chore(skills): graphify dist refresh 0.8.45 -> 0.9.6

Generator-owned files updated by the out-of-band 'make plugin' run
(SKILL.md, extraction-spec, query reference, version marker). Committed
deliberately after diff review; CHANGELOG Unreleased notes the bump.

skills/graphify/references/extraction-spec.md

@@ -58,7 +58,7 @@ confidence_score is REQUIRED on every edge - never omit it, never use 0.5 as a d
   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.
+Node ID format: lowercase, only `[a-z0-9_]`, no dots or slashes. Format: `{stem}_{entity}` where stem is the **full repo-relative path with the extension dropped**, every path segment kept and joined with `_` (each segment lowercased with non-alphanumeric chars replaced by `_`), and entity is the symbol name similarly normalized. Use every directory level, not just the immediate parent — this keeps same-named files in different directories distinct. Examples: `src/auth/session.py` + `ValidateToken` → `src_auth_session_validatetoken`; `lib/utils/helpers.py` + `parse_url` → `lib_utils_helpers_parse_url`; `tests/test_foo.py` + `_helper` → `tests_test_foo_helper`; `docs/v1/api/README.md` + `getUser` → `docs_v1_api_readme_getuser`. 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 only the immediate parent (e.g., `auth_session_validatetoken`) will create orphan ghost-duplicate nodes. If you are re-extracting a project built under the old immediate-parent 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":"auth_session_validatetoken","label":"Human Readable Name","file_type":"code|document|paper|image|rationale|concept","source_file":"<FILE_LIST path verbatim>","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":"<FILE_LIST path verbatim>","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":"<FILE_LIST path verbatim>"}],"input_tokens":0,"output_tokens":0}

skills/graphify/references/query.md

@@ -31,7 +31,7 @@ Fix this **without inventing tokens** by expanding the query against the actual
 $(cat graphify-out/.graphify_python) -c "
 import json, re
 from pathlib import Path
-data = json.loads(Path('graphify-out/graph.json').read_text())
+data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
 vocab = set()
 for n in data['nodes']:
     for c in re.findall(r'[^\W\d_]+', n.get('label','') or '', re.UNICODE):
@@ -40,7 +40,7 @@ for n in data['nodes']:
             t = p.lower()
             if 3 <= len(t) <= 30:
                 vocab.add(t)
-Path('graphify-out/.vocab.txt').write_text('\n'.join(sorted(vocab)))
+Path('graphify-out/.vocab.txt').write_text('\n'.join(sorted(vocab)), encoding='utf-8')
 print(f'vocab: {len(vocab)} tokens')
 "
 ```
@@ -83,7 +83,7 @@ from networkx.readwrite import json_graph
 import networkx as nx
 from pathlib import Path
 
-data = json.loads(Path('graphify-out/graph.json').read_text())
+data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
 G = json_graph.node_link_graph(data, edges='links')
 
 question = 'QUESTION'
@@ -173,6 +173,14 @@ $(cat graphify-out/.graphify_python) -m graphify save-result --question "ORIGINA
 
 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.
 
+**Work memory (self-improving loop).** Add an `--outcome` so future sessions learn from this one — append `--outcome useful|dead_end|corrected` to the `save-result` command (and `--correction "the right answer"` when correcting):
+
+- `useful` — the cited nodes answered the question well (they become *preferred sources*).
+- `dead_end` — the question/path led nowhere; don't re-derive it next time.
+- `corrected` — the saved answer was wrong; `--correction` records what was right.
+
+At the **start** of graph work, refresh and read the lessons: run `graphify reflect --if-stale` (cheap, deterministic, no LLM; `--if-stale` makes it a no-op when `LESSONS.md` is already newer than every input, e.g. when the git hook just refreshed it), then read `graphify-out/reflections/LESSONS.md`. It lists **preferred sources** (start there), **known dead ends** (skip them), and prior **corrections**. Running `reflect` yourself keeps the lessons current even without the git hook installed; if the post-commit hook *is* installed, `--if-stale` means your session-start run costs almost nothing.
+
 ---
 
 ## For /graphify path
@@ -192,7 +200,7 @@ import networkx as nx
 from networkx.readwrite import json_graph
 from pathlib import Path
 
-data = json.loads(Path('graphify-out/graph.json').read_text())
+data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
 G = json_graph.node_link_graph(data, edges='links')
 
 a_term = 'NODE_A'
@@ -260,7 +268,7 @@ import networkx as nx
 from networkx.readwrite import json_graph
 from pathlib import Path
 
-data = json.loads(Path('graphify-out/graph.json').read_text())
+data = json.loads(Path('graphify-out/graph.json').read_text(encoding='utf-8'))
 G = json_graph.node_link_graph(data, edges='links')
 
 term = 'NODE_NAME'