@oriro/orirocli 0.1.8 → 0.1.9

package/skills/graphify/skills/amp/references/update.md

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+# graphify reference: incremental update and cluster-only
+
+Load this only when the user passed `--update` or `--cluster-only`. A first-time full build never reads this file.
+
+## For --update (incremental re-extraction)
+
+Use when you've added or modified files since the last run. Only re-extracts changed files - saves tokens and time.
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import sys, json
+from graphify.detect import detect_incremental, save_manifest
+from pathlib import Path
+
+result = detect_incremental(Path('INPUT_PATH'))
+new_total = result.get('new_total', 0)
+print(json.dumps(result, indent=2, ensure_ascii=False))
+Path('graphify-out/.graphify_incremental.json').write_text(json.dumps(result, ensure_ascii=False), encoding=\"utf-8\")
+deleted = list(result.get('deleted_files', []))
+if new_total == 0 and not deleted:
+    print('No files changed since last run. Nothing to update.')
+    raise SystemExit(0)
+if deleted:
+    print(f'{len(deleted)} deleted file(s) to prune.')
+if new_total > 0:
+    print(f'{new_total} new/changed file(s) to re-extract.')
+"
+```
+
+Then populate `.graphify_detect.json` so Steps 3A–6 (which read it unconditionally) see the right state for an incremental run. `files` carries the changed subset (drives Step 3A AST + Step 3B0 cache check on only what changed); `all_files` carries the full corpus for any step that needs corpus-wide context:
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json
+from pathlib import Path
+r = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
+Path('graphify-out/.graphify_detect.json').write_text(json.dumps({
+    'files': r.get('new_files', {}),
+    'all_files': r.get('files', {}),
+    'total_files': r.get('new_total', 0),
+    'total_words': r.get('total_words', 0),
+    'skipped_sensitive': r.get('skipped_sensitive', []),
+    'needs_graph': True,
+}, ensure_ascii=False), encoding=\"utf-8\")
+"
+```
+
+If new files exist, first check whether all changed files are code files:
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json
+from pathlib import Path
+
+result = json.loads(open('graphify-out/.graphify_incremental.json', encoding='utf-8').read()) if Path('graphify-out/.graphify_incremental.json').exists() else {}
+code_exts = {'.py','.ts','.js','.go','.rs','.java','.cpp','.c','.rb','.swift','.kt','.cs','.scala','.php','.cc','.cxx','.hpp','.h','.kts','.lua','.toc','.f','.F','.f90','.F90','.f95','.F95','.f03','.F03','.f08','.F08'}
+new_files = result.get('new_files', {})
+all_changed = [f for files in new_files.values() for f in files]
+code_only = all(Path(f).suffix.lower() in code_exts for f in all_changed)
+print('code_only:', code_only)
+"
+```
+
+If `code_only` is True: print `[graphify update] Code-only changes detected - skipping semantic extraction (no LLM needed)`, run only Step 3A (AST) on the changed files, skip Step 3B entirely (no subagents), then go straight to merge and Steps 4–8.
+
+If `code_only` is False (any changed file is a doc/paper/image): run the full Steps 3A–3C pipeline as normal.
+
+
+If no new files exist (only deletions), create an empty extraction so the merge step can prune:
+
+```bash
+if [ ! -f graphify-out/.graphify_extract.json ]; then
+    echo '[graphify update] Only deletions -- creating empty extraction for merge.'
+    $(cat graphify-out/.graphify_python) -c "
+import json
+from pathlib import Path
+Path('graphify-out/.graphify_extract.json').write_text(json.dumps({'nodes':[],'edges':[],'hyperedges':[],'input_tokens':0,'output_tokens':0}), encoding='utf-8')
+"
+fi
+```
+
+
+Then:
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json
+from pathlib import Path
+from graphify.build import build_merge
+from graphify.detect import save_manifest
+
+# Load new extraction and incremental state
+new_extraction = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
+incremental = json.loads(Path('graphify-out/.graphify_incremental.json').read_text(encoding=\"utf-8\"))
+deleted = list(incremental.get('deleted_files', []))
+# Also prune old nodes for re-extracted (changed) files before inserting fresh AST.
+# Without this, build_merge's dedup pass tries to reconcile old and new versions of
+# the same file's nodes and can collapse same-named symbols across files (#1178).
+changed = [f for files in incremental.get('new_files', {}).values() for f in files]
+prune = list(dict.fromkeys(deleted + changed)) or None
+
+# Use build_merge() — reads graph.json directly without NetworkX round-trip
+# so edge direction (calls, implements, imports) is always preserved (#801).
+G = build_merge(
+    [new_extraction],
+    graph_path='graphify-out/graph.json',
+    prune_sources=prune,
+)
+print(f'[graphify update] Merged: {G.number_of_nodes()} nodes, {G.number_of_edges()} edges')
+
+# Write merged result back to .graphify_extract.json so Step 4 sees the full graph
+merged_out = {
+    'nodes': [{'id': n, **d} for n, d in G.nodes(data=True)],
+    'edges': [
+        # Explicit source/target last so they win over any stale attrs in d.
+        {**{k: val for k, val in d.items() if k not in ('_src', '_tgt', 'source', 'target')},
+         'source': d.get('_src', u), 'target': d.get('_tgt', v)}
+        for u, v, d in G.edges(data=True)
+    ],
+    # G.graph["hyperedges"] holds hyperedges from both existing graph.json
+    # and new_extraction (build_merge combines them). Falling back to
+    # new_extraction only would silently drop prior-run hyperedges (#801).
+    'hyperedges': list(G.graph.get('hyperedges', [])),
+    'input_tokens': new_extraction.get('input_tokens', 0),
+    'output_tokens': new_extraction.get('output_tokens', 0),
+}
+Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out, ensure_ascii=False), encoding=\"utf-8\")
+print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
+
+# Save manifest so next --update diffs against today's state, not the
+# prior run's baseline (prevents ghost-node reports on subsequent updates).
+save_manifest(incremental['files'])
+print('[graphify update] Manifest saved.')
+"
+```
+
+Then run Steps 4–8 on the merged graph as normal.
+
+After Step 4, show the graph diff:
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json
+from graphify.analyze import graph_diff
+from graphify.build import build_from_json
+from networkx.readwrite import json_graph
+import networkx as nx
+from pathlib import Path
+
+# Load old graph (before update) from backup written before merge
+old_data = json.loads(Path('graphify-out/.graphify_old.json').read_text(encoding=\"utf-8\")) if Path('graphify-out/.graphify_old.json').exists() else None
+new_extract = json.loads(Path('graphify-out/.graphify_extract.json').read_text(encoding=\"utf-8\"))
+G_new = build_from_json(new_extract)
+
+if old_data:
+    G_old = json_graph.node_link_graph(old_data, edges='links')
+    diff = graph_diff(G_old, G_new)
+    print(diff['summary'])
+    if diff['new_nodes']:
+        print('New nodes:', ', '.join(n['label'] for n in diff['new_nodes'][:5]))
+    if diff['new_edges']:
+        print('New edges:', len(diff['new_edges']))
+"
+```
+
+Before the merge step, save the old graph: `cp graphify-out/graph.json graphify-out/.graphify_old.json`
+Clean up after: `rm -f graphify-out/.graphify_old.json`
+
+---
+
+## For --cluster-only
+
+Skip Steps 1–3. Re-run clustering on the existing graph:
+
+```bash
+graphify cluster-only .
+```
+
+Then run Steps 5–9 as normal (label communities, generate viz, benchmark, clean up, report).

package/skills/graphify/skills/claude/references/add-watch.md

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+# graphify reference: add a URL and watch a folder
+
+Load this when the user ran `/graphify add <url>` or passed `--watch`. Neither is part of the default build.
+
+## For /graphify add
+
+Fetch a URL and add it to the corpus, then update the graph.
+
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import sys
+from graphify.ingest import ingest
+from pathlib import Path
+
+try:
+    out = ingest('URL', Path('./raw'), author='AUTHOR', contributor='CONTRIBUTOR')
+    print(f'Saved to {out}')
+except ValueError as e:
+    print(f'error: {e}', file=sys.stderr)
+    sys.exit(1)
+except RuntimeError as e:
+    print(f'error: {e}', file=sys.stderr)
+    sys.exit(1)
+"
+```
+
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+
+Supported URL types (auto-detected):
+- YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
+- Twitter/X → fetched via oEmbed, saved as `.md` with tweet text and author
+- arXiv → abstract + metadata saved as `.md`
+- PDF → downloaded as `.pdf`
+- Images (.png/.jpg/.webp) → downloaded, Claude vision extracts on next run
+- Any webpage → converted to markdown via html2text
+
+---
+
+## For --watch
+
+Start a background watcher that monitors a folder and auto-updates the graph when files change.
+
+```bash
+python3 -m graphify.watch INPUT_PATH --debounce 3
+```
+
+Replace INPUT_PATH with the folder to watch. Behavior depends on what changed:
+
+- **Code files only (.py, .ts, .go, etc.):** re-runs AST extraction + rebuild + cluster immediately, no LLM needed. `graph.json` and `GRAPH_REPORT.md` are updated automatically.
+- **Docs, papers, or images:** writes a `graphify-out/needs_update` flag and prints a notification to run `/graphify --update` (LLM semantic re-extraction required).
+
+Debounce (default 3s): waits until file activity stops before triggering, so a wave of parallel agent writes doesn't trigger a rebuild per file.
+
+Press Ctrl+C to stop.
+
+For agentic workflows: run `--watch` in a background terminal. Code changes from agent waves are picked up automatically between waves. If agents are also writing docs or notes, you'll need a manual `/graphify --update` after those waves.

package/skills/graphify/skills/claude/references/exports.md

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+# graphify reference: extra exports and benchmark
+
+Load this when the user passed one of the export flags (`--wiki`, `--neo4j`, `--neo4j-push`, `--svg`, `--graphml`, `--mcp`), or when the corpus is large enough for the token-reduction benchmark. Each step runs only for its own flag.
+
+### Step 6b - Wiki (only if --wiki flag)
+
+**Only run this step if `--wiki` was explicitly given in the original command.**
+
+Run this before Step 9 (cleanup) so `.graphify_labels.json` is still available.
+
+```bash
+graphify export wiki
+```
+
+### Step 7 - Neo4j export (only if --neo4j or --neo4j-push flag)
+
+**If `--neo4j`** - generate a Cypher file for manual import:
+
+```bash
+graphify export neo4j
+```
+
+**If `--neo4j-push <uri>`** - push directly to a running Neo4j instance. Ask the user for credentials if not provided:
+
+```bash
+graphify export neo4j --push bolt://localhost:7687 --user neo4j --password PASSWORD
+```
+
+Default URI is `bolt://localhost:7687`, default user is `neo4j`. Uses MERGE - safe to re-run without creating duplicates.
+
+### Step 7b - SVG export (only if --svg flag)
+
+```bash
+graphify export svg
+```
+
+### Step 7c - GraphML export (only if --graphml flag)
+
+```bash
+graphify export graphml
+```
+
+### Step 7d - MCP server (only if --mcp flag)
+
+```bash
+python3 -m graphify.serve graphify-out/graph.json
+```
+
+This starts a stdio MCP server that exposes tools: `query_graph`, `get_node`, `get_neighbors`, `get_community`, `god_nodes`, `graph_stats`, `shortest_path`. Add to Claude Desktop or any MCP-compatible agent orchestrator so other agents can query the graph live.
+
+To configure in Claude Desktop, add to `claude_desktop_config.json`:
+```json
+{
+  "mcpServers": {
+    "graphify": {
+      "command": "python3",
+      "args": ["-m", "graphify.serve", "/absolute/path/to/graphify-out/graph.json"]
+    }
+  }
+}
+```
+
+### Step 8 - Token reduction benchmark (only if total_words > 5000)
+
+If `total_words` from `graphify-out/.graphify_detect.json` is greater than 5,000, run:
+
+```bash
+graphify benchmark
+```
+
+Print the output directly in chat. If `total_words <= 5000`, skip silently - the graph value is structural clarity, not token compression, for small corpora.

package/skills/graphify/skills/claude/references/extraction-spec.md

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+# graphify reference: extraction subagent prompt
+
+Load this in Step 3 Part B when the corpus has at least one doc, paper, or image chunk. A pure-code corpus skips Part B and never reads this file. Each semantic subagent receives the prompt below verbatim (substitute FILE_LIST, CHUNK_NUM, TOTAL_CHUNKS, DEEP_MODE, and CHUNK_PATH).
+
+```
+You are a graphify extraction subagent. Read the files listed and extract a knowledge graph fragment.
+Output ONLY valid JSON matching the schema below - no explanation, no markdown fences, no preamble.
+
+Files (chunk CHUNK_NUM of TOTAL_CHUNKS):
+FILE_LIST
+
+Rules:
+- EXTRACTED: relationship explicit in source (import, call, citation, "see §3.2")
+- INFERRED: reasonable inference (shared data structure, implied dependency)
+- AMBIGUOUS: uncertain - flag for review, do not omit
+
+Code files: focus on semantic edges AST cannot find (call relationships, shared data, arch patterns).
+  Do not re-extract imports - AST already has those.
+Doc/paper files: extract named concepts, entities, citations. For rationale (WHY decisions were made, trade-offs, design intent): store as a `rationale` attribute on the relevant concept node — do NOT create a separate rationale node or fragment node. Only create a node for something that is itself a named entity or concept. Use `file_type:"rationale"` for concept-like nodes (ideas, principles, mechanisms, design patterns). `file_type` MUST be one of exactly these six values: `code`, `document`, `paper`, `image`, `rationale`, `concept`. Any other value is invalid and will be rejected.
+Code files: when adding `calls` edges, source MUST be the caller (the function/class doing the calling), target MUST be the callee. Never reverse this direction. `calls` edges MUST stay within one language: a Python function cannot `calls` a JS/TS/Go/Rust/Java symbol and vice versa — cross-language call edges are phantom artifacts, never emit them.
+Image files: use vision to understand what the image IS - do not just OCR.
+  UI screenshot: layout patterns, design decisions, key elements, purpose.
+  Chart: metric, trend/insight, data source.
+  Tweet/post: claim as node, author, concepts mentioned.
+  Diagram: components and connections.
+  Research figure: what it demonstrates, method, result.
+  Handwritten/whiteboard: ideas and arrows, mark uncertain readings AMBIGUOUS.
+
+DEEP_MODE (if --mode deep was given): be aggressive with INFERRED edges - indirect deps,
+  shared assumptions, latent couplings. Mark uncertain ones AMBIGUOUS instead of omitting.
+
+Semantic similarity: if two concepts in this chunk solve the same problem or represent the same idea without any structural link (no import, no call, no citation), add a `semantically_similar_to` edge marked INFERRED with a confidence_score reflecting how similar they are (0.6-0.95). Examples:
+- Two functions that both validate user input but never call each other
+- A class in code and a concept in a paper that describe the same algorithm
+- Two error types that handle the same failure mode differently
+Only add these when the similarity is genuinely non-obvious and cross-cutting. Do not add them for trivially similar things.
+
+Hyperedges: if 3 or more nodes clearly participate together in a shared concept, flow, or pattern that is not captured by pairwise edges alone, add a hyperedge to a top-level `hyperedges` array. Examples:
+- All classes that implement a common protocol or interface
+- All functions in an authentication flow (even if they don't all call each other)
+- All concepts from a paper section that form one coherent idea
+Use sparingly — only when the group relationship adds information beyond the pairwise edges. Maximum 3 hyperedges per chunk.
+
+If a file has YAML frontmatter (--- ... ---), copy source_url, captured_at, author,
+  contributor onto every node from that file.
+
+confidence_score is REQUIRED on every edge - never omit it, never use 0.5 as a default:
+- EXTRACTED edges: confidence_score = 1.0 always
+- INFERRED edges: pick exactly ONE value from this set — never 0.5:
+    0.95  direct structural evidence (shared data structure, named cross-file reference).
+    0.85  strong inference (clear functional alignment, no direct symbol link).
+    0.75  reasonable inference (shared problem domain + similar shape, requires interpretation).
+    0.65  weak inference (thematically related, no shape evidence).
+    0.55  speculative but plausible (surface-level co-occurrence only).
+  Models follow discrete rubrics better than continuous ranges; the bimodal
+  distribution observed in production (>50% at 0.5, >40% at 0.85+) shows the
+  range guidance is being collapsed to a binary. If no value above fits, mark
+  the edge AMBIGUOUS rather than picking 0.4 or below.
+- AMBIGUOUS edges: 0.1-0.3
+
+Node ID format: lowercase, only `[a-z0-9_]`, no dots or slashes. Format: `{stem}_{entity}` where stem is `{parent_dir}_{filename_without_ext}` (the **immediate** parent directory name + the filename stem, both lowercased with non-alphanumeric chars replaced by `_`) and entity is the symbol name similarly normalized. Only one level of parent is used — not the full path. Examples: `src/auth/session.py` + `ValidateToken` → `auth_session_validatetoken`; `lib/utils/helpers.py` + `parse_url` → `utils_helpers_parse_url`; `tests/test_foo.py` + `_helper` → `tests_test_foo_helper`. Top-level files (no parent dir, e.g. `setup.py`) use just the filename stem: `setup_my_func`. This must match the ID the AST extractor generates — using just the filename (e.g., `session_validatetoken`) or the full path (e.g., `src_auth_session_validatetoken`) will create orphan ghost-duplicate nodes. If you are re-extracting a project that had ghost duplicates under the old format, the user should run `graphify extract --force` to rebuild cleanly. CRITICAL: never append chunk numbers, sequence numbers, or any suffix to an ID (no `_c1`, `_c2`, `_chunk2`, etc.). IDs must be deterministic from the label alone — the same entity must always produce the same ID regardless of which chunk processes it.
+
+Generate the extraction JSON matching this schema exactly:
+{"nodes":[{"id":"session_validatetoken","label":"Human Readable Name","file_type":"code|document|paper|image|rationale|concept","source_file":"relative/path","source_location":null,"source_url":null,"captured_at":null,"author":null,"contributor":null}],"edges":[{"source":"node_id","target":"node_id","relation":"calls|implements|references|cites|conceptually_related_to|shares_data_with|semantically_similar_to|rationale_for","confidence":"EXTRACTED|INFERRED|AMBIGUOUS","confidence_score":1.0,"source_file":"relative/path","source_location":null,"weight":1.0}],"hyperedges":[{"id":"snake_case_id","label":"Human Readable Label","nodes":["node_id1","node_id2","node_id3"],"relation":"participate_in|implement|form","confidence":"EXTRACTED|INFERRED","confidence_score":0.75,"source_file":"relative/path"}],"input_tokens":0,"output_tokens":0}
+
+Then write the JSON to disk using the Write tool at this exact absolute path (no relative paths — Write resolves relative paths against an undefined cwd and the file will be silently lost):
+CHUNK_PATH
+```

package/skills/graphify/skills/claude/references/github-and-merge.md

@@ -0,0 +1,46 @@
+# graphify reference: GitHub clone and cross-repo merge
+
+Load this when the user passed one or more `https://github.com/...` URLs, or named several local subfolders to merge into one graph.
+
+### Step 0 - Clone GitHub repo(s) (only if a GitHub URL was given)
+
+**Single repo:**
+```bash
+LOCAL_PATH=$(graphify clone <github-url> [--branch <branch>])
+# Use LOCAL_PATH as the target for all subsequent steps
+```
+
+**Multiple repos (cross-repo graph):**
+```bash
+# Clone each repo, run the full pipeline on each, then merge
+graphify clone <url1>   # → ~/.graphify/repos/<owner1>/<repo1>
+graphify clone <url2>   # → ~/.graphify/repos/<owner2>/<repo2>
+# Run /graphify on each local path to produce their graph.json files
+# Then merge:
+graphify merge-graphs \
+  ~/.graphify/repos/<owner1>/<repo1>/graphify-out/graph.json \
+  ~/.graphify/repos/<owner2>/<repo2>/graphify-out/graph.json \
+  --out graphify-out/cross-repo-graph.json
+```
+
+Graphify clones into `~/.graphify/repos/<owner>/<repo>` and reuses existing clones on repeat runs. Each node in the merged graph carries a `repo` attribute so you can filter by origin.
+
+**Multiple local subfolders (monorepo or multi-service layout):**
+
+The skill pipeline writes all intermediate and final outputs to `graphify-out/` in the current working directory. Running the skill on each subfolder separately will clobber the same output dir. Instead, use the CLI directly for each subfolder — it places `graphify-out/` *inside* the scanned path:
+
+```bash
+graphify extract ./core/     # → ./core/graphify-out/graph.json
+graphify extract ./service/  # → ./service/graphify-out/graph.json
+graphify extract ./platform/ # → ./platform/graphify-out/graph.json
+# Add --backend gemini|kimi|openai|deepseek|claude-cli depending on which API key you have set
+
+# Then merge at the project root:
+graphify merge-graphs \
+  ./core/graphify-out/graph.json \
+  ./service/graphify-out/graph.json \
+  ./platform/graphify-out/graph.json \
+  --out graphify-out/graph.json
+```
+
+Once `graphify-out/graph.json` exists, the fast path above takes over: any codebase question runs `graphify query` directly on the merged graph — no re-extraction, no size gate.

package/skills/graphify/skills/claude/references/hooks.md

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+# graphify reference: commit hook and native CLAUDE.md integration
+
+Load this when the user asked to install the post-commit hook or wire graphify into a project's CLAUDE.md.
+
+## For git commit hook
+
+Install a post-commit hook that auto-rebuilds the graph after every commit. No background process needed - triggers once per commit, works with any editor.
+
+```bash
+graphify hook install    # install
+graphify hook uninstall  # remove
+graphify hook status     # check
+```
+
+After every `git commit`, the hook detects which code files changed (via `git diff HEAD~1`), re-runs AST extraction on those files, and rebuilds `graph.json` and `GRAPH_REPORT.md`. Doc/image changes are ignored by the hook - run `/graphify --update` manually for those.
+
+If a post-commit hook already exists, graphify appends to it rather than replacing it.
+
+---
+
+## For native CLAUDE.md integration
+
+Run once per project to make graphify always-on in Claude Code sessions:
+
+```bash
+graphify claude install
+```
+
+This writes a `## graphify` section to the local `CLAUDE.md` that instructs Claude to check the graph before answering codebase questions and rebuild it after code changes. No manual `/graphify` needed in future sessions.
+
+```bash
+graphify claude uninstall  # remove the section
+```

package/skills/graphify/skills/claude/references/query.md

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+# graphify reference: query, path, explain
+
+Load this when the user asks a question against an existing graph, or runs `/graphify path` or `/graphify explain`. The core's query stub points here for the full traversal flow.
+
+Two traversal modes - choose based on the question:
+
+| Mode | Flag | Best for |
+|------|------|----------|
+| BFS (default) | _(none)_ | "What is X connected to?" - broad context, nearest neighbors first |
+| DFS | `--dfs` | "How does X reach Y?" - trace a specific chain or dependency path |
+
+### Step 0 — Constrained query expansion (REQUIRED before traversal)
+
+graphify's `query` CLI matches nodes via case-folded substring + IDF — there is **no stemming, no synonyms, no cross-language match** inside the binary. If the user's question uses different language or different domain vocabulary than the graph's labels (user says "обработчик" / graph says "handler"; user says "authentication" / graph says "Guardian"), the literal matcher returns 0 hits and the answer collapses to noise.
+
+Fix this **without inventing tokens** by expanding the query against the actual graph vocabulary first:
+
+1. Extract the token vocabulary from node labels:
+```bash
+$(cat graphify-out/.graphify_python) -c "
+import json, re
+from pathlib import Path
+data = json.loads(Path('graphify-out/graph.json').read_text())
+vocab = set()
+for n in data['nodes']:
+    for c in re.findall(r'[^\W\d_]+', n.get('label','') or '', re.UNICODE):
+        parts = re.findall(r'[A-Z]+(?=[A-Z][a-z])|[A-Z]?[a-z]+|[A-Z]+', c) or [c]
+        for p in parts:
+            t = p.lower()
+            if 3 <= len(t) <= 30:
+                vocab.add(t)
+Path('graphify-out/.vocab.txt').write_text('\n'.join(sorted(vocab)))
+print(f'vocab: {len(vocab)} tokens')
+"
+```
+
+2. Read `graphify-out/.vocab.txt`. Then for the user's question, select **up to 12 tokens from this exact list** that semantically match the query intent. Hard constraints:
+   - You MUST pick only tokens present in the vocabulary file. Do NOT invent tokens.
+   - If a query concept has no plausible token in the vocab, skip it — do not substitute a near-synonym from training memory.
+   - If **no** vocab tokens match the query at all, output an empty list and tell the user the corpus has no relevant vocabulary for this question. Do not fabricate a search.
+   - Translate cross-language: Russian "аутентификация" → look for `auth`, `credential`, `token`, `security` IFF present in vocab.
+   - Morphology: "handlers" maps to `handler` IFF present; "todos" maps to `todo` IFF present.
+
+3. Print the selection explicitly to the user before running the query, so the expansion is auditable:
+```
+Query expanded to (from graph vocab, N tokens): [token1, token2, ...]
+```
+If the list is empty, say so plainly and stop — do not proceed to traversal.
+
+### Step 1 — Traversal
+
+Build the **expanded query string** by joining the selected tokens with spaces. Use this string as `QUESTION` below — NOT the original user question. (The original question is preserved only for `save-result` at the end.)
+
+```bash
+graphify query "QUESTION"
+# or: graphify query "QUESTION" --dfs --budget 3000
+```
+
+Answer using **only** what the graph output contains. Quote `source_location` when citing a specific fact. If the graph lacks enough information, say so - do not hallucinate edges.
+
+After writing the answer, save it back into the graph so it improves future queries. Include the expanded tokens inside the `--answer` text (e.g. `"Expanded from original query via vocab: [tokens]. Then traversed..."`) so the next `--update` extracts the expansion history as a graph node:
+
+```bash
+$(cat graphify-out/.graphify_python) -m graphify save-result --question "ORIGINAL_QUESTION" --answer "ANSWER" --type query --nodes NODE1 NODE2
+```
+
+Replace `ORIGINAL_QUESTION` with the user's verbatim question, `ANSWER` with your full answer text (containing the expanded-token trace), `NODE1 NODE2` with the list of node labels you cited. This closes the feedback loop: the next `--update` will extract this Q&A as a node in the graph.
+
+---
+
+## For /graphify path
+
+Find the shortest path between two named concepts in the graph.
+
+```bash
+graphify path "NODE_A" "NODE_B"
+```
+
+Replace `NODE_A` and `NODE_B` with the actual concept names. Then explain the path in plain language - what each hop means, why it's significant.
+
+After writing the explanation, save it back:
+
+```bash
+$(cat graphify-out/.graphify_python) -m graphify save-result --question "Path from NODE_A to NODE_B" --answer "ANSWER" --type path_query --nodes NODE_A NODE_B
+```
+
+---
+
+## For /graphify explain
+
+Give a plain-language explanation of a single node - everything connected to it.
+
+```bash
+graphify explain "NODE_NAME"
+```
+
+Replace `NODE_NAME` with the concept the user asked about. Then write a 3-5 sentence explanation of what this node is, what it connects to, and why those connections are significant. Use the source locations as citations.
+
+After writing the explanation, save it back:
+
+```bash
+$(cat graphify-out/.graphify_python) -m graphify save-result --question "Explain NODE_NAME" --answer "ANSWER" --type explain --nodes NODE_NAME
+```

package/skills/graphify/skills/claude/references/transcribe.md

@@ -0,0 +1,48 @@
+# graphify reference: transcribe video and audio
+
+Load this only when `detect` reported one or more `video` files. A corpus with no video never reads this.
+
+### Step 2.5 - Transcribe video / audio files (only if video files detected)
+
+Skip this step entirely if `detect` returned zero `video` files.
+
+Video and audio files cannot be read directly. Transcribe them to text first, then treat the transcripts as doc files in Step 3.
+
+**Strategy:** Read the god nodes from `graphify-out/.graphify_detect.json` (or the analysis file if it exists from a previous run). You are already a language model — write a one-sentence domain hint yourself from those labels. Then pass it to Whisper as the initial prompt. No separate API call needed.
+
+**However**, if the corpus has *only* video files and no other docs/code, use the generic fallback prompt: `"Use proper punctuation and paragraph breaks."`
+
+**Step 1 - Write the Whisper prompt yourself.**
+
+Read the top god node labels from detect output or analysis, then compose a short domain hint sentence, for example:
+
+- Labels: `transformer, attention, encoder, decoder` → `"Machine learning research on transformer architectures and attention mechanisms. Use proper punctuation and paragraph breaks."`
+- Labels: `kubernetes, deployment, pod, helm` → `"DevOps discussion about Kubernetes deployments and Helm charts. Use proper punctuation and paragraph breaks."`
+
+Set it as `WHISPER_PROMPT` to use in the next command.
+
+**Step 2 - Transcribe:**
+
+```bash
+GRAPHIFY_WHISPER_MODEL=base  # or whatever --whisper-model the user passed
+$(cat graphify-out/.graphify_python) -c "
+import json, os
+from pathlib import Path
+from graphify.transcribe import transcribe_all
+
+detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
+video_files = detect.get('files', {}).get('video', [])
+prompt = os.environ.get('GRAPHIFY_WHISPER_PROMPT', 'Use proper punctuation and paragraph breaks.')
+
+transcript_paths = transcribe_all(video_files, initial_prompt=prompt)
+print(json.dumps(transcript_paths, ensure_ascii=False))
+" > graphify-out/.graphify_transcripts.json
+```
+
+After transcription:
+- Read the transcript paths from `graphify-out/.graphify_transcripts.json`
+- Add them to the docs list before dispatching semantic subagents in Step 3B
+- Print how many transcripts were created: `Transcribed N video file(s) -> treating as docs`
+- If transcription fails for a file, print a warning and continue with the rest
+
+**Whisper model:** Default is `base`. If the user passed `--whisper-model <name>`, set `GRAPHIFY_WHISPER_MODEL=<name>` in the environment before running the command above.