Update design docs and add implementation runbook per ADR-011/012
Update CLAUDE.md: clarify the knowledge layer now specifies the ~/Documents/SecondBrain vault, six-facet taxonomy, and reference the locked decisions (ADR-011, ADR-012). Update 02-system-design.md: align with faceted taxonomy (type/ client/project/domain/tool/convention/ plus scope/), express hierarchy via hubs + wikilinks + Graphify edges rather than nested paths, name the vault explicitly, update build-plan timestamp. Add 05-implementation-process.md: concrete build runbook integrating the locked decisions — seven steps bottom-up from vault migration through plugin packaging, with the Graphify + Ollama model benchmark (Step 2c) marked as the critical gate. Open questions deferred or defaulted; most are non-blocking. Design milestone: tag taxonomy and vault location locked.
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jared
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235fd45ff7
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@ -45,10 +45,9 @@ the design, update this paragraph (and the relevant `docs/memory-system/` files
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match.** Keep it accurate, don't preserve it for its own sake.
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Two memory types kept as **separate systems**: **episodic** ("what happened, when") handled by
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**memsearch** (Milvus Lite, embedded), and **semantic/knowledge** ("how do we…") handled by a
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flat **Obsidian markdown vault** as the single source of truth. Notes keep `summary` +
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namespaced tags (`tool/`/`client/`/`domain/`/`convention/`/`scope/`) as metadata, and the vault
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is queried via a **Graphify knowledge graph** (local Ollama SLM for doc extraction, free
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**memsearch** (Milvus Lite, embedded), and **semantic/knowledge** ("how do we…") handled by the
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existing **`~/Documents/SecondBrain` Obsidian vault** as the single source of truth. Notes keep
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`summary` + six flat, parallel namespaced facets (`type/`/`client/`/`project/`/`domain/`/`tool/`/`convention/`) plus `scope/` as metadata; hierarchy and relationships are expressed via hub notes (`type/hub`), wikilinks, and Graphify graph edges — not nested tag paths. The vault is queried via a **Graphify knowledge graph** (local Ollama SLM for doc extraction, free
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tree-sitter AST for code). Retrieval is hook-injected + on-demand so project repos stay thin;
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freshness is lazy
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(write-time hook + SessionStart reconcile, no daemon/cron); the vault syncs to a VPS while
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@ -59,6 +58,8 @@ tag-index CLI and also covers the deferred QMD semantic layer. `04-build-plan.md
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`06-graphify-evaluation.md` reflect this; if an older doc still describes the Ruby CLI, defer
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to those two and fix the stale doc.
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**Decisions locked (2026-06-04):** Six-facet tag taxonomy + `scope/` (ADR-011); reuse `~/Documents/SecondBrain` vault rather than creating a new one (ADR-012).
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## OpenSpec workflow
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Changes are managed spec-driven via OpenSpec. Use the matching skills rather than editing spec
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@ -1,7 +1,9 @@
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# System Design
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_Status: approved 2026-06-03; knowledge layer revised 2026-06-04 (Graphify replaces the Ruby
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tag-index CLI and the deferred QMD layer — see ADR-010). Implementation not yet started._
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tag-index CLI and the deferred QMD layer — see ADR-010); tag taxonomy and vault location locked
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2026-06-04 (six-facet taxonomy — see ADR-011; reuse ~/Documents/SecondBrain — see ADR-012).
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Implementation not yet started._
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## Goals (what this system must do)
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@ -39,8 +41,8 @@ forcing one tool to do both is what made every earlier design feel forced.
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│ auto-captured session/journal notes · NL semantic recall │
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│ answers "when did we…", "what was I doing yesterday" │
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├─────────────────────────────────────────────────────────────────┤
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│ KNOWLEDGE ── flat Obsidian vault (single source of truth) │
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│ notes carry summary + namespaced tags (metadata) │
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│ KNOWLEDGE ── ~/Documents/SecondBrain Obsidian vault (single SOT) │
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│ notes carry summary + six facet tags + scope/ (metadata) │
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│ + Graphify knowledge graph (local SLM over docs; AST over code) │
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│ graph queries (god nodes / query / path) · answers "how do we…",│
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│ "what do we know about X for client Y", "what relates to Y" │
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@ -72,8 +74,7 @@ filters), it is just no longer backed by a bespoke index.
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The heart of the system, and the part we build.
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### Vault
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- **Flat markdown directory**, single source of truth, **configurable location** (NOT forced
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into `~/.claude/`; symlink if a tool insists). Browsable in Obsidian as a viewer.
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- **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.
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- **Replaces project-local documentation**: instead of docs scattered per repo, knowledge
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lives once in the vault and is pulled into any project on demand.
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@ -83,14 +84,20 @@ The heart of the system, and the part we build.
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summary: One line, written at creation. The router shows this so the AI can pick a
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file without opening it.
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tags:
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- tool/semrush # namespaced, nested (slash = Obsidian nested tag)
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- type/reference # listed first by convention; e.g. type/hub, type/how-to
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- client/sesame3g
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- project/website-redesign
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- domain/seo
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- tool/semrush
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- convention/api-style
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- scope/project # or scope/global
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---
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```
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- **Namespaces** are the "virtual indexes": `tool/`, `client/`, `domain/`, `convention/`,
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`scope/`. `#tool` matches all children — native prefix filtering, no folders needed.
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- **Six flat facets** (ADR-011): `type/`, `client/`, `project/`, `domain/`, `tool/`,
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`convention/` — plus `scope/`. Each facet is independent and parallel (never nested into each
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other). `#tool` matches all `tool/*` values — native Obsidian prefix filtering, no folders
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needed. Hierarchy and relationships are expressed via **hub notes** (`type/hub`),
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**wikilinks**, and **Graphify graph edges**, not nested tag paths.
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- **Two knowledge scopes** via `scope/global` vs `scope/project` (+ a `client/` tag): global =
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broadly useful tool/domain knowledge; project = how a specific client uses it. Both are
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globally queryable; the scope tag is the shortcut that avoids scanning every client's usage.
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@ -113,11 +120,12 @@ layer (ADR-010): one graph gives both structured and semantic retrieval, without
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- **Query** (via CLI and an MCP server exposing `query_graph` / `get_node` / `shortest_path`):
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ask for **god nodes first**, then scalpel down with `graphify query` / `path` / `explain`.
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Prompt the graph; don't dump the corpus into context.
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- **Metadata still matters**: the `summary` + namespaced tags remain first-class note
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- **Metadata still matters**: the `summary` + six facet tags remain first-class note
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attributes — `summary` is the human-written router hint Graphify does **not** generate, and
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the `tag/` namespaces stay useful for Obsidian filtering and as node attributes. They are
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retained even though they no longer back a bespoke index. *(How tightly metadata feeds graph
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queries is a refinement for build time.)*
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the facet namespaces (`type/`, `client/`, `project/`, `domain/`, `tool/`, `convention/`,
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`scope/`) stay useful for Obsidian filtering and as node attributes. They are retained even
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though they no longer back a bespoke index. *(How tightly metadata feeds graph queries is a
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refinement for build time.)*
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- **Source of truth rule**: markdown is authoritative; the graph (`graphify-out/`) is a
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rebuildable artifact that is **never synced** and can be deleted/rebuilt anytime
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(`graphify ... --force`).
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@ -179,6 +187,6 @@ similarity would clearly win, revisit then (the video's "only level up when it b
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| Goal | Met by |
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|------|--------|
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| 1. Thin projects | Knowledge in the vault, not repos; CLAUDE.md holds tags/pointers; on-demand `index query` |
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| 2. Cross-project/client knowledge, global vs project scopes | Flat vault + namespaced tags + `scope/` + `client/`; Graphify knowledge graph (god nodes + traversal) over it |
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| 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 |
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| 3. Timeline | memsearch episodic layer + session-end journal hook |
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| 4. Remote, local-fast | Markdown vault synced via git/Syncthing; disposable per-machine graphs/indexes |
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@ -0,0 +1,306 @@
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# Implementation Process
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_Last updated: 2026-06-04_ | _Status: Ready to plan — awaiting Step 2c benchmark results_
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This document distills `04-build-plan.md` into a concrete, staged build process and folds in
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two locked decisions: **ADR-011** (faceted six-namespace taxonomy) and **ADR-012** (reuse the
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existing `~/Documents/SecondBrain` vault rather than creating a new one). Read `04-build-plan.md`
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for the underlying rationale, query/CRUD conventions, and plugin internals; read
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`03-architecture-decisions.md` for the decision log. This document is the runbook.
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> This is still a build process outline, not a detailed implementation plan. The recommended
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> next move is to feed Step 2 (the critical path) into the **writing-plans skill** to produce an
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> executable, task-level plan. Most open questions in Steps 3–6 can be defaulted; Step 2c's
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> model benchmark is the genuine gate that the rest depends on — do not hardcode a model before
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> it runs.
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---
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## Build order
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Bottom-up: vault migration first (usable standalone), then Graphify, then hooks, then plugin.
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---
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## Step 1 — Adopt and migrate the SecondBrain vault
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**Per ADR-012:** reuse `~/Documents/SecondBrain` as the knowledge vault rather than creating a
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new `~/brain`. The vault is already flat, already scoped to durable knowledge, and already
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articulates the correct governance philosophy. Migration cost is mechanical.
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### 1a — Initialize git
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The vault has no `.git` yet. Initialize it so ADR-008's sync strategy works:
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```bash
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git init ~/Documents/SecondBrain
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```
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### 1b — Update vault governance notes
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Update three files to the new schema:
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- **`CLAUDE.md`** — update vault path references, Graphify commands, ADR-011 namespace list.
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- **`vault-conventions.md`** — update tag-namespace list to the six-facet form; keep the
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existing "act without being asked" proactive-retrieval section intact (it's better than
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what cc-os had — adopt it, don't overwrite it).
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- **Project-config hub note(s)** — update the tag-inference table values to namespaced form
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(e.g. `semrush-work → tool/semrush`, `pest-control → domain/pest-control`). Keep the
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table; it operationalizes auto-tagging by path pattern and should be preserved.
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**Frontmatter contract** (apply to all notes, new and migrated):
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```yaml
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---
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summary: "One-line, human-written router hint (required; Graphify does not generate this)"
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tags:
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- type/<kind> # listed first by convention
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- client/<name> # as applicable
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- project/<name> # as applicable — first-class for a freelancer
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- domain/<topic> # as applicable
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- tool/<name> # as applicable
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- convention/<name> # as applicable
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- scope/global # or scope/project
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---
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```
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`type/` listed first preserves the vault's existing type-first ordering habit and makes note
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kind immediately visible.
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### 1c — Migrate existing notes (~20)
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For each existing note:
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1. Add `summary:` frontmatter (one line; write it now — it's the human-authored router hint).
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2. Convert flat unnamespaced tags to the six-facet namespaced form. Examples:
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- `research` → `type/research`
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- `pest-control` → `domain/pest-control`
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- `niche-automation-prospecting` → `domain/niche-automation-prospecting` (or split across
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`domain/` + `project/` if the note is project-specific)
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- `semrush` → `tool/semrush`
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3. Add `scope/global` or `scope/project` to each note.
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Keep 5–10 migrated notes aside as representative test cases for Step 2c's extraction benchmark.
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Include variety: a tool note, a client/project note, a convention note, a domain note, and at
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least one note dense with relationships between concepts.
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### 1d — Create `_templates` for core note types only
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Add templates for: `research`, `howto`, `adr`, `hub`. The long tail stays freeform until a
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pattern earns a template (per ADR-011). Consistent per-type structure improves Graphify's
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local-SLM extraction reliability.
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### 1e — Fix the broken vault search reference
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`vault-conventions.md` (or `CLAUDE.md`) currently references
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`~/.claude/scripts/vault_search.rb`, which does not exist. Replace every reference to that
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script with `graphify query` (per ADR-010).
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---
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## Step 2 — Graphify + Ollama setup (CRITICAL PATH)
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This step is the genuine gate. All hook behavior, model selection, and extraction tuning depend
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on the benchmark in 2c. Do not skip or defer 2c.
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### 2a — Install and verify Graphify
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The PyPI package name has a double-y — this is the correct install command:
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```bash
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pip install graphifyy
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```
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Verify: `graphify --version`
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### 2b — Configure Ollama
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Set these in your shell profile (or the plugin env block in Step 6):
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```bash
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OLLAMA_FLASH_ATTENTION=1 # 30–50% VRAM savings on KV cache — always set
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GRAPHIFY_OLLAMA_NUM_CTX=8192 # 8K is sufficient for vault notes (200–2000 words)
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# leaves comfortable headroom for prompt overhead
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GRAPHIFY_OLLAMA_KEEP_ALIVE=5 # set when packaging in Step 6
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```
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Verify context allocation after the first extraction call: `ollama ps` shows allocated context.
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### 2c — Model benchmark (THE GATE)
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Run a small extraction test before committing to any model. Use the 5–10 representative
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migrated notes from Step 1c as the test set.
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**Models to benchmark:**
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| Model | Backend | Size | Notes |
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|---|---|---|---|
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| `gemma4:e2b` | Ollama local | 7.2 GB | Primary candidate — fast, large context |
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| `qwen3.5:2b` | Ollama local | 2.7 GB | Smallest; fallback if VRAM is constrained |
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| `gemma4:e4b` | Ollama local | 9.6 GB | Highest local quality; slower |
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| `claude-haiku-4-5` | Claude API | — | API baseline |
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| `claude-sonnet-4-6` | Claude API | — | Mid-tier reference |
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| `claude-opus-4-8` | Claude API | — | **Gold standard — score local models against this** |
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**What to measure per model:**
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1. Extraction speed (wall-clock time per note)
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2. Entity quality: right concepts extracted, no hallucinated entities
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3. Relationship quality: edges plausible and correctly typed, no missing key edges
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4. Confidence tag accuracy: `INFERRED` vs `AMBIGUOUS` appropriately flagged
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**Decision rule:** choose the fastest local model whose entity/relationship quality is "close
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enough" to Opus output. Do not hardcode `gemma4:e2b` — the benchmark decides.
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Review god-node quality in `GRAPH_REPORT.md` after each run. Opus output is the scoring rubric.
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### 2d — Build the initial vault graph
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After 2c picks a model:
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```bash
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graphify extract --path ~/Documents/SecondBrain \
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--backend ollama --model <chosen-model> \
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--token-budget 512 --max-concurrency 2
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```
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Review `GRAPH_REPORT.md`. God nodes should be the most-connected tools, clients, and domain
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concepts — confirm they make sense given the vault's content.
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### 2e — Per-project code graphs (free; no model)
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For each active client project:
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```bash
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graphify extract --path ~/projects/<client>/<project> --no-docs
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```
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`--no-docs` runs only tree-sitter AST — zero token cost. Use `--update` on subsequent runs;
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use `--force` when files have been deleted (to clear stale nodes). Keep each project's
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`graphify-out/` alongside the project; do not merge client projects into one graph.
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---
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## Step 3 — Hooks
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Thin shell wrappers around Graphify. The logic lives in Graphify; the hooks only invoke it.
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| Hook | Trigger | Action |
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|---|---|---|
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| **PostToolUse** | AI writes/edits a vault `.md` | `graphify update --file <path>` |
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| **SessionStart** | Session opens | Stale check → `--force` rebuild if needed → inject context |
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| **SessionEnd** | Session closes | Append dated journal note to vault |
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**Stale-check mechanism (SessionStart):** read the mtime of
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`~/.cache/graphify/vault-rebuild.stamp`. If older than N days (7 is the starting guess — tune
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after observing drift), run `graphify --force` on the vault and write a new stamp. Then inject:
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god-node summary from `GRAPH_REPORT.md` + `convention/*` note summaries + journal pointer.
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**Note on `--update` vs `--force`:** `graphify update --file` does not prune deleted nodes.
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Stale/ghost nodes accumulate from manual deletes and renames. The periodic `--force` rebuild
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triggered by the stale check is the mitigation — it rebuilds the graph clean.
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---
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## Step 4 — Episodic layer (memsearch)
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Install memsearch for time-anchored "what happened / what was I working on" queries. Graphify
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does **not** replace this — they serve different query patterns (knowledge graph vs timeline
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recall).
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|
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```
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/plugin marketplace add zilliztech/memsearch
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plugin install memsearch
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```
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Verify daily memory files appear after a few conversations. The open question of whether
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memsearch indexes SessionEnd journal notes or only its own auto-capture is deferred to build
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time (see Open questions §7).
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---
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## Step 5 — Vault sync
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Sync the markdown vault to the VPS. Pick one:
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- **git** — versioned, hourly push/pull via cron; explicit audit trail.
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- **Syncthing** — continuous, bidirectional, zero-thought after setup.
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**What to sync:** the vault only (`~/Documents/SecondBrain`).
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**What NOT to sync:** `graphify-out/` directories, Milvus Lite caches, Ollama models. These are
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disposable — rebuilt per machine from the vault (markdown is the single source of truth, per
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ADR-008).
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---
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## Step 6 — Package as a global Claude Code plugin
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One global install so every project and machine shares the same vault conventions, hooks, and
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Graphify config.
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**Plugin contents:**
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- **Hooks** registered in settings: SessionStart, PostToolUse, SessionEnd — shell wrappers from
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Step 3, parameterized by vault path and Graphify output dir.
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- **Graphify CLI on PATH** — the AI calls `graphify query`, `graphify path`, `graphify explain`
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via the Bash tool. No server process per graph; project-specific graphs are queried with
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`--graph <project-root>/graphify-out/graph.json`.
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- **Skills** (carry the know-how to the model):
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- `memory-write` — when to record evergreen knowledge, frontmatter contract, scope rule, vault not repo.
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- `memory-query` — `graphify query` vs memsearch; god-node discipline; `--budget`/`--dfs`; cross-client lookups; progressive disclosure via `summary`.
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- `memory-reorganize` — plan-mode consolidation/promotion procedure; when to trigger `--force` rebuild; human-approval guardrails.
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- **Env vars** baked in: `OLLAMA_FLASH_ATTENTION=1`, `GRAPHIFY_OLLAMA_NUM_CTX=8192`,
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`GRAPHIFY_OLLAMA_KEEP_ALIVE=5`.
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- **Config** (set once at user level): vault path, Graphify output dir, Ollama model name,
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||||
stale-rebuild threshold in days.
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---
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## Open questions / decisions still to settle
|
||||
|
||||
These are deferred to build time. Most can be defaulted without blocking; the only genuine gate
|
||||
is **§6 (Step 2c benchmark)** — model selection is blocked until it runs.
|
||||
|
||||
1. **Vault symlink** — `~/Documents/SecondBrain` is confirmed as the vault (RESOLVED per
|
||||
ADR-012). The open sub-question: symlink it into `~/.claude/memory` or not? Only needed if
|
||||
a tool requires that path.
|
||||
|
||||
2. **Sync mechanism** — git (versioned, hourly) vs Syncthing (continuous). Both are valid;
|
||||
choose at build time based on preference.
|
||||
|
||||
3. **Stale rebuild threshold** — 7 days is the starting guess. Tune after observing how quickly
|
||||
ghost-node drift becomes noticeable in practice.
|
||||
|
||||
4. **Per-project graph path convention** — how does SessionStart know which `graph.json` to
|
||||
inject? Proposed convention: `<project-root>/graphify-out/graph.json`, injected only if the
|
||||
file exists at that path. Not yet made explicit in the plugin spec.
|
||||
|
||||
5. **`summary` field discipline** — Graphify extracts entities and edges but does not write
|
||||
summaries. The human (or AI at note-creation time) must write `summary:` frontmatter. Confirm
|
||||
this holds in practice and add a lint/reminder to the memory-write skill if it drifts.
|
||||
|
||||
6. **Model benchmark results (Step 2c)** — all model choices are deferred until the benchmark
|
||||
runs. Do not hardcode `gemma4:e2b` (it's the primary candidate, not the confirmed pick).
|
||||
|
||||
7. **memsearch + journal integration** — does memsearch index SessionEnd journal notes or only
|
||||
its own auto-capture? How does the journal pointer injected at SessionStart reference the
|
||||
vault? Nail down at memsearch install time (Step 4).
|
||||
|
||||
8. **MCP server management** — vault graph + N project graphs = N+1 potential instances. The
|
||||
build plan leans toward a single Graphify CLI on PATH with `--graph <path>` rather than
|
||||
running multiple `graphify serve` instances, but this is not yet made explicit in the plugin
|
||||
spec. Confirm the CLI-only approach or define the server lifecycle.
|
||||
|
||||
**Resolved:** The type-tag taxonomy is settled via ADR-011 (faceted, six independent namespaces;
|
||||
`type/` listed first). No further debate needed on taxonomy shape.
|
||||
|
||||
---
|
||||
|
||||
## Recommended next move
|
||||
|
||||
Turn **Step 2** into a detailed implementation plan via the **writing-plans skill**. It is the
|
||||
critical path: Graphify install, Ollama configuration, the model benchmark (2c), and the initial
|
||||
graph build are the smallest set of tasks that unblock everything else. Open questions §1–5 and
|
||||
§7–8 can be defaulted or deferred; only §6 (the benchmark) genuinely blocks model-dependent
|
||||
decisions.
|
||||
Loading…
Reference in New Issue