Graphify CLI

Reusable contract for querying a Graphify code graph. The graph is read-only material: this skill covers finding it, querying it, and degrading gracefully — never building it. The division of paths is fixed:

Graph	Path	Who
Repository's own (.ai/graphify-out/graph.json)	graphify MCP tools (query_graph, get_neighbors, …)	Agents
Cross-repository global (~/.graphify/global-graph.json)	graphify-global MCP tools + ~/.graphify/global-manifest.json	Agents
Either graph, by hand	Read-only CLI with explicit --graph	Humans only
Lifecycle (first indexing, refresh)	/graphify-index command + graphify-init plugin	Human and plugin only — never agents

Availability detection

1. The per-repository graph lives at .ai/graphify-out/graph.json (repo root). Check that literal path. If the file exists and parses, the graph is available; record graphify: available.
2. If the graph file is missing, record graphify: absent and skip Graphify entirely. Do not build it: first indexing is human-gated behind the /graphify-index command, and the graphify-init OpenCode plugin owns refreshes afterwards. Mention /graphify-index to the user once as the way to enable the graph, then continue without it.
3. Check freshness: compare the graph's built_at_commit with git rev-parse HEAD, and check whether .ai/graphify-out/.opencode-extract-lock exists (a refresh is in flight). On a commit mismatch or a present lock, downgrade the record to graphify: stale: still query the graph, but treat every answer as an approximate locator — verify each claim against the current files before citing it, and never base impact or blast-radius conclusions on the stale graph alone. The graphify-init plugin refreshes it on the next session; never refresh it yourself.
4. Documentation coverage depends on the recorded indexing mode — read .ai/graphify-out/.opencode-index-mode (one JSON line): docs means markdown and other documents are indexed as document and concept nodes, so documentation questions are graph-first too; code-only means the graph holds no documentation and docs questions go straight to filesystem tools. When the mode file is missing (a graph indexed before it existed), fall back to .ai/graphify-out/.graphify_semantic_marker — Graphify writes it only when a semantic docs pass ran, so present means docs coverage, absent means code-only.

Never conclude "no graph" from a wildcard search. Patterns like **/graphify-out/graph.json do not match inside dot-directories, so they silently miss .ai/graphify-out/graph.json. An empty glob is inconclusive, not evidence of absence — check the literal path before reporting graphify: absent.

Querying the local graph (MCP)

The Graphify MCP tools are the agent path to the repository's graph: query_graph, get_node, get_neighbors, shortest_path, god_nodes, graph_stats, get_community. They answer over the graph the server was started with, read-only.

• Omit the optional project_path argument unless you genuinely need another repository. Passing it makes the server ignore the graph it was started with and resolve <project_path>/<GRAPHIFY_OUT>/graph.json from its own environment instead; if the server was launched without GRAPHIFY_OUT exported, that path does not exist and the tool reports no graph for a repository that has one. When a project_path call comes back empty, retry without it before concluding anything.
• If the MCP tools are unavailable, fall back to the runtime's filesystem tools directly — the CLI is not an agent fallback for the local graph.
• Cite the underlying file:line for every claim the graph resolves; the graph is a locator, not evidence by itself. Graphs may also contain documentation, paper, and image nodes when the repository owner enabled semantic indexing — treat them like any other node.

Cross-repository global graph (MCP)

~/.graphify/global-graph.json merges every indexed repository under a repo tag; the graphify-global MCP server exposes the same tool set over it.

Trigger: any question that names a repository or project other than the current one, not only questions that explicitly span several. Before Context7, web search, or a clarifying question, read ~/.graphify/global-manifest.json — an indexed tag means it is a local repo question, and wins over library documentation. Answer structural questions with the graphify-global tools. For content questions (what its documentation says, what a file contains), the tag's source_path points at that repo's .ai/graphify-out/graph.json — the repository root is two directories up; read the actual files there and cite them.

Caveat: node labels are not namespaced — two repositories defining the same class contribute two same-label nodes. Keep symbol-addressed queries on the repository's own graph, where labels are unambiguous; use the global graph for open-ended questions.

Manual CLI verbs (human use)

The read-only verbs (query, explain, path, affected, god-nodes) are for a human in a terminal — never an agent path. Always pass --graph explicitly; the CLI's default (./<GRAPHIFY_OUT>/graph.json) resolves only with GRAPHIFY_OUT=.ai/graphify-out exported from the repo root:

graphify global list                                                  # repos and node counts
graphify query "<question>" --graph ~/.graphify/global-graph.json
graphify query "<question>" --graph .ai/graphify-out/graph.json --budget 2000
graphify explain "<NodeLabel>" --graph .ai/graphify-out/graph.json

Hard rule: never lifecycle commands

Never run graphify extract, update, watch, global add, global remove, or any graphify ... install variant. They mutate state, and update/watch recreate graphify-out/ at the repository root, outside .ai/. First indexing belongs to the human-invoked /graphify-index command, refreshing belongs to the graphify-init plugin, and recovery belongs to the user.

Fallback

When the graph or the MCP tools are unavailable, continue with the runtime's normal read, LSP, grep, and glob tools without friction, and state the fallback in your output. Needing more than ~3 files for one structural question usually means the graph query was too broad — narrow it before crawling files.