From 98f5e3b71c7f425d5dbe9ad4dd74efb9beeeaba6 Mon Sep 17 00:00:00 2001 From: cdeust Date: Wed, 1 Jul 2026 06:24:16 +0200 Subject: [PATCH] =?UTF-8?q?docs(readme):=20global=20review=20=E2=80=94=20v?= =?UTF-8?q?3.25.0=20refresh?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - version badge 3.24.0 → 3.25.0 - companion projects: automatised-pipeline no longer "driven via run_pipeline" (that tool is not in this server, see CLAUDE.md); Cortex ingests its codebase analysis via the optional ingest_codebase / change_impact tools - What's new: add v3.25.0 (headless authoring hardening + active forgetting) and v3.24.0–3.24.1 (MCPB manifest + cross-backend recall fix); drop the two oldest entries (3.20/3.19) to keep the section to the five most recent releases - Science: add the active-forgetting mechanism (two Drosophila dopaminergic circuits — Rac1 permanent erosion + DAMB transient block; Davis & Zhong 2017, Sabandal et al. 2021), shipped in #69 but absent from the doc All counts verified against code: 42 canonical scopes (SCOPES tuple), 13 file sections (FILE_DOC_SECTIONS), 23 neuroscience mechanisms (ablation.py), codebase_context/impact/query tool names. Co-Authored-By: Claude Opus 4.8 (1M context) Claude-Session: https://claude.ai/code/session_019o58McF4LRfvGNNXaqG2Au --- README.md | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 34ae1635..6f0e72fb 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,7 @@ Python 3.10+ Tests References - Version 3.24.0 + Version 3.25.0

@@ -25,7 +25,7 @@ Companion projects:
cortex-beam-abstain (repo cortex-know-when-to-stop-training-model) — community-trained retrieval abstention model for RAG systems
zetetic-team-subagents — specialist Claude Code agents Cortex orchestrates with
- automatised-pipeline — automated 11-stage pipeline (findings → PRs) that Cortex drives via run_pipeline
+ automatised-pipeline — automated 11-stage pipeline (findings → PRs); Cortex ingests its codebase analysis via the optional ingest_codebase / change_impact tools
cortex-viz — read-only visualization MCP (galaxy graph, execution trace, wiki browser) over the same store

@@ -164,16 +164,16 @@ You rarely call these by hand: the lifecycle hooks (plugin install) inject the r ## What's new +**v3.25.0 — headless wiki-authoring hardened + active forgetting.** The headless wiki worker now delegates read-only codebase analysis to your **full zetetic specialist roster** (architect, engineer, code-reviewer, test-engineer, security-auditor, …) under a hard `Write/Edit/Bash` deny ceiling that propagates to delegated subagents; it bills a logged-in **Claude subscription by default** (API key opt-in), and no-ops every Cortex hook in the child process to stop consolidation→authoring recursion and memory pollution. Root-cause fix: a variadic `--add-dir` had been swallowing the authoring prompt, silently failing every drain with a source root since 3.24. New memory mechanism — **active forgetting**: two *Drosophila* dopaminergic circuits (permanent Rac1 trace erosion under chronic interference + transient DAMB retrieval block), shipped with a falsification harness left failing where the model genuinely diverges from biology. Also: Windows cross-platform portability. *(Davis & Zhong 2017; Sabandal et al. 2021)* + +**v3.24.0–3.24.1 — MCPB manifest fix + cross-backend recall fix.** 3.24.1 fixes `recall` (and every read tool) on **PostgreSQL**: the PG store returned `numpy.float32` scores and `datetime` timestamps where FastMCP needs JSON-native values, so a non-native field silently dropped `structuredContent` and the host rejected the call — on PostgreSQL only, while SQLite-backed tests stayed green. Normalized at the `safe_handler` boundary every tool crosses. 3.24.0: MCPB manifest schema fix + PyPI install docs. Also adds mutation testing (mutmut) scoped per-change. + **v3.23.0 — single-click bundle + registry-indexer build fix.** Cortex now ships as an MCP bundle (`.mcpb`) with a `uv` runtime and a selectable storage backend — **SQLite by default, PostgreSQL optional** — so it installs in one click with zero setup. Also: a `neuro-cortex-memory` console script so `uv run neuro-cortex-memory` resolves from a checkout; registry indexers that build with `uv sync` and launch via that script now start the server and register all 43 standalone tools **without** a PostgreSQL connection (46 when the automatised-pipeline + prd-spec-generator integrations are configured; so `tools/list` answers inside a DB-less container). **v3.22.0 — security + reliability hardening (P0/P1 audit).** Security: a headless-authoring RCE fix (the subprocess toolset is restricted and the untrusted repo's settings/hooks are ignored), DSN/secret redaction (libpq `?password=` query params and psycopg exception leaks), and pip supply-chain hardening. Fixed: the SQLite backend's incomplete `heat→heat_base` rename — all 11 indexes were never created (full table scans) and search/stats queried a dropped column; both are corrected, with a dedicated SQLite-backend CI job and deployment docs (WSL, TLS client-cert `DATABASE_URL`, remote PostgreSQL). 46 MCP tools. **v3.21.0 — visualization extracted to cortex-viz.** The entire visualization stack — the galaxy graph, execution trace, the Knowledge / Board / Wiki / Pipeline views, and their HTTP server — moves to a standalone companion MCP, **[cortex-viz](https://github.com/cdeust/cortex-viz)**, which reads this same store read-only. Cortex is a focused memory engine again (−50k lines). **Breaking:** the `open_visualization`, `get_methodology_graph`, and `query_workflow_graph` MCP tools are removed from Cortex — install cortex-viz to get them back (its `/cortex-visualize` skill replaces the old one). 46 MCP tools remain; no memory, retrieval, or wiki behaviour changed; full suite green (3214 tests). -**v3.20.0 — graph intelligence + memory knowledge-updates.** The codebase graph gains Leiden community detection, centrality and god-node analysis, and native tree-sitter symbol extraction across 7 languages — no `automatised-pipeline` dependency required. Memory learns to handle *knowledge updates*: a memory that supersedes prior knowledge records an explicit supersession edge so recall ranks the newest version above what it replaces; a MinHash entity-dedup engine (with AST-symbol origin flagging) collapses near-duplicate entities during a consolidate-time merge cycle; and a new `include_related` recall mode returns a memory's graph neighbours in one call. - -**v3.19.0 — memory hygiene + scoring integrity.** A fix to an auto-capture scoring inversion at all three roots: prospective-trigger injection no longer harvests garbage keyword triggers from raw tool dumps; WRRF fusion excludes mechanical freshness (`post_tool_capture`) from the hot/recency pools so churn isn't mistaken for importance; and `rate_memory` feedback now wires into rank as a metamemory confidence prior (Kraaij 2002). Oversized auto-captures store a deterministic gist plus a content-addressed artifact pointer — full output one `Read` away, no truncation. Benchmarks regression-free (LongMemEval R@10 98.4% / MRR 0.9124; LoCoMo MRR 0.8278). - → **[Full changelog and release notes](https://github.com/cdeust/Cortex/releases)** --- @@ -194,6 +194,8 @@ Cortex doesn't store memories the way a database stores rows. It treats them the **Similar memories stay distinct.** Pattern separation, modeled on the dentate gyrus, keeps "Tuesday's standup" separate from "Wednesday's standup" even though they're nearly identical — without it, retrieval returns the same generic match for every similar query. *(Leutgeb et al. 2007; Yassa & Stark 2011)* +**Forgetting is active, not just passive decay.** Beyond the slow cooling of the heat model, Cortex runs two independent dopaminergic forgetting circuits from *Drosophila*: a permanent one that erodes a memory's trace under chronic interference (Rac1), and a transient one that blocks retrieval of a memory without erasing it (DAMB). Interference-heavy, low-value memories are actively removed rather than left to linger — the same way your brain prunes what competes without paying off. *(Davis & Zhong 2017; Sabandal et al. 2021)* + The two arXiv-ready papers go deeper: **[Thermodynamic Memory vs. Flat-Importance Stores (PDF, 34 pages)](docs/arxiv-thermodynamic/main.pdf)** · **[Stage-Aware Context Assembly (PDF, 39 pages)](docs/arxiv-context-assembly/main.pdf)**. ---