release-v1.2.0

Author: voidstackloop

.claude/CLAUDE.md

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+# graphify
+- **graphify** (`.claude/skills/graphify/SKILL.md`) - any input to knowledge graph. Trigger: `/graphify`
+When the user types `/graphify`, use the installed graphify skill or instructions before doing anything else.

.claude/settings.json

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+{
+  "hooks": {
+    "PreToolUse": [
+      {
+        "matcher": "Bash|Grep",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "/home/saldev/.local/bin/graphify hook-guard search"
+          }
+        ]
+      },
+      {
+        "matcher": "Read|Glob",
+        "hooks": [
+          {
+            "type": "command",
+            "command": "/home/saldev/.local/bin/graphify hook-guard read"
+          }
+        ]
+      }
+    ]
+  }
+}

.claude/skills/graphify/.graphify_version

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+0.9.29

.claude/skills/graphify/SKILL.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
+$(cat graphify-out/.graphify_python) -c "
+import sys
+from graphify.ingest import ingest
+from pathlib import Path
+
+try:
+    out = ingest('URL', Path('./raw'), author='AUTHOR', contributor='CONTRIBUTOR')
+    print(f'Saved to {out}')
+except ValueError as e:
+    print(f'error: {e}', file=sys.stderr)
+    sys.exit(1)
+except RuntimeError as e:
+    print(f'error: {e}', file=sys.stderr)
+    sys.exit(1)
+"
+```
+
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+
+Supported URL types (auto-detected):
+- YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
+- Twitter/X → fetched via oEmbed, saved as `.md` with tweet text and author
+- arXiv → abstract + metadata saved as `.md`
+- PDF → downloaded as `.pdf`
+- Images (.png/.jpg/.webp) → downloaded, Claude vision extracts on next run
+- Any webpage → converted to markdown via html2text
+
+---
+
+## For --watch
+
+Start a background watcher that monitors a folder and auto-updates the graph when files change.
+
+```bash
+$(cat graphify-out/.graphify_python) -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.

.claude/skills/graphify/references/add-watch.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`, `--falkordb`, `--falkordb-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 7a - FalkorDB export (only if --falkordb or --falkordb-push flag)
+
+**If `--falkordb`** - generate a Cypher file. The statements are OpenCypher, but FalkorDB's `GRAPH.QUERY` runs one statement at a time (no bulk script import like Neo4j's `cypher-shell`), so prefer `--falkordb-push` to load a graph. Use this only when you want the portable `cypher.txt` artifact:
+
+```bash
+graphify export falkordb
+```
+
+**If `--falkordb-push <uri>`** - push directly to a running FalkorDB instance. Credentials are optional; ask the user only if the instance requires auth:
+
+```bash
+graphify export falkordb --push falkordb://localhost:6379
+```
+
+Default URI is `falkordb://localhost:6379` (the scheme is informational - `redis://` or a bare `host:port` work too), auth is optional, and the target graph defaults to `graphify`. 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
+$(cat graphify-out/.graphify_python) -m graphify.serve graphify-out/graph.json
+```
+
+This starts a stdio MCP server that exposes tools: `query_graph`, `get_node`, `get_neighbors`, `get_community`, `god_nodes`, `graph_stats`, `shortest_path`. Add to Claude Desktop or any MCP-compatible agent orchestrator so other agents can query the graph live.
+
+To configure in Claude Desktop, add to `claude_desktop_config.json`. Claude Desktop can't run `$(...)`, and under `uv tool install` the system `python3` can't import graphify — so set `command` to the **absolute interpreter path** printed by `cat graphify-out/.graphify_python`:
+```json
+{
+  "mcpServers": {
+    "graphify": {
+      "command": "<absolute path from: cat graphify-out/.graphify_python>",
+      "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.

.claude/skills/graphify/references/exports.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 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}
+
+source_file RULE (every node, edge, and hyperedge): set source_file to the path of the originating file EXACTLY as it appears in FILE_LIST — verbatim and absolute. Do NOT shorten to a basename, do NOT re-relativize, do NOT strip any directory prefix, and do NOT change separators (the engine canonicalizes separators and relativizes against the build root downstream). Copy the FILE_LIST entry character-for-character. This keeps the full build and incremental --update on the same base, so build_merge's replace-on-re-extract matches the existing node instead of accumulating a duplicate.
+
+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
+```

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

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+# 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.

.claude/skills/graphify/references/github-and-merge.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
+```