Mnemoscope README

An open-source observability layer for LLM agent memory on Markdown vaults.
Predict context rot before it happens · audit every agent write with a signed journal · tier your knowledge the way the science says you should.

_{Demo · Workflow · Tools · Quickstart · Architecture · Science}

[!NOTE] The dominant 2025–2026 narrative on X — "Markdown trips up the LLM at scale" — is partially wrong. Markdown does not trip up the LLM. Long-context loading trips up the LLM (Chroma, Context Rot, July 2025). Mnemoscope is built on that distinction.

👀 See it in action

Real output, captured from the bundled examples/demo-vault — a 13-note synthetic vault built so every rot factor moves. Reproduce locally with mnemoscope-init examples/demo-vault (full transcript: SAMPLE-OUTPUT.md).

predict_rot — score, factors, top-risk notes

predict_rot card showing rot risk 52/100, dominant factor semanticRedundancy, factor breakdown bars, and the top 5 risk notes.

mnemoscope-verify — clean run vs. tamper detection

Two verify outputs side by side: a clean run with three valid entries and exit 0, and a tampered run with one signature-mismatch FAIL and exit 1.

Full overview (click) — gauge, factors, top-risk notes, both verify states, tier counts, hash chain — all on one page

Full demo page showing every Mnemoscope view at once.

✨ What is Mnemoscope?

Mnemoscope is not another memory store. It is an instrument that sits between your LLM agent and your Markdown vault and gives you three things nobody else gives you in one tool:

🎯 Predict the rot risk of a corpus before injection, with a citation-backed score across 5 factors.
📝 Witness every read and write your agent performs, in an Ed25519-signed, hash-chained journal that detects field-level tampering, deletion, and reordering.
🧱 Tier the corpus into a working / episodic / semantic hierarchy, drawing on the 2025–2026 science instead of the GraphRAG hype.

It ships as an MCP server (Claude Code, Cursor, ChatGPT desktop, anything MCP-compatible), an Obsidian plugin, and a Claude Code PostToolUse hook. Everything runs 100% locally. No cloud. No telemetry without explicit opt-in.

🔄 How it fits your workflow

Imagine you start a brand-new project — a folder of Markdown notes you'll grow with Claude Code over the next year. Mnemoscope plugs into the lifecycle in five places:

Code

   [create project]
        │
        ▼
   mnemoscope-init                     ◄─── 1× at the very start
        │                                   creates .mnemoscope/, generates Ed25519 keypair
        ▼
   ┌───────────────────────────────────────────────────────────┐
   │  [you work with Claude Code on the vault]                 │
   │                                                           │
   │   predict_rot       ──┐                                   │
   │                       ├─►  on demand (or before sessions) │
   │   get_tiered_read   ──┘    "is the vault healthy?"        │
   │                            "what should the agent read?"  │
   │                                                           │
   │   PostToolUse hook  ────►  passive, on every Write/Edit   │
   │                            "what did the agent just do?"  │
   └───────────────────────────────────────────────────────────┘
        │
        ▼
   mnemoscope-verify                   ◄─── on demand, or in CI
                                            "has anyone tampered?"

Phase	Tool / command	When to use it	What you get
1. Bootstrap	`mnemoscope-init`	Once, at project creation	`.mnemoscope/` + per-vault Ed25519 keypair
2. Predict	`predict_rot` (MCP tool)	Before injecting a vault into the LLM	A 0–100 risk score + factor breakdown + top-risk notes
3. Compact	`get_tiered_read` (MCP tool)	When the vault grows past your model's effective context	Working / episodic / semantic split
4. Witness	`mnemoscope-record-hook` (Claude Code PostToolUse hook)	Wired once in `~/.claude/settings.json`, then passive	Every agent write becomes a signed journal entry
5. Audit	`mnemoscope-verify`	Any time, or as a pre-commit / CI step	Exit 0 if all entries verify, exit 1 if tampered

🛠️ The four MCP tools

Tool	Input	What it returns
`predict_rot`	`vault_path`	Score 0–100, dominant factor, full factor breakdown, top 5 risk notes, vault stats
`get_tiered_read`	`vault_path`, optional age thresholds	Note paths grouped into `working` / `episodic` / `semantic`
`record_journal`	`vault_path`, `session_id`, `op`, `target_path`, optional content	The signed entry, including its `sig`, `keyFingerprint`, and `prevHash`
`read_journal`	`vault_path`, optional `session_id`	All journal entries, or a single session's entries

Example — `predict_rot` on a real vault

config.json

{
  "rot_risk": 41,
  "dominant_factor": "tokenVolume",
  "factors": {
    "tokenVolume": 100, "semanticRedundancy": 0,
    "distractorDensity": 2.65, "structuralCoherence": 100, "freshnessSpread": 0
  },
  "top_risk_notes": [
    { "relPath": "brainstorms/.../transcript.md", "approxTokens": 13439, "reason": "very large note" },
    { "relPath": "brainstorms/.../sylvie-signaux.md", "approxTokens": 12605, "reason": "very large note" }
  ],
  "vault_stats": { "noteCount": 113, "approxTokens": 506823 },
  "baseline_model": "v0-heuristic",
  "version": "0.2.0"
}

🚀 Quickstart

bash

git clone https://github.com/toonight/Mnemoscope
cd Mnemoscope
npm install
npm run build
npm test                           # 47 tests across core + mcp-server
npm audit                          # 0 vulnerabilities

# Make the CLI binaries available on your PATH
npm link --workspace @mnemoscope/cli

Bootstrap a vault

bash

mnemoscope-init /path/to/your/vault
# → state dir, Ed25519 keypair, fingerprint

Add .mnemoscope/ to your vault's .gitignore — the per-vault private key must never be committed.

Connect the MCP server to Claude Code (or Cursor / any MCP client)

json

// ~/.claude/settings.json
{
  "mcpServers": {
    "mnemoscope": {
      "command": "node",
      "args": ["/absolute/path/to/Mnemoscope/packages/mcp-server/dist/index.js"]
    }
  }
}

The four tools (predict_rot, get_tiered_read, record_journal, read_journal) become available to the agent immediately.

(Optional) wire the auto-journal hook

Asking the agent to call record_journal on every write is a recipe for forgetting. Wire the bundled hook instead:

json

// ~/.claude/settings.json
{
  "hooks": {
    "PostToolUse": [
      {
        "matcher": "Write|Edit|MultiEdit",
        "hooks": [{ "type": "command", "command": "mnemoscope-record-hook" }]
      }
    ]
  }
}

The hook resolves the vault root via MNEMOSCOPE_VAULT_PATH or by walking up to the closest .mnemoscope/ directory. It never blocks the tool call: any internal error is caught, logged to stderr, and the process exits 0. Full setup including safety properties: docs/claude-code-hook.md.

Verify the journal

bash

mnemoscope-verify /path/to/vault
# ok    2026-04-26T19:42:13.001Z  write  /vault/notes/foo.md
# ok    2026-04-26T19:43:01.220Z  write  /vault/notes/bar.md
# 2 entries; 2 valid; 0 invalid

mnemoscope-verify exits non-zero on any of:

field-level tampering (signature mismatch),
deletion or reordering (prevHash chain break),
entries signed by a key the current vault does not own.

(Optional) back up the per-vault private key

If you lose <vault>/.mnemoscope/keys/ed25519.key, the journal becomes unverifiable. The bundled backup CLIs encrypt the key with a passphrase (scrypt + AES-256-GCM, no extra deps) and let you restore it later:

bash

mnemoscope-backup-key /path/to/vault /path/to/off-vault-backup.enc.json
# … prompts for a passphrase, writes chmod 0600 …

mnemoscope-restore-key /path/to/vault /path/to/off-vault-backup.enc.json
# … prompts for the same passphrase, writes the key back into the vault …

Full flow including threat model: docs/key-escrow.md.

(Optional) anchor the journal in time with OpenTimestamps

The signed hash chain proves order. To prove absolute time and stay safe against retroactive rewrites if the per-vault key is ever compromised, anchor each entry's signature to a public Bitcoin-backed OTS calendar:

bash

mnemoscope-timestamp /path/to/vault
# … POSTs SHA-256(sig) per entry to the calendar, writes .ots proofs
# under <vault>/.mnemoscope/timestamps/. Idempotent on re-run.

Pending proofs are upgraded to fully self-verifying Bitcoin proofs with the upstream ots upgrade / ots verify CLIs — that part is intentionally not reimplemented. Full threat model and flow: docs/timestamping.md.

✅ What works today

	What	How verified
✅	`predict_rot` returns a 5-factor breakdown, each factor citation-backed in source	14 unit tests; smoke-tested on a real 506 K-token vault — sensible top-risk ordering
✅	`get_tiered_read` splits a vault into working / episodic / semantic by freshness	integration test on fixture vault; freshness-based, access-frequency aware in a future revision
✅	`record_journal` produces a real Ed25519 signature with prevHash chaining	9 journal tests, including 4 tamper tests + 2 chain-integrity tests (truncation, reordering)
✅	`mnemoscope-init` bootstraps a vault idempotently	manual run on multiple fresh + existing vaults
✅	`mnemoscope-verify` CLI replays and exits non-zero on any invalid entry	wired to the same `verifyAll`
✅	`mnemoscope-record-hook` Claude Code `PostToolUse` hook auto-journals every Write/Edit/MultiEdit	docs/claude-code-hook.md, never blocks
✅	`mnemoscope-backup-key` / `mnemoscope-restore-key` encrypt the per-vault Ed25519 key with scrypt + AES-256-GCM	7 unit tests, full flow in docs/key-escrow.md
✅	`mnemoscope-timestamp` anchors each entry's signature to a Bitcoin-backed OpenTimestamps calendar; pending `.ots` proofs upgraded with the official `ots` CLI	12 unit tests + smoke-tested 3 entries → 3 `.ots` files round-trip through `verifyOtsHeaderForDigest`; full flow in docs/timestamping.md
✅	MCP server passes 5 end-to-end tests over real JSON-RPC stdio	`server.test.ts` spawns the binary
✅	Obsidian plugin: sidebar view with SVG rot gauge, factor bars, top-risk list, settings tab, auto-onboarding modal on first launch	single-file bundle, no runtime deps; `eslint-plugin-obsidianmd` clean in CI
✅	Research sub-project: predictive classifier calibrated on real LLM measurements (Random Forest R² = 0.58 on 50 rows graded by Gemma 4 26B), MarkdownMemBench v0.1 schema + sample dataset + harness, Chroma replication protocol with position-of-needle sweep	self-contained Python project under `research/`; CI runs `ruff` + 14 pytest cases on every push; classifier metadata audited in `research/classifier/model.json`
✅	CI green on Node 22 + Python 3.11, 0 npm vulnerabilities, `npm audit --audit-level=moderate` and `eslint-plugin-obsidianmd` enforced on every push	GitHub Actions on every push and PR
✅	Three npm packages (`@mnemoscope/{core,mcp-server,cli}@0.2.0`) live on the public npm registry, published via OIDC Trusted Publishing (no rotating token, automatic provenance)	`npm view @mnemoscope/core` etc.; release workflow at `.github/workflows/release.yml`
✅	The MCP server is listed on the Official MCP Registry under `io.github.toonight/mnemoscope @ 0.2.0` — automatic fan-out to PulseMCP and other downstream catalogs	`server.json` at repo root, registered via `mcp-publisher` CLI

🏗️ Architecture

mermaid

flowchart LR
    A["Obsidian vault<br/>Markdown files"] --> B["mnemoscope/core<br/>signatures · rot · tiering · Ed25519 chained journal"]
    B --> C["mnemoscope/mcp-server<br/>stdio MCP - 4 tools"]
    B --> D["mnemoscope/obsidian-plugin<br/>UI · rot gauge"]
    B --> G["mnemoscope/cli<br/>init · record-hook · verify"]
    C -->|tools| E(("Claude Code<br/>Cursor<br/>ChatGPT desktop"))
    G -->|PostToolUse hook| E
    F["research/<br/>classifier · benchmark · replication"] -.->|trained ONNX classifier| B
    style A fill:#1a2444,stroke:#a78bfa,color:#cbd5e1
    style B fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style C fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style D fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style G fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style E fill:#1a2444,stroke:#7cf09d,color:#cbd5e1
    style F fill:#1a2444,stroke:#fbbf24,color:#cbd5e1

Code

mnemoscope/
├── packages/
│   ├── core/              # rot scoring, tiering, Ed25519 hash-chained journal, signatures
│   ├── mcp-server/        # MCP server (stdio); 4 tools, integration-tested via spawn
│   ├── obsidian-plugin/   # Obsidian plugin: rot gauge, factor bars, top-risk list, settings
│   └── cli/               # mnemoscope-init, mnemoscope-record-hook, mnemoscope-verify
├── examples/
│   └── demo-vault/        # 13-note synthetic vault — every rot factor moves
├── research/              # Python (uv): classifier, MarkdownMemBench v0.1, Chroma replication
└── docs/                  # banner, logo, claude-code-hook setup, demo page, screenshots

🔐 The signed journal in one diagram

mermaid

flowchart TD
    K["Per-vault Ed25519 keypair<br/>.mnemoscope/keys/ed25519.key (mode 0600)"]
    E1["Entry 1<br/>prevHash = GENESIS<br/>sig = σ1"]
    E2["Entry 2<br/>prevHash = SHA256 of σ1<br/>sig = σ2"]
    E3["Entry 3<br/>prevHash = SHA256 of σ2<br/>sig = σ3"]
    K -->|signs| E1
    K -->|signs| E2
    K -->|signs| E3
    E1 -.->|chain| E2
    E2 -.->|chain| E3
    style K fill:#1a2444,stroke:#a78bfa,color:#cbd5e1
    style E1 fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style E2 fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1
    style E3 fill:#0e1530,stroke:#5fd9d1,color:#cbd5e1

Attack	Detected by
Edit a field of any single entry	per-entry signature mismatch
Delete an entry	next entry's `prevHash` no longer matches
Reorder two entries	both signatures still verify, but the chain breaks
Forge an entry with a different key	`keyFingerprint` flagged as foreign

🤝 Voisins (not competitors)

Project	What it does	Where Mnemoscope sits
Anthropic Memory tool	Official, file-based, primitive	We add the rot scoring + signed chained journal Anthropic does not provide
Letta / MemGPT	Runtime-stateful agents	Different layer — we sit under the agent
Mem0, Zep, Cognee	Generic memory stores	Different scope — we are MD-vault-native
MemPalace	Viral OSS memory MCP	Not Obsidian-specific; complementary
Smart Connections	RAG-vector for Obsidian	Co-installable; we are runtime / forensics, they are search
Basic Memory MCP	Semantic graph over markdown	Closest in spirit — we want to interop, not duplicate
claude-memory-compiler	MD-compiler approach	Reach out before duplicating

[!IMPORTANT] If you maintain one of these projects and see overlap or complementarity, please open an issue — collaboration is the explicit design goal.

🔬 Scientific posture

Mnemoscope is meant to be a tool and a contribution to the public empirical record on agent memory.

Research thread	Status	Why it matters
MarkdownMemBench v0.1	🟢 schema + sample dataset + harness shipping	Today's benchmarks (LongMemEval, LoCoMo) are conversational and English-only. There is no public bench for vault-native, MD-native agent memory.
Predictive Context Rot classifier	🟢 trained on 50 real `(signature, observed_loss)` rows graded by `gemma4:26b` (Q4_K_M, `num_ctx=40000`). Random Forest wins out — R² = 0.58, MAE = 0.14 on a held-out 10-row split — confirming the rot surface has interactions a linear model can't capture (Ridge collapses from 0.85 on the synthetic baseline to 0.14 on real data). First public observation of Chroma 2025's "structured > shuffled is worse" effect on real Markdown vaults graded by a real LLM (`structural_coherence` r = +0.30 vs observed loss). Audit metadata	Every existing benchmark measures degradation after injection. We predict it before, with a calibrated baseline anyone can extend by dropping a fresh `measurements.csv` next to the existing one and re-training.
Replication of Chroma's "structured > shuffled is worse"	🟢 runner + offline & online grading shipping; real-corpus runs pending vault contributions	Chroma showed coherent haystacks underperform shuffled ones on NIAH. Nobody has replicated or refuted this on real Obsidian vaults yet. The runner (`research/replication/`) needs only an API key and a vault path.

Each thread lives in research/ and will produce a preprint alongside the code.

🛣️ Roadmap

Done

Publish the three packages on npm at v0.2.0 with OIDC Trusted Publishing — @mnemoscope/{core,mcp-server,cli} are live on the npm registry. CI publishes automatically on tag push, no rotating token required, provenance attestations emitted on every publish.
List the MCP server on the Official MCP Registry — io.github.toonight/mnemoscope @ 0.2.0 is indexed. PulseMCP ingests the official registry daily, so the server appears there too within ~7 days, no separate submission required.
Submit the Obsidian plugin to the community plugins directory — obsidianmd/obsidian-releases#12354 passes automated validation; awaiting human review (typical 2–4 weeks).
Periodic remote attestation — OpenTimestamps anchoring of every journal-entry signature, upgradable to a Bitcoin-backed proof via the upstream ots CLI (docs/timestamping.md).
Calibrate the predictive classifier on real LLM measurements — 50 (signature, observed_loss) rows graded by gemma4:26b, Random Forest wins at R² = 0.58 / MAE = 0.14 on the held-out split; first public observation of the Chroma 2025 "structured > shuffled is worse" effect on real Markdown vaults graded by a real LLM (model.json).
Lint locally with the same plugin the Obsidian reviewer uses — eslint-plugin-obsidianmd is wired into the project (root eslint.config.mjs, npm run lint) and gates CI, so reviewer-bot findings land at commit time instead of review time.

Dogfood the auto-journal hook on the author's vault for two full weeks; tune heuristics against observed Claude Code session outcomes
Wire the calibrated model.onnx into @mnemoscope/core via onnxruntime-node (optional dependency) so predict_rot returns the model's prediction next to the v0 heuristic
Release MarkdownMemBench v1 with 50–200 contributed real vaults
Preprint #1: replication of Chroma Context Rot on real Obsidian vaults
List on Glama (catalog ingestion path complementary to PulseMCP)

Full history: CHANGELOG.md.

🧑‍🤝‍🧑 Contributing

PRs are welcome but the most useful first step is opening an issue describing what you want to do. See CONTRIBUTING.md for code style and process.

If you are a researcher at Letta, Chroma, Mem0, Cognee, OSU-NLP, Snap Research or any related lab and you see overlap with the Predictive Context Rot or MarkdownMemBench axes, please reach out — the project is explicitly designed for this.

📜 License

Apache License 2.0. Apache-2.0 was chosen over MIT for its explicit patent grant, which we believe is appropriate for a project introducing novel scoring methods in an active research area.

🙏 Acknowledgements

Mnemoscope's framing borrows directly from public work by:

Without their public artifacts, this project would not be possible.

_{🧠 predict · witness · tier 🧠}

👀 See it in action

✨ What is Mnemoscope?

🔄 How it fits your workflow

🛠️ The four MCP tools

Example — predict_rot on a real vault

🚀 Quickstart

Bootstrap a vault

Connect the MCP server to Claude Code (or Cursor / any MCP client)

(Optional) wire the auto-journal hook

Verify the journal

(Optional) back up the per-vault private key

(Optional) anchor the journal in time with OpenTimestamps

✅ What works today

🏗️ Architecture

🔐 The signed journal in one diagram

🤝 Voisins (not competitors)

🔬 Scientific posture

🛣️ Roadmap

Done

Next

🧑‍🤝‍🧑 Contributing

📜 License

🙏 Acknowledgements

Example — `predict_rot` on a real vault