003). When supplied it records the plan's declared files_deleted — built by the per-plan worktree gate exactly like PLAN_FILES, from the plan's own frontmatter — as a declared_deletions array on the entry. It is the opt-in the deletions guard reads (see below). A blank or omitted --deletions writes no field, leaving the on-disk shape untouched and the guard's original unconditional block in force. Like --files, values are compared against a diff and never opened or passed to a shell.

Intentional deletions (gate, #3003)

cleanup-wave blocks the merge of any executor branch whose diff deletes a file — a net against a mass-deletion accident. A plan whose scope legitimately includes removing a file declares those paths in its files_deleted frontmatter, which reaches the entry as declared_deletions; the guard then blocks only the deletions not in that list.

Branch deletes	Entry declares	Result
nothing	—	merges
tests/a.ts	(no field)	blocked — unchanged pre-#3003 behavior
tests/a.ts	["tests/a.ts"]	merges
tests/a.ts, src/b.ts	["tests/a.ts"]	blocked, and the block detail names only src/b.ts
tests/a.ts	["tests"]	blocked — a directory does not authorize its children
tests/a.ts	["*.ts"]	blocked — globs are literal paths here, matching nothing

Matching is exact after normalization: git's C-quoting is decoded, backslashes become forward slashes, and a leading ./ and any trailing / are stripped — on both sides. The decode matters more than it looks: with core.quotepath at its git default, a path like tests/é.ts is reported as the literal "tests/\303\251.ts", which would never compare equal to the plainly-declared path, so a correctly declared deletion of any non-ASCII path would block forever with nothing pointing at the encoding. It is deliberately neither a prefix nor a glob match — either would let one declaration authorize a whole set of deletions, which is the accident the guard exists to catch. A declared path that was not in fact deleted is inert. A blocked entry still isolates: the rest of the wave proceeds (#2852). If the deletion check itself fails the entry blocks on deletion_check_failed and is never filtered — a broken check is not an authorization.

A declared deletion is also treated as in-scope by the advisory below, so authorizing a removal does not then warn that the removed path was out of the declared scope. That is done by subtracting declared deletions from the advisory's findings, not by adding them to the declared scope it matches against — the advisory reads its scope list with prefix-and-glob semantics, so adding them would quietly give declared_deletions a second, wider matching rule than the table above, and ["*.md"] would go from inert to silencing the advisory entirely. One field, one matching rule, on every surface. Subtraction also means the advisory's activation is unchanged: it still runs only when files_modified is recorded, so a plan that declares deletions alone stays as silent as it was before #3003.

One limit worth knowing, shared with --files and failing closed: a declared path containing a space cannot be expressed, because the flag value is whitespace-separated — such a path splits into fragments, matches nothing, and the entry blocks. Flag values are also read positionally and never re-inspected for shape, so a malformed --deletions --files src/a.ts records the literal --files as the declaration; that is harmless (it is a path git never reports as deleted, so it authorizes nothing) and --files still resolves to src/a.ts on its own lookup.

Scope conformance at merge (advisory, #2596)

When a manifest entry carries a declared files_modified, cleanup-wave compares the branch's actual committed diff (HEAD...<branch>) against it and appends one entry to the result's warnings array for every path outside the declared scope, with code: "scope_out_of_declared" and the offending path. If the diff itself cannot be computed the entry gets a single code: "scope_check_unavailable" warning instead, so an unknown result is never mistaken for a clean one. Warnings are also aggregated on the top-level warnings array, each tagged with its branch.

This is advisory: it does not change ok, reason, the per-entry status, or the exit code, and the merge proceeds either way. Promotion to a hard gate would be a separate, disclosed change.

Two deliberate limits keep it from crying wolf. .planning/**/*SUMMARY.md paths are always exempt — the executor writes a SUMMARY by orchestration contract and no plan declares it. Glob patterns are matched by their literal prefix only, so src/**/*.ts covers everything under src/, and a pattern with no literal prefix (*.md) suppresses warnings for that entry rather than reporting every file.

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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.agy      "gemini-3.1-pro-preview"
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