cdeust/Cortex

• fix: format 5 files to pass ruff formatting check
• fix: resolve all CodeQL security alerts + update auto-backfill tests
• fix: resolve ReDoS vulnerability in CamelCase regex (CodeQL py/redos)
• feat: consolidation pipeline, board view, replay tracking, auto-backfill (v3.4.0)
• fix: make .mcp.json work in both plugin and project context
• docs: fix cowork install command to cortex-cowork
• docs: add Cortex-cowork link for Cowork users
• fix: bump marketplace.json version to 3.3.0, update description
• docs: add marketplace installation as recommended setup path
• fix: format embedding_engine.py
• merge: security hardening + setup-project rebuild_profiles fix
• revert: restore original http_launcher.py — PYTHONPATH inherited from env
• fix: setup-project skill adds rebuild_profiles as Phase 2
• fix: viz server inherits CLAUDE_PLUGIN_DATA deps in PYTHONPATH
• security: harden code without touching install flow
• revert: security audit merge — broke marketplace plugin flow
• merge: security audit fixes — verified from bare metal
• fix: setup.sh registers MCP server in ~/.claude.json
• security: fix all findings from audit
• docs: add Getting Started section with installation guide
• docs: add Neural Graph section, update hooks/module counts
• docs: update agent team from 11 to 18 specialists
• fix: Docker — install hooks as cortex user, add CORTEX_RUNTIME env
• feat: discussions in neural graph, conversation viewer, fix all tests
• fix: hooks use exit 0 for skip cases, not exit 1
• fix: format install_hooks.py, remove dead code
• feat: runtime-aware storage, user-level hooks, autonomous setup
• fix: install psycopg before MCP server starts, use correct PYTHONPATH
• revert: remove broken memory neural graph integration (5 commits)
• fix: unified graph uses in-process server + materialized links + batch loading
• fix: single-command setup — DATABASE_URL default, backfill, env propagation
• fix: standalone viz server uses PostgreSQL + navigation API routes
• feat: complete Obsidian-like navigation — timeline, entity detail, live editing
• feat: Obsidian-like knowledge navigation — local graph, backlinks, breadcrumbs
• feat: neural evolution wave 2 — faithful DA RPE, schema acceleration, single-command setup
• chore: clean tasks — 6 development axes, remove 9 obsolete files
• fix: test report issues — checkpoint created_at, narrative cleanup, output caps
• fix: brighten text-dim for readability on dark backgrounds
• feat: dashboard UI updates for v3.2.0 — agent colors, protection rings, team badges
• feat: seamless auto-recall hook + full plugin hook registration
• fix: replace Mermaid with SVG diagrams for consistent rendering
• fix: replace ASCII diagrams with Mermaid for GitHub rendering

Full Changelog: https://github.com/cdeust/Cortex/compare/v3.2.0...v3.4.0