ferrox-graphify

name	ferrox-graphify
description	You want to build, query or inspect the knowledge graph of this project
argument-hint	[build|query <term>|status|diff]
allowed-tools	["Read","Bash"]

STOP -- DO NOT READ THIS FILE. You are already reading it. This prompt was injected into your context by Claude Code's command system. Using the Read tool on this file wastes tokens. Begin executing Step 0 immediately.

CJS-only (graphify): graphify subcommands are not registered on ferrox-tools query. Use the ferrox_run launcher shim (defined in each bash block below) or invoke the binary directly: node <runtime-home>/ferrox-core/bin/ferrox-tools.cjs graphify … where <runtime-home> is your runtime's config directory (e.g. ~/.claude, ~/.hermes, ~/.cursor). See docs/CLI-TOOLS.md for details. Other tooling may still use ferrox-tools query where a handler exists.

Step 0 -- Banner

Before ANY tool calls, display this banner:

Ferrox > GRAPHIFY

Then proceed to Step 1.

Step 1 -- Config Gate

Check if graphify is enabled by reading .planning/config.json directly using the Read tool.

DO NOT use the ferrox-tools config-get command -- it hard-exits on missing keys unless --default is passed.

1. Read .planning/config.json using the Read tool
2. If the file does not exist: display the disabled message below and STOP
3. Parse the JSON content. Check if config.graphify && config.graphify.enabled === true
4. If graphify.enabled is NOT explicitly true: display the disabled message below and STOP
5. If graphify.enabled is true: proceed to Step 2

Disabled message:

Ferrox > GRAPHIFY

Knowledge graph is disabled. To activate:

  node <runtime-home>/ferrox-core/bin/ferrox-tools.cjs config-set graphify.enabled true

Then run /ferrox-graphify build to create the initial graph.

---

Step 2 -- Parse Argument

Parse $ARGUMENTS to determine the operation mode:

Argument	Action
build	Run inline build (Step 3)
query <term>	Run inline query (Step 2a)
status	Run inline status check (Step 2b)
diff	Run inline diff check (Step 2c)
No argument or unknown	Show usage message

Usage message (shown when no argument or unrecognized argument):

Ferrox > GRAPHIFY

Usage: /ferrox-graphify <mode>

Modes:
  build           Build or rebuild the knowledge graph
  query <term>    Search the graph for a term
  status          Show graph freshness and statistics
  diff            Show changes since last build

Step 2a -- Query

Run:

_FERROX_SHIM_NAME="ferrox-tools.cjs"; _FERROX_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/ferrox-core/bin/${_FERROX_SHIM_NAME}"; if [ -f "$FERROX_TOOLS" ]; then ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif command -v ferrox-tools >/dev/null 2>&1; then FERROX_TOOLS="$(command -v ferrox-tools)"; () {  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };    >&2;  1; ;  [ -n  ] && [ -n  ];     >>  2>/dev/null || ; 
ferrox_run graphify query <term>

Parse the JSON output and display results:

• If the output contains "disabled": true, display the disabled message from Step 1 and STOP
• If the output contains "error" field, display the error message and STOP
• If no nodes found, display: No graph matches for '<term>'. Try /ferrox-graphify build to create or rebuild the graph.
• Otherwise, display matched nodes grouped by type, with edge relationships and confidence tiers (EXTRACTED/INFERRED/AMBIGUOUS)

STOP after displaying results. Do not spawn an agent.

Step 2b -- Status

Run:

_FERROX_SHIM_NAME="ferrox-tools.cjs"; _FERROX_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/ferrox-core/bin/${_FERROX_SHIM_NAME}"; if [ -f "$FERROX_TOOLS" ]; then ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif command -v ferrox-tools >/dev/null 2>&1; then FERROX_TOOLS="$(command -v ferrox-tools)"; () {  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };    >&2;  1; ;  [ -n  ] && [ -n  ];     >>  2>/dev/null || ; 
ferrox_run graphify status

Parse the JSON output and display:

• If exists: false, display the message field
• Otherwise show last build time, node/edge/hyperedge counts, and STALE or FRESH indicator
• If built_at_commit is non-null, also display a Source commit: line:
  • commit_stale === false (rebuilt at HEAD): Source commit: <built_at_commit> (current)
  • commit_stale === true (graph behind HEAD): Source commit: <built_at_commit> (<commits_behind> commits behind HEAD)
  • commit_stale === null (unreachable commit / no git): Source commit: <built_at_commit> (freshness unknown)
• If built_at_commit is null (pre-graphify-v0.7 graph), omit the source-commit line entirely — do not render "Source commit: unknown"

The mtime-based STALE/FRESH flag and the commit-based commit_stale measure different things and can disagree (e.g., a CI-built graph rebuilt minutes ago against an old checkout reads as FRESH on mtime but commit_stale: true). Surface both so the agent can choose.

STOP after displaying status. Do not spawn an agent.

Step 2c -- Diff

Run:

_FERROX_SHIM_NAME="ferrox-tools.cjs"; _FERROX_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/ferrox-core/bin/${_FERROX_SHIM_NAME}"; if [ -f "$FERROX_TOOLS" ]; then ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif command -v ferrox-tools >/dev/null 2>&1; then FERROX_TOOLS="$(command -v ferrox-tools)"; () {  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };    >&2;  1; ;  [ -n  ] && [ -n  ];     >>  2>/dev/null || ; 
ferrox_run graphify diff

Parse the JSON output and display:

• If no_baseline: true, display the message field
• Otherwise show node and edge change counts (added/removed/changed)

If no snapshot exists, suggest running build twice (first to create, second to generate a diff baseline).

STOP after displaying diff. Do not spawn an agent.

---

Step 3 -- Build (Inline)

Run the pre-flight check first:

_FERROX_SHIM_NAME="ferrox-tools.cjs"; _FERROX_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/ferrox-core/bin/${_FERROX_SHIM_NAME}"; if [ -f "$FERROX_TOOLS" ]; then ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif command -v ferrox-tools >/dev/null 2>&1; then FERROX_TOOLS="$(command -v ferrox-tools)"; () {  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };    >&2;  1; ;  [ -n  ] && [ -n  ];     >>  2>/dev/null || ; 
ferrox_run graphify build

Parse the JSON output:

• If disabled: true: display the disabled message from Step 1 and STOP
• If error: display the error message and STOP
• If action: "spawn_agent": pre-flight passed -- proceed with the inline build below

(The spawn_agent action name is historical. The skill now performs the build inline because graphify v0.7+ split the build into a fast AST-extraction phase and a separate clustering + report-write phase. Sub-agent isolation kept the cached extraction phase alive but SIGTERM'd the post-extraction phase when the agent exited, leaving the cache populated but no graph.json artifacts written. The CLI still emits the spawn_agent signal so external callers and tests keep working.)

Display:

Ferrox > Building knowledge graph...

Run the build, copy artifacts, write the diff snapshot, and report the summary in a single foreground Bash call so the whole pipeline survives to completion. Use a timeout of 600000 ms (10 minutes), which covers the graphify.build_timeout ceiling (default 300 s) with margin:

_FERROX_SHIM_NAME="ferrox-tools.cjs"; _FERROX_RUNTIME_ROOT="${RUNTIME_DIR:-$(git rev-parse --show-toplevel 2>/dev/null || pwd)}"; FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/ferrox-core/bin/${_FERROX_SHIM_NAME}"; if [ -f "$FERROX_TOOLS" ]; then ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.claude/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif [ -f "${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}" ]; then FERROX_TOOLS="${_FERROX_RUNTIME_ROOT}/.codex/ferrox-core/bin/${_FERROX_SHIM_NAME}"; ferrox_run() { node "$FERROX_TOOLS" "$@"; }; elif command -v ferrox-tools >/dev/null 2>&1; then FERROX_TOOLS="$(command -v ferrox-tools)"; () {  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };  [ -f  ];  FERROX_TOOLS=; () { node  ; };    >&2;  1; ;  [ -n  ] && [ -n  ];     >>  2>/dev/null || ; 
graphify update . \
  &&  graphify-out/graph.json .planning/graphs/graph.json \
  && { [ -f graphify-out/graph.html ] &&  graphify-out/graph.html .planning/graphs/graph.html || ; } \
  &&  graphify-out/GRAPH_REPORT.md .planning/graphs/GRAPH_REPORT.md \
  && ferrox_run graphify build snapshot \
  && ferrox_run graphify status

Do NOT pass run_in_background: true. Typical builds complete in 15-60 seconds and the entire chain must run foreground.

If the chain fails (non-zero exit):

• Display: ## GRAPHIFY BUILD FAILED followed by the captured stderr
• Do NOT delete .planning/graphs/ -- the prior valid graph remains available
• STOP

If the chain succeeds:

• Parse the trailing graphify status JSON
• Display: ## GRAPHIFY BUILD COMPLETE with the node, edge, and hyperedge counts

---

MVP-Mode Node Rendering

MVP-mode rendering. When a phase has **Mode:** mvp in ROADMAP.md (resolved via ferrox-tools query roadmap.get-phase --pick mode), render its graph node with two distinct visual signals:

1. Distinct fill color. Use #22c55e (green) for MVP-mode phase nodes. Standard phases keep the default fill color. Two-channel signaling (color + label) handles color-blind and grayscale renders.
2. MVP label suffix. Append (MVP) to the node's label text. Example: a phase originally labeled Phase 1: User Auth renders as Phase 1: User Auth (MVP).

Both signals fire together — never just one. Per PRD Q5 decision, the goal is unambiguous visual distinction in any render context.

When the phase mode is null/absent, render with the standard color and label — no behavioral change for non-MVP phases.

---

Anti-Patterns

1. DO NOT spawn an agent for any operation -- build, query, status, and diff all run inline. Sub-agent isolation terminates background bash when the agent exits, which previously truncated graphify builds mid-write and left only the cache populated (#3166).
2. DO NOT pass run_in_background: true for the build chain -- the operation is fast and must complete in the foreground.
3. DO NOT modify graph files directly -- always go through graphify update . and the snapshot CLI.
4. DO NOT skip the config gate check.
5. DO NOT use ferrox-tools config-get for the config gate -- it exits on missing keys unless --default is passed.