release: v3.19.4 — fix failing cortex MCP server in the plugin repo itself

Bumps manifest + marketplace + pyproject to 3.19.4, marks the CHANGELOG
Unreleased section released, and adds release notes for the -32000
shadow-registration fix (405f557): the repo-root .mcp.json was
double-read as project-scoped MCP config where ${CLAUDE_PLUGIN_ROOT}
is never substituted, spawning a phantom failing `cortex` server next
to the healthy plugin:cortex:cortex. Config is now inline in
plugin.json mcpServers; .mcp.json is gone; the contract test pins its
absence.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

Author: cdeust

.claude-plugin/marketplace.json

@@ -6,14 +6,14 @@
   },
   "metadata": {
     "description": "Persistent memory and cognitive profiling plugins for Claude Code",
-    "version": "3.19.3"
+    "version": "3.19.4"
   },
   "plugins": [
     {
       "name": "cortex",
       "source": "./",
       "description": "Persistent memory and cognitive profiling for Claude Code — thermodynamic memory with heat/decay, intent-aware retrieval, biological plasticity, codebase intelligence, and cognitive profiling. 49 MCP tools with enriched schemas. PostgreSQL + pgvector in CLI mode; automatic SQLite fallback in Cowork/sandboxed mode. v3.17.0 — autonomous per-project wiki: SessionStart auto-spawns a 6-hour consolidate cycle; a headless `claude -p` worker drains the curation-gap queue, calls codebase-intelligence MCP tools to ground each section in the real call graph, and authors missing anchor pages (architecture / services / api / data-flow / operations / decisions / PRD) per project from the source tree. 15 canonical scopes × 13 file sections; per-project dashboards under `wiki/_dashboards/`. Mermaid diagrams have a 🔍 lens with zoom + pan. Workflow graph with caller-qualified CALLS chains rendering full method-to-method dependencies (native tree-sitter, no AP required). Side panel humanized for non-technical users. Ingests codebase analysis (ai-automatised-pipeline) and PRDs (prd-spec-generator) into wiki + memory + knowledge graph. Docker image available.",
-      "version": "3.19.3",
+      "version": "3.19.4",
       "author": {
         "name": "Clement Deust",
         "email": "admin@ai-architect.tools"

.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "cortex",
   "description": "Persistent memory for Claude Code — remembers across sessions automatically. Install and forget. Scientific retrieval backed by 41 published papers.",
-  "version": "3.19.3",
+  "version": "3.19.4",
   "author": {
     "name": "Clement Deust",
     "email": "admin@ai-architect.tools"

CHANGELOG.md

@@ -6,6 +6,8 @@ adheres to [Semantic Versioning](https://semver.org/).
 
 ## [Unreleased]
 
+## [3.19.4] - 2026-06-12
+
 ### Fixed
 
 - **`/mcp` showed a failing `cortex` server (-32000) whenever the plugin

docs/release-notes/v3.19.4.md

@@ -0,0 +1,54 @@
+# v3.19.4 — fix failing `cortex` MCP server when working in the plugin repo
+
+Fourth entry in the 3.19.x reliability series. This one fixes a confusing
+failure that only appeared when the Cortex plugin source repo itself was the
+working directory: `/mcp` showed a failing `cortex` server with
+"MCP error -32000: Connection closed", alongside the healthy
+`plugin:cortex:cortex` server.
+
+## What it fixes
+
+The repo-root `.mcp.json` served double duty:
+
+1. **Plugin MCP config** — `.claude-plugin/plugin.json` referenced it as
+   `"mcpServers": "./.mcp.json"`.
+2. **Project-scoped MCP config** — unintentionally. Claude Code picks up a
+   repo-root `.mcp.json` as project configuration whenever that repo is the
+   working directory.
+
+In project scope `${CLAUDE_PLUGIN_ROOT}` is never substituted (it is a
+plugin-scope-only variable), so the project-scoped registration spawned a
+literal `python3 '<repo>/${CLAUDE_PLUGIN_ROOT}/scripts/launcher.py'` →
+ENOENT → -32000. The phantom `cortex` entry shadowed the healthy
+plugin-scoped server (which connected in ~1.7 s in the same session's logs)
+and made the plugin look broken to anyone developing it.
+
+## The fix
+
+- The MCP server config moved **inline** into `.claude-plugin/plugin.json`
+  `mcpServers` (the documented object form) — inline plugin config is
+  invisible to project-scope discovery.
+- The repo-root `.mcp.json` was **deleted**.
+- The contract test (`tests_py/scripts/test_mcp_json_contract.py`) now reads
+  the inline object and pins the absence of a repo-root `.mcp.json` as a
+  regression guard.
+
+## Verification
+
+- Post-restart, only `plugin:cortex:cortex` registers; the failing `cortex`
+  log stream (`mcp-logs-cortex/`) received no new entries.
+- `pytest tests_py/scripts/` — 12 passed.
+- `claude plugin validate .` — passes.
+
+## Diagnosis notes (for future -32000 triage)
+
+Two distinct -32000 root causes are now on record:
+
+- **2026-06-09:** stale `postmaster.pid` after unclean PostgreSQL shutdown.
+- **2026-06-12 (this release):** project-scope shadow registration of the
+  plugin's `.mcp.json`.
+
+Per-project MCP logs live at
+`~/Library/Caches/claude-cli-nodejs/<project>/mcp-logs-<server>/` (JSONL,
+parse per-line). Two log directories for one conceptual server = two
+registrations — check scope before debugging the server itself.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "neuro-cortex-memory"
-version = "3.19.3"
+version = "3.19.4"
 description = "Scientifically-grounded memory system based on computational neuroscience research"
 readme = "README.md"
 license = "MIT"