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  "IssueTotal": 16,
  "Held": 16,
  "Issues": [
    {
      "Title": "checkpoint: every call fails client-side output validation — outputSchema requires 'action' but no return path includes it",
      "Excerpt": "**Environment:** Cortex plugin 4.13.1, Windows 11, Claude Code as MCP client (validates structured tool results against the declared `outputSchema`).\n\n## Summary\n\nEvery `checkpoint` call fails client-side with:\n\n```\nOutput validation error: 'action' is a required property\n```\n\nThe declared output schema requires `action`, but **no return path in the handler ever includes it** — so a strict MCP client rejects every response, including successful saves.\n\n## Where\n\n- `mcp_server/handlers/checkpoint",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/99",
      "PublishedAt": "2026-07-12T10:21:19.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "Registered tool signatures drift from handler schemas: remember lacks supersedes_id/write_class, wiki_write lacks memory_ids — promotion loop cannot be closed over MCP",
      "Excerpt": "**Environment:** Cortex plugin 4.13.1, Windows 11, Claude Code as MCP client (validates tool calls against the declared input schema; `additionalProperties` violations are rejected client-side).\n\n## Summary\n\nThe client-visible input schemas for `remember` and `wiki_write` are derived by FastMCP from the registered wrapper signatures — and those signatures have drifted from the handlers' own schemas and from the instructions your grooming planners emit. Net effect: **the documented lesson-promoti",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/98",
      "PublishedAt": "2026-07-12T10:21:18.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "Windows: _pip_install's commit destroys existing deps packages while the MCP server is running (rmtree + os.replace vs locked .pyd) — armed on every session start when the ML stack is missing",
      "Excerpt": "**Environment:** Windows 11 Pro (build 26200), Python 3.13.13, cortex plugin **4.13.0** installed through the marketplace. Same box as #91–#95. Found while diagnosing the SessionStart charmap crash (#96).\n\n## Setup that arms the bug\n\nThe 4.13.0 plugin cache's active deps dir (`~\\.claude\\plugins\\cache\\cortex-plugins\\cortex\\4.13.0\\deps`) came up with the base stack (~200 top-level entries) but **without the ML stack** (no `sentence_transformers` / `torch` / `flashrank`). Since `session_start` is t",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/97",
      "PublishedAt": "2026-07-11T21:23:11.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Windows: session_start hook dies with UnicodeEncodeError ('charmap' can't encode U+27E6 ⟦) — entire SessionStart memory injection lost",
      "Excerpt": "**Environment:** Windows 11 Pro (build 26200), Python 3.13.13, cortex plugin **4.13.0** installed through the marketplace, Western locale (ANSI code page 1252). Same box as #91–#95.\n\n## Symptom\n\nEvery Claude Code session start shows:\n\n```\nSessionStart:startup hook error\nFailed with non-blocking status code: [cortex-launcher] Failed to run mcp_server.hooks.session_start: 'charmap' codec can't encode character '⟦' in position 25: character maps to <undefined>\n```\n\nand — the actual damage — **no me",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/96",
      "PublishedAt": "2026-07-11T21:22:52.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Windows: first `remember` can deadlock on the lazy scipy/sklearn import inside a FastMCP worker thread — eager-import at startup fixes it",
      "Excerpt": "## Environment\r\n\r\nSame as #91: Cortex 4.3.0, Windows 11, Python 3.13.13, FastMCP 3.2.4/3.4.4, Claude Code client.\r\n\r\n## Symptom\r\n\r\nDistinct from the `_git_root` hang (reported separately in #91): before I found that one, the *first* `remember` on a fresh server process could wedge a worker thread permanently. `faulthandler.dump_traceback_later` on the live server showed:\r\n\r\n```\r\nThread (AnyIO worker thread):\r\n  ...\r\n  deps\\scipy\\linalg\\blas.py:247        <module>\r\n  deps\\scipy\\linalg\\_misc.py:3 ",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/92",
      "PublishedAt": "2026-07-09T19:44:19.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "`remember` hangs indefinitely on Windows: `_git_root`'s subprocess timeout is defeated by `subprocess.run`'s post-kill `communicate()` (pipe handle-inheritance race)",
      "Excerpt": "## Environment\r\n\r\n- Cortex plugin **4.3.0** (Claude Code marketplace install), PostgreSQL backend (pgvector/pg17, Docker)\r\n- Windows 11 Pro (26200), Python **3.13.13**\r\n- Client: Claude Code desktop; reproduced on FastMCP 3.2.4 **and** 3.4.4 (version-independent)\r\n\r\n## Symptom\r\n\r\nCalling the `remember` tool over a live MCP connection never returns — the call sits 10–30 minutes until the client's idle timeout aborts it (or the user cancels). Meanwhile:\r\n\r\n- `memory_stats` on the **same connection",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/91",
      "PublishedAt": "2026-07-09T19:43:20.000Z",
      "State": "closed",
      "Comments": 4,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "recall tool fails MCP output validation: schema requires 'memories' but handler returns 'results'",
      "Excerpt": "## Summary\n\nEvery call to the `recall` MCP tool fails with:\n\n```\nOutput validation error: 'memories' is a required property\n```\n\nThe declared `outputSchema` for `recall` requires the key `memories`, but the handler returns `results`. Two related schema/handler drifts compound this.\n\n## Reproduction\n\nCortex 3.17.0, plugin install via cortex-plugins marketplace, PG backend healthy (`memory_stats` returns valid stats with 73K+ memories, `pgvector` enabled).\n\nAny recall call fails:\n\n```\n# From an MC",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/46",
      "PublishedAt": "2026-05-24T15:26:04.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "auto_recall hook queries non-existent 'heat' column instead of 'heat_base'",
      "Excerpt": "## Summary\n\n`mcp_server/hooks/auto_recall.py` queries `memories.heat`, but the actual schema column is `heat_base`. As a result, every UserPromptSubmit hook fire fails with:\n\n```\n[cortex-auto-recall] FTS query failed: column \"heat\" does not exist\nLINE 2:             SELECT id, content, heat, domain, agent_context,...\n                                        ^\n```\n\nThe hook then exits 0 with no injection — silent failure on every user prompt. Per-prompt memory injection is broken.\n\n## Reproducer\n\n",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/20",
      "PublishedAt": "2026-05-05T16:55:36.000Z",
      "State": "closed",
      "Comments": 2,
      "Reporter": "Contributor",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "FastMCP: remember/recall/get_telemetry return 'structured_content must be a dict' despite success",
      "Excerpt": "## Summary\n\nThree MCP tools return a FastMCP runtime error to the client even though the underlying memory operation succeeds and persists correctly:\n\n- `mcp__cortex__remember`\n- `mcp__cortex__recall`\n- `mcp__cortex__get_telemetry`\n\nError message:\n\n> structured_content must be a dict or None. Got str: '{...}'. Tools should wrap non-dict values based on their output_schema.\n\nThe data inside the error payload is the correct JSON; it's just being returned as a stringified JSON instead of a dict, so",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/17",
      "PublishedAt": "2026-05-05T16:16:33.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "Contributor",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "seed_project: delete_memories_by_tag('seeded') is global, ignores domain scope",
      "Excerpt": "## Summary\n\n`mcp_server/handlers/seed_project.py:180` purges memories globally by tag, regardless of the `domain` argument:\n\n```python\npurged = 0\nif not dry_run:\n    purged = _get_store().delete_memories_by_tag(\"seeded\")\n```\n\nThis means every call to `seed_project` wipes all previously-seeded memory rows across every domain — only the most recent seed survives.\n\n## Reproducer\n\nSequentially seed two repos with distinct domains:\n\n```\nseed_project(directory=\"/path/to/repoA\", domain=\"repo-a\")\n# stor",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/16",
      "PublishedAt": "2026-05-05T16:13:49.000Z",
      "State": "closed",
      "Comments": 2,
      "Reporter": "Contributor",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "backfill_memories misses subagent/teammate sessions due to non-recursive glob in discover_files",
      "Excerpt": "## Summary\n\n`backfill_memories` silently skips most session transcripts because `discover_files` in `mcp_server/handlers/backfill_helpers.py:210` uses non-recursive `project_dir.glob(\"*.jsonl\")`. Claude Code persists parent and subagent / teammate sessions across **four** layouts that the walker never descends into when nested.\n\n## Concrete impact\n\nVerified taxonomy on a real corpus with active subagent / teammate use, all 802 `*.jsonl` accounted for:\n\n| layout | path shape | count | walker sees",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/15",
      "PublishedAt": "2026-05-02T17:24:50.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "Cortex 3.12.0 — `consolidate` field report",
      "Excerpt": "The previous report were done on copies of this db.  I upgraded my main install to 3.12 and this was the results of running consolidate.\n\n\n# Cortex 3.12.0 — `consolidate` field report\n\n**Date:** 2026-04-16\n**Version:** cortex 3.12.0 (MCP plugin, alloy Postgres backend)\n**Store size:** 66,277 memories (25,603 episodic / 40,675 semantic, 3,111 protected)\n**Context:** First `consolidate` run after upgrade to 3.12.0; store includes a recent large claude-mem backfill import.\n\n---\n\n## Summary\n\n`consol",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/14",
      "PublishedAt": "2026-04-16T18:35:09.000Z",
      "State": "closed",
      "Comments": 6,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "Cortex `consolidate` — Performance Report",
      "Excerpt": "# Cortex `consolidate` — Performance Report\n\n**Plugin:** `cortex` (v3.9.1, per skill path)\n**Date:** 2026-04-15\n**Environment:** macOS 25.4.0 (Darwin), Mac M2 Max, 64 GB RAM\n\n## Summary\n\nA full `consolidate({decay, compress, cls, memify})` run on a memory\nstore of ~66K memories took **35 min 50 s** (2,150,496 ms). Most of\nthe work appears to be O(N) per-row updates across stages that could\nplausibly be batched. One stage scanned but produced nothing, and the\nhomeostatic stage reported `health_sc",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/13",
      "PublishedAt": "2026-04-15T14:26:01.000Z",
      "State": "closed",
      "Comments": 8,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "hooks.json file fix (needed on my system anyway)",
      "Excerpt": "# hooks.json uses flat structure instead of required nested `hooks` array\n\n**Affected repos:** `zetetic-team-subagents` (v2.0.0), `Cortex` (v3.9.0)\n**Files:** `hooks/hooks.json` (subagents), `.claude/hooks/hooks.json` (Cortex)\n**Severity:** Plugin fails to load — all hooks are broken\n\n## Problem\n\nClaude Code's hook schema requires each hook entry to wrap `type`/`command` inside a nested `hooks` array. Both repos use a flat structure that puts `type` and `command` as siblings of `matcher`/`when`,",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/12",
      "PublishedAt": "2026-04-13T14:00:28.000Z",
      "State": "closed",
      "Comments": 2,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    },
    {
      "Title": "Enhancement: Cache engram slot list in allocate_engram_slot",
      "Excerpt": "# Enhancement: Cache engram slot list in allocate_engram_slot\n\n## Problem\n\n`allocate_engram_slot()` is called on every `remember()` invocation. Each call:\n\n1. `init_engram_slots()` — `SELECT COUNT(*)` to check if slots exist\n2. `get_all_engram_slots()` — `SELECT *` fetching all 5,000 engram slot rows\n3. `find_best_slot()` — CPU scan over the 5,000 slots (cheap)\n4. `assign_memory_slot()` — `UPDATE` + `COMMIT`\n5. `update_engram_slot()` — `UPDATE` + `COMMIT`\n6. `get_memories_in_slot()` — `SELECT *`",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/11",
      "PublishedAt": "2026-04-12T16:56:32.000Z",
      "State": "closed",
      "Comments": 3,
      "Reporter": "External",
      "Rank": "top",
      "Extractor": "github_issue"
    },
    {
      "Title": "plugin.json hardcoded DATABASE_URL overrides user's shell environment",
      "Excerpt": "Summary\nThe plugin-bundled MCP server config in [.claude-plugin/plugin.json] hardcodes DATABASE_URL=postgresql://localhost:5432/cortex in the mcpServers.cortex.env block. Claude Code merges this over the user's shell environment when launching the MCP server, so users running Postgres on any non-localhost host (remote DB, separate LXC, Docker network hostname, non-default port, or requiring credentials) hit a silent connection failure — regardless of what they set in ~/.claude/settings.json or t",
      "SourceUrl": "https://github.com/cdeust/Cortex/issues/9",
      "PublishedAt": "2026-04-08T17:25:33.000Z",
      "State": "closed",
      "Comments": 1,
      "Reporter": "External",
      "Rank": "recent",
      "Extractor": "github_issue"
    }
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