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19 Commits

Author SHA1 Message Date
Safi d23ae1774d v2: hypergraph support - hyperedges in graph.json, shaded regions in HTML, report section 2026-04-05 23:18:25 +01:00
Safi e6fefa8a2c v2: semantic similarity edges, scored higher in surprising connections 2026-04-05 23:12:47 +01:00
Safi 0f11f6a32d v2: confidence scores on INFERRED edges, avg shown in report 2026-04-05 23:06:07 +01:00
Safi e8b8e2039d v2: fast --update for code-only changes, parallel AST+semantic, graphify claude install 2026-04-05 23:00:24 +01:00
Safi 0a31c0862b add git commit hook - auto-rebuilds graph after every commit 2026-04-05 22:40:34 +01:00
Safi 2a8b6c16ad fix test_watch: update import after _run_update renamed to _notify_only 2026-04-05 20:58:23 +01:00
Safi fd2cc8d8a7 Surface all options post-run; wiki-first follow-ups; --update regenerates wiki 2026-04-05 17:07:57 +01:00
Safi ef06d7d8d9 Add --wiki export: agent-crawlable knowledge wiki from graph 2026-04-05 16:54:50 +01:00
Safi a7f8cab1a9 test: add end-to-end pipeline integration test 
Covers detect → extract → build → cluster → analyze → report → export
using existing fixtures. AST-only (no LLM calls), catches regressions
in how modules connect, not just individual module behaviour.
 2026-04-05 00:42:30 +01:00
Safi 8708333484 feat: vis.js HTML graph, token reduction benchmark, repo cleanup 
- Replace pyvis with custom vis.js renderer: node size by degree,
  click-to-inspect panel with clickable neighbors, search box,
  community filter, physics clustering by community
- HTML graph generated by default on every run (no --html flag needed)
- Token reduction benchmark auto-runs after every /graphify on corpora >5k words
- Fix 292 edge warnings: silently skip stdlib/external edges in build.py
- Fix build() to merge extractions before building (cross-extraction edges were dropped)
- Add 5 HTML renderer tests (223 total)
- Remove unnecessary files: lib/, tests/eval_attention.py, misplaced eval reports
- Add graphify-out/ and .graphify_*.json to .gitignore
- Bump version to 0.1.4, remove pyvis dependency
- README: token reduction as top-level selling point, vis.js in tech stack,
  graph.html in output listing, correct test count and install command
 2026-04-05 00:20:56 +01:00
Safi a7d1969f02 docs: update surprising connections description, test count 
style: replace all em dashes with hyphens

fix: explain hidden .graphify/ folder in skill output and README

fix: rename .graphify/ to graphify-out/ so output is visible by default
 2026-04-05 00:20:56 +01:00
Safi 258eff3e9f feat: composite surprise score — cross-type, cross-repo, community distance, peripheral→hub 2026-04-05 00:20:56 +01:00
Safi a7f910667d feat: GraphML export (--graphml flag) for Gephi and yEd 2026-04-05 00:20:56 +01:00
Safi 81a43f028f feat: 13-language AST support and token benchmark 
Java, C, C++, Ruby, C#, Kotlin, Scala, PHP via tree-sitter (13 total)
benchmark.py measures BFS subgraph tokens vs corpus tokens
5 skill bug fixes (cohesion crash, dead step, missing MCP tool)
 2026-04-04 18:56:38 +01:00
Safi 41e4e3576a security: SSRF protection, HTML escaping, path guards, encoding hardening 
- graphify/security.py (new): centralised security module
    - validate_url(): blocks file://, ftp://, data:, any non-http/https scheme
    - _NoFileRedirectHandler: re-validates redirect targets, blocks file:// redirects
    - safe_fetch(): streams response, 50MB hard cap, non-2xx raises, timeout
    - safe_fetch_text(): safe_fetch + UTF-8 decode with errors=replace
    - validate_graph_path(): resolves path, requires inside .graphify/, base must exist
    - sanitize_label(): strip control chars, cap 256, html.escape() — mirrors
      code-review-graph's _sanitize_name pattern
- graphify/ingest.py: _fetch_html() and _download_binary() now use safe_fetch*;
  ingest() validates URL scheme and wraps network calls in try/except;
  YAML frontmatter: newlines stripped from question before embedding
- graphify/extract.py: all 33 bare .decode() → .decode("utf-8", errors="replace")
  — non-UTF-8 source files degrade gracefully instead of crashing extraction
- graphify/export.py: sanitize_label() on all node labels and edge titles
  before pyvis embeds them in HTML output
- graphify/serve.py: _load_graph() validates graph_path via validate_graph_path()
  and wraps JSONDecodeError with recovery message; sanitize_label() on MCP
  text output
- graphify/detect.py: os.walk(..., followlinks=False) made explicit
- SECURITY.md (new): threat model, mitigations table, reporting process
- tests/test_security.py (new): 20 tests covering all security.py functions
 2026-04-04 18:56:38 +01:00
Safi 0b7460a9e3 perf+fix: parallel extraction, faster imports, bug fixes 
45x faster cluster import, 135x faster detect, parallel subagent extraction,
auto-exclude venvs/caches, suggest_questions fix, manifest fix, install CLI
 2026-04-04 18:56:38 +01:00
Safi e7a03a0539 feat: cache, multi-language extraction, MCP, memory feedback 
call-graph INFERRED edges, multi-language semantic extraction, SHA256 cache,
MCP stdio server with shortest_path, Q&A memory feedback loop
 2026-04-04 18:56:38 +01:00
Safi ce47198be1 feat: Claude Code skill, Obsidian vault, install, tests 
skill.md with full pipeline steps, Obsidian as default output (canvas, tags,
dataview, graph colors), two-command install, 71 tests, .gitignore, deps
 2026-04-04 18:53:43 +01:00
Safi 77966a7622 feat: core pipeline 
detect, extract (AST + call-graph), build, cluster, analyze, report, export
PDF extraction, tree-sitter AST, pyvis HTML, schema validation
 2026-04-04 18:52:44 +01:00