cdeust/Cortex

• release: v3.14.6 — silent AP self-heal + canonical domain ids
• fix(ap): silent self-heal for stale graph slots + multi-roster resolver — install/setup-project never errors
• docs(adr): ADR-0049 — Cortex stays local on main; server-side deferred
• fix(ci): ruff format 4 files + add pre-commit-ruff hook for CI parity
• refactor: sync clean pii-fixtures + secret-shield hook from zetetic (post-scrub)
• fix(domains): canonicalise domain ids — kill worktree-path noise in viz + list_domains
• feat(hooks/briefing): dynamic _SPECIALIST_AGENTS load + zetetic bridge ADR
• fix(ci): remove 2 unused imports from pii-daemon (ruff check F401)
• fix(ci): apply ruff format to 3 files (CI was failing on Lint)
• fix(security): remove TP secret-fixture corpus (working tree + history)
• release: v3.14.5 — adopt canonical uvx pattern (per modelcontextprotocol/servers)
• refactor: complete sync — add missing memory commands + drain hook
• refactor: sync spawn-agent.sh + .mcp.json wiring from zetetic-team-subagents
• refactor: sync genius agents batch B (51-98) from zetetic-team-subagents
• refactor: sync genius agents batch A (1-50) from zetetic-team-subagents
• refactor: sync 19 team agents from zetetic-team-subagents (Batch 2)
• refactor: sync memory infrastructure from zetetic-team-subagents (Batch 1)
• release: v3.14.4 — launcher self-installs full base runtime
• release: v3.14.3 — align MCP wiring with Anthropic-official plugin convention
• release: bump marketplace.json to v3.14.2
• release: v3.14.2 — native AST CALLS chains + humanized panel + Dijkstra compliance
• refactor(compliance): Dijkstra YELLOW items — all UI files under 300 LOC
• fix(ci+compliance): ruff format + Dijkstra RED items (panel split, dead param)
• fix(ui): humanization corrections from Eco + Vygotsky + Feynman audits
• feat(ui): humanize workflow-graph detail panel for non-technical users
• fix(ci): install [codebase] extra + skip tree-sitter tests without it
• fix(graph): CALLS edges were silently dropped — cross-verified by Wu + Feynman
• feat(graph): caller-qualified CALLS — full method-to-method dependency chain
• refactor(ap): remove legacy CORTEX_ENABLE_AP env var — single source of truth
• feat(ap): flip default to ON, make user-overridable via MCP config
• feat(graph): native AST source — L6 depth without automatised-pipeline
• docs: GitNexus competitive analysis + 5-move science-grounded plan
• docs: gap analysis v2 — CORRECTED after reading AP source + web search
• docs: gap analysis — codebase analysis as first-class Cortex core
• docs(darval): reply draft for issue #14 OB4 fix + O1 resolution
• refactor(homeostatic): tighten OB4 fix — fold clips, flag estimate
• fix(homeostatic): issue #14 OB4 — emit bimodality_after on scale-invariant paths
• test(main): bump tool-count assertion to 46 for Gap 1 (query_workflow_graph)
• feat(graph): Gap 1 — query_workflow_graph MCP tool + README refresh
• feat(graph): Gap 6 — confidence + reason on WorkflowEdge
• fix(graph): populate Calls_* / Imports_* rel tables via AP resolve pass
• fix(security): replace ancestor-walk loop with Path.is_relative_to
• fix(security): werkzeug-style whitelist + Path.is_relative_to for CWE-22
• fix(security): apply CodeQL's exact canonical sanitizer patterns
• test(invariants): bump I2 allowlist for handlers/anchor.py after ruff format
• fix(security): satisfy CodeQL on response-splitting + path-injection
• feat(mcp): add title + annotations + outputSchema to every tool
• fix(security): clear remaining CodeQL path-injection + response-splitting alerts
• fix(security): add explicit path-containment checks (CWE-22)
• docs: bump test count to 2500+ across README, CLAUDE.md, linkedin post
• docs(readme): document L6 AST-symbol layer in Graph View
• docs(readme): correct companion project name to automatised-pipeline
• docs(readme): add ai-architect automated pipeline to companion projects
• style: ruff format workflow_graph_source_ast
• release: v3.14.1 — hero screenshot + version bump
• docs(legend): expand L6 section with every AST symbol-type color
• fix(ui): Board + Knowledge crash on symbol-label 'constructor'
• fix(ui+ast): board/knowledge hang + multi-language symbol coverage
• feat(ui): surface code-symbol impact in Knowledge + Board views
• docs(readme): rewrite v3.14.0 callout without internal code names
• docs+ui: L6 filter options, taller legend, README v3.14.0 callout
• feat(viz): phase-driven graph build, AST integration, diff/legend polish
• docs(adr): ADR-0046 — integrate with automatised-pipeline
• style: fix ruff check — drop unused re-exports, retarget imports
• style: apply ruff format to workflow-graph modules
• docs(readme): new hero screenshot + workflow-graph section
• fix(viz): eliminate alpha-box artifact + make Graph the default view
• feat(viz): full file-access coverage + timestamps + compact filter row
• feat(viz): Claude-workflow graph — radial hierarchy, filters, full diff coverage
• fix(lint): drop remaining unused imports in pipeline_impact_bump test
• docs(darval): github issue #14 O1 instrumentation ask
• fix(lint): drop unused imports flagged by CI
• feat(wiki): plain-language top-level README generator
• feat(darval-o1): heat_delta instrumentation on cohort_correction output
• fix(i2): allow-list pipeline_impact_bump heat_base writer
• fix(darval-v3.13.2): forgetting_curve fit_quality + schema_acceleration bootstrap guard
• feat(grooming): wiki templates + auditor + cortex-wiki-groomer agent
• feat(pipeline-4): /cortex:cortex-setup-project handles optional pipeline
• feat(pipeline-3): PostToolUse heat bump via pipeline detect_changes
• feat(pipeline-2): SessionStart async re-analyze when graph stale
• feat(pipeline-1): auto-wire ai-automatised-pipeline into mcp-connections.json
• feat(doctor): optional codebase-pipeline detection with install guidance
• style: ruff format + lint sweep for Phase 2-7 additions
• fix(v3.13.2): revert plugin.json to launcher path (Claude Code marketplace install)
• fix(v3.13.1): SQLite A3 migration + pinned plugin.json versions
• docs(readme): v3.13.0 scalability release note + cortex-doctor + pool architecture
• feat(marketplace): no-Python-required install + uvx-consistent hooks
• bench(phase-5): LongMemEval 500-Q regression gate PASSED — exact match
• release(v3.13.0): bump version + cortex-doctor CLI for marketplace users
• feat(phase-7): hardening — content normalization, metrics, Dockerfile
• feat(phase-4): chunked consolidate + streaming homeostatic moments
• feat(phase-2): JOIN replacements for plasticity / synaptic tagging / co-activation
• test(phase-5-step-6): I10 invariant — pool capacity vs cycle worker fanout
• feat(phase-5-step-4c): asyncio.to_thread wrap handlers at registration
• feat(phase-5-step-4b): migrate 14 external store._conn.execute sites to pool
• feat(phase-5-step-4a): _execute borrows from interactive_pool per call
• feat(phase-5-step-5): per-tool admission semaphore middleware
• feat(phase-5-step-3): latency-class registry for MCP tool handlers
• feat(phase-5-step-2): ConnectionPool infrastructure in PgMemoryStore
• feat(phase-5-step-1): psycopg_pool dep + pool config knobs
• docs(phase-5): ConnectionPool + to_thread + admission design spec
• docs(darval): github issue #14 A3 delivery reply draft
• bench(a3-step-9): BEAM-100K regression gate PASSED — exact zero delta
• bench(a3-step-9): LoCoMo 1982-Q regression gate PASSED
• bench(a3-step-9): LongMemEval 500-Q regression gate PASSED
• fix(a3): effective_heat underflow guards for multi-year age rows
• feat(a3-step-8): delete legacy heat path — single A3 canonical implementation
• feat(a3-step-7): flag-gated decay cycle no-op under A3_LAZY_HEAT
• feat(a3-step-6): recall_memories_lazy PL/pgSQL function + get_a3_ddl
• feat(a3-step-5): dual-path heat writers (anchor, preemptive_context, stale, sqlite)
• chore(settings): add project permission allowlist for read-only ops
• style: ruff format + drop unused import in Phase 6 fixes
• feat(reranker): Platt calibration from rate_memory feedback (AF-2)
• feat(a3-step-4): bump_heat_raw canonical writer + homeostatic_state helpers
• feat(write_gate): auto-calibrate threshold from observed acceptance rate (AF-5)
• feat(a3-step-2): effective_heat() + effective_heat_frozen() PL/pgSQL functions
• feat(a3-step-1): CORTEX_MEMORY_A3_LAZY_HEAT flag + migration SQL scaffolding
• fix(recall_hierarchical): require domain or memory_ids — kill O(N^2) uncapped fallback
• style: ruff check --fix unused imports in Phase 1 tests
• style: ruff format Phase 1 changes — line length + minor normalisation
• fix(profile-store): per-domain split — bound write amplification per session
• fix(compression): eliminate redundant gist encode on 0→2 transitions
• fix(homeostatic): Welford one-pass moments for heat-distribution health
• fix(wiki-sync): surface errors in remember handler, stop silent swallowing
• fix(codebase-analyze): bounded-candidate rglob — ADR-0045 R2/R3
• style: ruff format v3.12.x commits (CI format-check fix)
• fix(validation): bounded tags envelope on remember (ADR-0045 R2)
• fix(validation): tighten remember.content maxLength 50K→10K (ADR-0045 R2)
• fix(embedding_cache): SHA256[:16] keys, never raw text (ADR-0045 R5)
• fix(import_sessions): delete full_read path — streaming only (ADR-0045 R2)
• release: v3.12.2 — darval field report fixes (#14)
• feat(entities): case-variant canonicalization + merge migration
• feat(diagnostics): cls + memify reason_for_zero signals (#14)
• feat(backfill+homeostatic): age-decayed initial_heat + bimodality-aware cohort correction (#14)
• release: v3.12.1 — hotfix: emergence_tracker import + I2 regression guard
• docs(scalability): Phase 0 program — ADR-0045 + invariants I1-I10 + memory_entities audit + Phase 0.4.5 backfill design
• chore(tools): TDQS A-grade rewrite across 53 MCP tool schemas + fix emergence_metrics import
• release: v3.12.0 — upstream MCP ingest (ingest_codebase + ingest_prd)
• feat(ingest): upstream MCP consumption — ingest_codebase + ingest_prd
• fix(tests): update exploding_decay signature to match Phase B memories= param
• release: v3.11.0 — consolidate batching + plasticity/CLS/cascade fixes
• perf(consolidate): v3.11 deferred fixes — batching, cache, plasticity, CLS, cascade (#13)
• perf(consolidate): per-stage telemetry + fix homeostatic import bug (#13)
• perf(consolidate): per-stage telemetry + fix homeostatic silent failure (#13)
• release: v3.10.1 — wiki_purge tool for cleaning audit-artefact pollution
• fix(wiki): reject audit artefacts (backfill, stage-N, path/URL titles)
• release: v3.10.0 — Cowork compat + TDQS schema enrichment
• chore(tools): TDQS schema enrichment (40 tools) + sqlite memory_entities
• style: ruff format memory_store after auto-fallback edit
• feat(memory_store): auto-fallback to SQLite when DATABASE_URL absent
• chore(plugin): declare CORTEX_RUNTIME in mcp env schema
• security: use compile-time filename constants + README Glama badge
• chore: add glama.json — maintainer manifest for Glama's evaluator
• docs: refresh Views → Wiki screenshot with post-edit rendered view
• docs: reposition Cortex as a scientific-authoring tool, not just memory+graph
• security: close 2 new CodeQL alerts (ReDoS + HTTP response splitting)
• feat(wiki ui): collapse duplicate-title entries in the sidebar tree
• fix(wiki export): strip frontmatter before pandoc; re-inject as --metadata
• fix(wiki export): clearer error messages; pre-check for LaTeX engine
• ci+ui: skip ccplugins workflows without PAT; surface export errors in UI
• feat(wiki redesign): Phase 10 — Pandoc export (PDF, LaTeX, DOCX, HTML)
• feat(wiki redesign): Phase 9 — academic extensions
• feat(wiki redesign): Phase 8 — inline editor with live KaTeX preview
• feat(wiki redesign): Phase 7.3 — seed wiki from existing repo docs
• feat(wiki redesign): Phase 7.1 + 7.2 — cold-start fix
• ci: keep ccplugins fork in sync continuously
• ci: auto-sync cortex plugin to ccplugins monorepo on release
• docs: add Wiki + Knowledge screenshots; refresh Graph + Board shots
• security: match CodeQL py/path-injection example verbatim (3rd attempt)
• security: switch sanitizer to startswith pattern for CodeQL recognition
• security: keep sanitized path on same variable through sink (CodeQL #48 #49)
• security: close 6 CodeQL alerts in wiki_store + wiki_view_executor
• feat(wiki redesign): Phase 6 — Frontend integration
• feat(wiki redesign): Phase 5 — Malleability (user rules + executable views)
• feat(wiki redesign): Phase 4 — Thermodynamics
• feat(wiki redesign): Phase 3 — Concept emergence (Strauss grounded theory)
• feat(wiki redesign): Phase 2.4 + 2.5 — Curate + Compile
• feat(wiki redesign): Phase 2.3 — Synthesize phase (Path A + Path B)
• feat(wiki redesign): Phase 2.2 — Resolve phase
• feat(wiki redesign): Phase 2.1 — Extract phase (claim_events from memories)
• fix(wiki migrate): accurate written/unchanged counter on idempotent re-runs
• feat(wiki redesign): Phase 1.2 + 1.3 — migration + self-hosting loader
• feat(wiki redesign): Phase 1.1 — wiki.* schema + IR models
• feat: invert wiki gate + harden path traversal check (security)
• fix: classifier tolerates markdown heading prefix in reject patterns
• fix: reject / slash-command framing in wiki
• release: v3.9.1 — hooks.json nested schema fix (#12)
• fix: hooks.json nested schema per Claude Code requirement (#12)
• style: apply ruff format + remove unused imports
• feat: 7-view frontend + wiki classifier + backend schema fixes
• fix: resolve ruff lint errors — unused/missing EmbeddingEngine imports
• release: v3.9.0 — engram slot cache (#11) + safe GPU embedding (#10)
• feat: safe GPU auto-detection for embedding engine (#10)
• perf: cache engram slots + COUNT(*) for allocate_engram_slot (#11)
• feat: sync all agents, skills, commands, hooks, tools from zetetic-team-subagents
• fix: remove unauthorized attribution from all agent files
• style: "powered by ai-architect.tools" right-aligned on two lines
• style: unify brand identity — teal accent + ai-architect.tools tag
• feat: add ASCII art banner — SVG for GitHub README
• security: fix command injection vectors (CodeQL CWE-78)
• docs: compiled arxiv PDF + LinkedIn endorser post draft
• fix: remove unused StageDetector import (ruff F401)
• style: ruff format run_benchmark + stage_detector
• feat: temporal assembler beats oracle — 0.471 MRR (+33.4%) on BEAM-10M
• fix: apply genius review corrections across all docs
• docs: arxiv-ready LaTeX paper for cs.IR submission
• fix: replace all LaTeX with Unicode + code blocks for GitHub rendering
• fix: LaTeX syntax issues in research papers
• docs: rewrite science.md + research post as arxiv-style papers
• docs: add per-category breakdowns under each benchmark
• docs: update agent count to 27 specialists
• docs: full narrative README rewrite — Zikkaron-style tutorial
• docs: full narrative README — hook, scenario, benchmarks with context
• docs: add auto-wiki feature + science table with brain analogies
• fix: remove unused own_budget variable (ruff F841)
• docs: move Scientific Foundation above Benchmarks
• docs: slim README from 680 to 416 lines — product page, not paper
• docs: slim README to product page, move science to docs/
• docs: rewrite How It Works + Architecture in plain language
• docs: reorganize scientific foundation into plain-language results
• style: ruff format all context_assembly + benchmark files
• docs: link README to public ai-prd-builder origin, not private repo
• docs: trace architecture origin to ai-prd-builder (public, Sep 2025)
• docs: add verifiable commit SHAs for prior art provenance
• docs: update README with BEAM-10M scores + research post
• feat: structured context assembly — 21.5% BEAM-10M improvement
• release: v3.8.0 — auto-promote decision memories to wiki
• release: v3.7.3 — fix Windows seed_project hang (#8)
• release: v3.7.2 — surface real Postgres connection errors (#9)
• chore: actually add traces/ to .gitignore
• chore: ignore traces/ runtime telemetry directory
• fix(recall): expose source column in recall_memories() PL/pgSQL
• feat(wiki): rewrite as first-class authored layer, not PG projection
• style(wiki): apply ruff format and fix import ordering
• feat(wiki): add read-only Markdown projection of memory state
• fix(setup): install benchmark and codebase deps in setup scripts
• style: format abstention_gate.py
• fix: restore validated 0.546 BEAM pipeline + benchmark setup docs
• fix: pin uvx to Python 3.13 for MCP server
• docs: link companion projects in README header
• docs: document full BEAM ablation log in README
• feat: instruction/preference typed retrieval + intent detection
• feat: MMR diversity module + ablation results (disabled for now)
• docs: correct benchmark scores, acknowledge database pollution error
• feat: event ordering + summarization intent detection and chrono reranking
• feat: emotional memory processing — retrieval, decay, reconsolidation
• style: format pg_store modules
• fix: stale prepared statement recovery + connection resilience
• docs: update README with new visualization screenshots and install options
• fix: cross-platform MCP via uvx, hooks via python detection
• fix: break CodeQL taint chain — separate subcommand and args parameters
• fix: remove unused os import in git_diff.py
• fix: sever CodeQL taint chain in subprocess.run — use _GIT_BINARY + fresh list
• fix: CORS headers for discussion detail fetch
• fix: format session_start.py
• fix: whitelist-based path security + deprecated utcnow
• fix: bump pyproject.toml version to 3.4.2 for PyPI release
• fix: remove unused os import in http_server.py
• fix: remove duplicate shell=False kwarg in git_diff.py
• style: format launcher.py and setup.py
• feat: cross-platform setup.py for Windows support
• fix: harden path sanitization for CodeQL — pre-validate before resolve()
• feat: pipeline tree with canvas bezier lines, scroll sync, surpriseScore
• fix: plugin.json hooks format + marketplace v3.4.1
• wip: pipeline tree improvements + surpriseScore + security fixes
• fix: resolve all remaining CodeQL path traversal and command injection alerts
• feat: pipeline tree view, board flow header, UI improvements (P2)
• feat: coordinated selection + minimizable detail panel
• feat: coordinated selection (brushing/linking) between graph and board views
• fix: format install_hooks.py and test_cold_start.py, bump pyproject.toml to 3.4.0
• 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
• docs: rewrite README for v3.2.0 — agent integration, hooks, skills
• fix: correct hook semantics + format reranker.py for CI
• feat: preemptive file context + agent briefing hooks
• feat: decision auto-protection, team memory bus, auto-dream consolidation
• feat: adaptive alpha reranking (disabled) + comprehensive ablation data
• data: BEAM signal weight ablation + cross-benchmark regression analysis
• chore: bump version to 3.1.0
• fix: remove unused imports and variable (ruff lint)
• style: format 13 files with ruff
• docs: rewrite README — science-first, full paper transparency
• fix: zetetic audit — remove invented constants, add ablation data
• feat: zetetic rewrite — faithful paper implementations across all 33 core modules
• docs: zetetic scientific standard reference document
• wip: Bruch 2023 TMM convex fusion + faithful Titans + zetetic standard
• fix: OR tsquery, benchmark isolation, Bruch 2023 TMM convex fusion
• style: format git_diff.py and http_standalone.py with ruff
• chore: bump version to 3.0.0
• feat: redesign unified graph visualization UX
• docs: update hero image alt text for v2.6.0 screenshots
• docs: update hero images with v2.6.0 unified graph screenshots
• fix: add HF model cache to release workflow
• fix: add sentence-transformers and networkx to dev deps for CI
• fix: move model pre-download after pip install, allow soft failure
• fix: cache HuggingFace model in CI to prevent download failures
• fix: ruff format http_standalone.py
• release: v2.6.0 — remove memory dashboard, global memory dedup fix, cleanup
• release: v2.5.5 — domain clustering in unified graph, per-project brain shells
• release: v2.5.4 — update script + cache workaround documentation
• release: v2.5.3 — auto-install embeddings, Docker one-liner, session warnings
• release: v2.5.2 — schema resilience, lint fixes, all backends aligned
• fix: ruff format + remove unused variable to pass CI lint
• fix: consistent per-statement schema init across PG, SQLite, and Docker
• feat: add cortex-remember-global and cortex-recall-global skills
• feat: global memories — cross-project knowledge with auto-detection and visualization
• fix: split DDL into individual statements to prevent cascading schema failures
• release: v2.5.1 — version bump (2.5.0 tarball burned on PyPI)
• fix: align package.json and safeskill-report.json to v2.5.0
• release: v2.5.0
• fix: 5 user-reported bugs — path validation, hierarchical recall, causal chain, narrative, seed
• fix: persistent memory across Docker container restarts
• fix: use shields.io badge for SafeSkill — their badge API is broken
• fix: SafeSkill badge uses dynamic API from published npm package
• fix: Docker entrypoint registers MCP in .claude.json, strips host config
• fix: badge links to local SafeSkill report
• docs: add SafeSkill 94/100 scan report, remove stale badge link
• fix: add minimal package.json for SafeSkill scanner, update badge to 94/100
• fix: remove legacy Node.js files flagged by SafeSkill security scan
• Merge pull request #2 from OyaAIProd/safeskill-scan-1774780323456

Full Changelog: https://github.com/cdeust/Cortex/compare/v2.4.1...v3.14.6