cc-os/docs/memory-system/02-system-design.md

System Design

Status: approved 2026-06-03; knowledge layer revised 2026-06-04 (Graphify replaces the Ruby tag-index CLI and the deferred QMD layer — see ADR-010); tag taxonomy and vault location locked 2026-06-04 (six-facet taxonomy — see ADR-011; reuse ~/Documents/SecondBrain — see ADR-012). Implementation not yet started.

Goals (what this system must do)

1. Thin projects — keep as little AI context inside each project repo as possible. Projects focus on project files; knowledge is pulled in on demand or injected by hooks.
2. Cross-project / cross-client knowledge — the AI learns something once (e.g. the SEMrush API) and references it from anywhere. Two scopes: global (broadly useful) and project/client-specific (how a given client uses a tool) — both globally reachable. Ask anything client- or project-related from any project.
3. Timeline awareness — from any project, lightweight awareness of recent activity ("what was I doing an hour ago / yesterday"), with the ability to drill deeper.
4. Remote, local-fast — accessible anywhere (VPS / personal OS) but runs local-fast; lazy sync (minutes/hourly) is fine; real-time is overkill.

Desired properties: lightweight (low tokens), fast (out of the way), flexible (cross project/client), self-evolving (AI maintains it under clear rules), easy to manage (AI-managed), semi-structured (organization that can evolve).

Core principle: two memory types, kept separate

Type	Question	Lifecycle	Write path	Our tool
Episodic	"What happened, when?"	accretes & decays	auto-captured	memsearch
Semantic / knowledge	"How do we…?"	deliberately maintained	curated by you/AI	Obsidian vault + Graphify knowledge graph

This is the classic episodic vs. semantic memory split. Keeping them separate is the key architectural decision — they have different lifecycles, write paths, and query patterns, and forcing one tool to do both is what made every earlier design feel forced.

The two layers

┌─────────────────────────────────────────────────────────────────┐
│ EPISODIC  ── memsearch (Milvus Lite, embedded, no Docker)         │
│   auto-captured session/journal notes · NL semantic recall        │
│   answers "when did we…", "what was I doing yesterday"            │
├─────────────────────────────────────────────────────────────────┤
│ KNOWLEDGE ── ~/Documents/SecondBrain Obsidian vault (single SOT)  │
│   notes carry summary + six facet tags + scope/ (metadata)        │
│   + Graphify knowledge graph (local SLM over docs; AST over code) │
│   graph queries (god nodes / query / path) · answers "how do we…",│
│   "what do we know about X for client Y", "what relates to Y"     │
└─────────────────────────────────────────────────────────────────┘

Both are local-first, markdown-as-truth, no Docker, no server, no API keys (Graphify extraction runs against a local Ollama model). An earlier design split the knowledge layer into a Ruby/SQLite tag index plus a deferred QMD vector layer; Graphify replaces both — it provides structured and semantic retrieval over the vault as a single graph (ADR-010). The summary + tag frontmatter is retained as note metadata (router hint + cross-cutting filters), it is just no longer backed by a bespoke index.

Layer 1 — Episodic (memsearch)

• What it is: a Claude Code plugin (by Zilliz) that auto-captures session notes as daily markdown, chunks them, and stores a shadow index in Milvus Lite (a single embedded file — no server, no Docker). Hybrid search = BM25 + dense vectors + RRF, local ONNX embeddings (bge-m3, no API key/cost). A FileWatcher (1500ms debounce) handles updates and deletions; markdown stays the source of truth.
• Why off-the-shelf: it already implements the OpenClaw daily-notes + "dreaming" pattern and the markdown-as-truth / disposable-shadow-index philosophy we'd otherwise hand-build.
• Role in our system: satisfies Goal 3 (timeline). The AI queries it in natural language ("what was decided about X last week"). We do not make it filter by our tags — it owns the episodic corpus only.

Layer 2 — Knowledge (vault + Graphify knowledge graph)

The heart of the system, and the part we build.

Vault

• Flat markdown directory, single source of truth — reuses the existing ~/Documents/SecondBrain Obsidian vault (ADR-012); not forced into ~/.claude/; symlink if a tool insists. Browsable in Obsidian as a viewer.
• Replaces project-local documentation: instead of docs scattered per repo, knowledge lives once in the vault and is pulled into any project on demand.

Frontmatter contract (every note)

---
summary: One line, written at creation. The router shows this so the AI can pick a
  file without opening it.
tags:
  - type/reference        # listed first by convention; e.g. type/hub, type/how-to
  - client/sesame3g
  - project/website-redesign
  - domain/seo
  - tool/semrush
  - convention/api-style
  - scope/project         # or scope/global
---

• Six flat facets (ADR-011): type/, client/, project/, domain/, tool/, convention/ — plus scope/. Each facet is independent and parallel (never nested into each other). #tool matches all tool/* values — native Obsidian prefix filtering, no folders needed. Hierarchy and relationships are expressed via hub notes (type/hub), wikilinks, and Graphify graph edges, not nested tag paths.
• Two knowledge scopes via scope/global vs scope/project (+ a client/ tag): global = broadly useful tool/domain knowledge; project = how a specific client uses it. Both are globally queryable; the scope tag is the shortcut that avoids scanning every client's usage.

Knowledge graph (Graphify)

Graphify (safishamsi/graphify, command graphify) turns the vault into a queryable knowledge graph — the disposable, rebuildable structure over the markdown. It replaces the earlier Ruby/SQLite tag index and the deferred QMD vector layer (ADR-010): one graph gives both structured and semantic retrieval, without vectors.

• Extraction:
  • Vault docs → a local Ollama SLM extracts entities + typed relationships from each note (confidence-tagged EXTRACTED / INFERRED / AMBIGUOUS). Local model = no API cost, no data leaving the machine.
  • Project code → free tree-sitter AST (--no-docs), no model, no token cost. Kept as separate per-project graphs, not merged with the vault graph.
• What it produces: graphify-out/ with graph.json, an interactive graph.html, and a GRAPH_REPORT.md whose top lists the god nodes (the most-connected concepts — your highest-value entry points).
• Query (via CLI and an MCP server exposing query_graph / get_node / shortest_path): ask for god nodes first, then scalpel down with graphify query / path / explain. Prompt the graph; don't dump the corpus into context.
• Metadata still matters: the summary + six facet tags remain first-class note attributes — summary is the human-written router hint Graphify does not generate, and the facet namespaces (type/, client/, project/, domain/, tool/, convention/, scope/) stay useful for Obsidian filtering and as node attributes. They are retained even though they no longer back a bespoke index. (How tightly metadata feeds graph queries is a refinement for build time.)
• Source of truth rule: markdown is authoritative; the graph (graphify-out/) is a rebuildable artifact that is never synced and can be deleted/rebuilt anytime (graphify ... --force).

Freshness (lazy — chosen Option A)

• AI writes → a PostToolUse hook on Write/Edit targeting vault .md files runs graphify ... --update to merge the changed note into the vault graph. Event-driven, no polling.
• Stale-node caveat: Graphify's --update merges (SHA-256 + dedup) but does not prune deleted notes/symbols — ghost nodes accumulate. A periodic --force rebuild clears them, triggered by the session-start reconcile when a rebuild stamp is older than N days (7 to start). No daemon, no cron.

Retrieval (hook-injected + on-demand)

• Session-start hook injects: (a) a compact overview — the vault graph's god nodes as the map of what's known, (b) the current project's declared convention/* notes resolved to their summaries (so coding conventions auto-pull and a convention edit propagates to every project using that tag), (c) a pointer to recent episodic journal.
• On demand: the AI runs graphify query / path / explain (or the MCP tools) to pull specific knowledge into context only when the task needs it. Projects stay thin — their CLAUDE.md holds tags/pointers, not content.

Semantic recall over the vault — covered by Graphify

The earlier design earmarked a separate vector layer (QMD) for "when structured tag filtering misses a note whose wording doesn't match the query." Graphify's knowledge graph covers that need without a second system or vectors: relationship traversal and explain surface notes by connection, not just exact tag match. So there is no separate deferred semantic layer — if graph traversal ever proves insufficient for a case where embedding similarity would clearly win, revisit then (the video's "only level up when it bites").

Timeline (Goal 3) details

• A session-end hook appends a daily journal note (one file per date) with pointers to the project/knowledge files touched. memsearch indexes these; today+yesterday are cheap to load, older entries are reachable by query for drill-down.

Self-evolution guardrails

• The AI writes only to the vault, never silently into project repos.
• Required frontmatter schema (summary + namespaced tags) is enforced so the index stays queryable.
• Daily notes are append-only; consolidation/reorg is a separate, reviewable step run in plan mode (Connelly's reorganize + Huryn's propose-and-approve loop).
• Promotion to scope/global requires a rule (e.g. a fact recurring N times) — not every stray note gets promoted.

Sync (Goal 4)

• The vault syncs to the VPS via git (versioned history, hourly) or Syncthing (continuous, zero-thought). Decision deferred to build time.
• Graphs/indexes are never synced — the Milvus Lite episodic index and the Graphify graphify-out/ graphs are rebuilt per machine. Sync only the markdown.

Packaging

• The whole thing ships as a global Claude Code plugin with skills (hooks + scripts + CRUD know-how) so every project, on every machine, knows how to use the vault effectively. See 04-build-plan.md.

How each goal is met

Goal	Met by
1. Thin projects	Knowledge in the vault, not repos; CLAUDE.md holds tags/pointers; on-demand index query
2. Cross-project/client knowledge, global vs project scopes	~/Documents/SecondBrain vault + six-facet tags (type//client//project//domain//tool//convention/) + scope/; Graphify knowledge graph (god nodes + traversal) over it
3. Timeline	memsearch episodic layer + session-end journal hook
4. Remote, local-fast	Markdown vault synced via git/Syncthing; disposable per-machine graphs/indexes