chore: track claude skills, tools, templates, reference code and research-wiki

- Add all claude skills (brainstorming, commit, debugging, TDD, etc.) - Add claude hooks (pre-commit-guard, post-edit-quality) - Add research templates (experiment plan, research brief, etc.) - Add claude tools (arxiv/semantic_scholar/openalex fetch, wiki, exa) - Add TRM4 reference implementation as algorithm fidelity baseline - Add research-wiki content (plans, index, graph, query_pack) - Update .gitignore to exclude .graphify_version runtime state
2026-07-06 20:59:03 -04:00
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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
+```