graphify

name	graphify
description	Build, refresh, query, explain, or trace Graphify repo and Vault knowledge.

Graphify in Pi / Codeflare

Use this skill for Graphify build, refresh, query, explain, path, and repo/Vault/global graph work.

Hard rules:

• Never use external/provider LLM backends for interactive Graphify work. Do not run graphify label, do not pass --backend, and do not use Gemini/OpenAI/Anthropic/DeepSeek/Kimi/Ollama extraction from this skill.
• Never use the graphify_build tool. Its semanticBackend parameter defaults to DeepSeek (an external provider requiring DEEPSEEK_API_KEY, which is NOT set in this container), so it fails with backend 'deepseek' requires DEEPSEEK_API_KEY. Use the local scripts/flows in this skill instead (build-graphify-ast.sh, safe-graphify-update.sh, graphify cluster-only).
• Vault graph rebuilds publish to Raw/Graphs/. After a local graphify cluster-only . from /home/user/Vault, copy graphify-out/graph.html to Raw/Graphs/vault-graph.html so the seeded Raw/Graphs/Vault Graph.md index link resolves through the SilverBullet .fs/ route. graphify-out/ is excluded from R2 bisync and the .fs/ route, so without the copy the link 404s.
• The Vault graph uses the canonical graphify schema. Vault nodes carry file_type + source_file (document/code) or file_type: "concept" with source_file: null; edges carry relation + confidence + confidence_score, identical to repo and global graphs. Never write the legacy type/path/mentions shape - graphify global add label-merges any node lacking source_file, collapsing document identity.
• Use the Pi main session agent for community labels. The main session writes graphify-out/.graphify_labels.json; then Graphify regenerates report/html locally from the graph's existing community assignments.
• Use Pi subagent tool calls only for uncached Full-mode semantic extraction chunks. Do not run headless semantic extraction for uncached docs/images.
• Use official Graphify flows for AST detection/extraction, graph build/merge, clustering, report generation, HTML generation, query/path/explain, global merge, and callflow export.
• Do not hand-edit graph output JSON. Do not add Codeflare-specific AST allowlists, import rewrites, or graph normalization.

Graph paths

Repo graph:   <repo>/graphify-out/graph.json
Vault graph:  /home/user/Vault/graphify-out/graph.json
Global graph: /home/user/.graphify/global-graph.json

There is normally no /home/user/workspace/graphify-out/graph.json.

Query workflow

Use the first-party native Pi tools for every graphify query - repo, Vault, and cross-repo/global alike:

• Broad context: graphify_query({ question, mode: "bfs" })
• Trace/path: graphify_query({ question, mode: "dfs" }) or graphify_path
• Node details: graphify_explain({ concept })

The native tool resolves the graph automatically: the active repo's graph when you are in a cloned repo, otherwise the merged global graph (/home/user/.graphify/global-graph.json, which holds the Vault plus every globally-added repo). You do not pass a graph path - this includes Vault/session/cross-repo memory questions, which resolve to the global graph.

After answering from a graphify_query / graphify_path / graphify_explain result, persist the Q&A back into the graph with graphify save-result so the next update extracts it as a node. For the CLI --graph fallback, the save-result feedback loop (--type query / path_query / explain), and the /graphify path and /graphify explain flows, see references/query.md.

Clone-time triage

Clone-time prompts must never authorize an automatic graph update. When a cloned repo has no graph, ask the user which graph action they want before running any build:

• Full repo AST-only build — free/local code graph.
• Full repo semantic build — intent to run Pi subagent semantic extraction after detection shows the actual uncached file/subagent counts.
• No graph action right now — stop without creating graphify-out.

When a cloned repo has a stale/unknown existing graph, ask before any update and offer only:

• Use the existing graph as-is — no files are modified.
• Full repo AST-only update — refresh code structure via the bounded wrapper.
• Full repo semantic refresh — intent to run the agent-driven semantic flow after detection shows the actual uncached file/subagent counts.

If the user already chose clone-time AST-only, treat that as the graph refresh choice after detection and do not ask the same mode question again. If the user chose clone-time Full semantic, treat it as intent only: after detection, show the actual uncached file/subagent counts and get confirmation before dispatching semantic subagents. Only re-prompt for a different mode if the chosen option is unavailable (for example, Full semantic was chosen but detection finds zero docs/papers/images).

Detect corpus

From the repo root:

/root/.local/share/uv/tools/graphifyy/bin/python - <<'PY'
import json
from pathlib import Path
from graphify.detect import detect
Path('.graphify_detect.json').write_text(json.dumps(detect(Path('.').resolve()), indent=2), encoding='utf-8')
PY
/root/.local/share/uv/tools/graphifyy/bin/python - <<'PY'
import json
from pathlib import Path
result = json.loads(Path('.graphify_detect.json').read_text())
print(f"Corpus: {result.get('total_files', 0)} files · ~{result.get('total_words', 0)} words")
for key in ['code', 'document', 'paper', 'image', 'video']:
    count = len(result.get('files', {}).get(key, []))
    if count:
        print(f"  {key}: {count}")
PY

If the user asks to ignore a file class (for example images), exclude that class from semantic extraction and/or pass matching --exclude flags to Graphify code-refresh commands. Do not alter code detection.

Mandatory graph refresh choice

After detection, present these choices and wait for the user to choose one, unless the current clone-time triage already captured an explicit Full repo AST-only or no-graph choice. If clone-time triage captured Full repo semantic, present only a post-detection cost/count confirmation before any semantic subagents run:

1. Architecture graph — recommended for large/noisy repos and daily navigation. Builds a smaller runtime-source graph by excluding tests, fixtures, generated files, docs/spec bulk, and build artifacts. Free/local.
2. Full repo AST-only — official Graphify AST/code graph for every detected code file. Free/local, but can be noisy on large repos.
3. Full repo semantic — Pi subagent tool calls produce semantic chunks for docs/papers/images, then Graphify consumes local semantic fragments and rebuilds locally.
4. No, I don't want to create/update a graph right now. — stop without modifying graphify-out.

If there are zero docs/papers/images, hide only the semantic option; still offer Architecture graph, Full repo AST-only, and the no-graph option. For repos with more than ~200 files, recommend Architecture graph unless the user explicitly wants exhaustive coverage.

If the user chooses the no-graph option, do not build, update, label, delete, or regenerate any Graphify outputs. Acknowledge and stop.

Architecture graph build

Use this when the user chooses Architecture graph:

bash /home/user/.pi/agent/scripts/build-graphify-architecture.sh .

The script uses Graphify’s own detect, extract, build, cluster, and report modules after applying generic architecture filters. It does not rewrite Graphify output. It deliberately defers user-facing graph.html and callflow.html until labels exist.

Then label communities using the Local main-session community labels section below. Do not push or present HTML outputs until label apply regenerates them from .graphify_labels.json.

Full repo AST-only initial build

Use this only when the user chooses Full repo AST-only and graphify-out/graph.json is missing:

bash /home/user/.pi/agent/scripts/build-graphify-ast.sh .

The script uses Graphify’s own detect, extract, build, cluster, and report modules only. It does not rewrite Graphify output. It deliberately defers user-facing graph.html and callflow.html until labels exist.

Then label communities using the Local main-session community labels section below. Do not push or present HTML outputs until label apply regenerates them from .graphify_labels.json.

Full repo AST-only refresh for an existing graph

Use this when the user chooses Full repo AST-only, graphify-out/graph.json exists, and source code changed:

bash /home/user/.pi/agent/scripts/safe-graphify-update.sh .

The safety wrapper only sets GRAPHIFY_MAX_WORKERS, applies ulimit -v, and runs upstream graphify update. Any graph.html produced by upstream update is provisional.

Then label communities using the Local main-session community labels section below. Do not push or present HTML outputs until label apply regenerates them from .graphify_labels.json.

Full build/update without provider LLMs

Use this when the user chooses Full repo semantic. Pi subagent tool calls produce semantic chunks for the uncached docs/papers/images, then Graphify consumes the local semantic fragments and rebuilds locally. Do not pass a model override when dispatching those subagents - they use the running session model. The full four-step flow (create semantic file list, dispatch subagents, merge chunks into the Graphify cache + local fragment, then rebuild from an AST baseline with build-graphify-ast.sh) lives in references/build.md. Load it only after the post-detection cost/count confirmation passes.

Then label communities using the Local main-session community labels flow below.

Local main-session community labels

This is the only allowed label path in Pi interactive Graphify - never run graphify label. The Pi main session agent prepares a worklist (local-graphify-labels.sh prepare .), inspects each community's nodes/sources, writes unique 2–6 word names to graphify-out/.graphify_labels.json, then applies them (local-graphify-labels.sh apply .), which regenerates GRAPH_REPORT.md + the final labeled graph.html + callflow.html without reclustering. Every completed build/update must finish by running label apply. See references/labels.md for the worklist/naming rules, the apply-script guarantees, and the callflow-html fallback.

Validation checklist

After build/refresh, verify:

• graphify-out/graph.json exists
• graphify-out/GRAPH_REPORT.md exists
• graphify-out/graph.html exists
• graphify-out/callflow.html exists
• node/edge counts are nonzero
• duplicate IDs = 0
• dangling edges = 0
• semantic cache was preserved for Full mode
• graphify-out/.graphify_labels.json exists and has complete, unique, non-placeholder, non-numbered labels for all communities

Global merge and git persistence

Merge into the global graph:

flock -w 5 /tmp/graphify-global.lock graphify global add graphify-out/graph.json --as "$(basename "$PWD")"

Commit only durable outputs when the user can push:

• graphify-out/graph.json
• graphify-out/GRAPH_REPORT.md
• graphify-out/graph.html
• graphify-out/.graphify_labels.json
• graphify-out/callflow.html
• optional graphify-out/wiki/

Do not commit caches, manifests, chunks, or .graphify_* intermediates other than .graphify_labels.json unless explicitly asked.

Ensure .gitattributes contains:

graphify-out/graph.json merge=graphify