---
id: "0010"
date: 2026-06-03
status: Accepted
supersedes: "0004, 0005, 0006"
superseded-by:
affected-paths: []
affected-components: []
migration_confidence: medium
migration_source: "docs/memory-system/03-architecture-decisions.md### ADR-010 — Graphify knowledge graph as the knowledge layer (supersedes ADR-004/005/006)"
---

# 0010 — Graphify knowledge graph as the knowledge layer (supersedes ADR-004/005/006)

## Context

ADR-004 specced a hand-built Ruby/Sequel/SQLite tag index (+ CLI) as the
  machine-queryable layer over the vault, with ADR-005/006 deferring meaning-based recall to a
  future QMD vector layer. Before building any of it, we evaluated **Graphify** (`graphify`,
  PyPI `graphifyy`) — a tool that turns a folder into a queryable knowledge graph (local
  tree-sitter AST for code, local-SLM entity/relationship extraction for docs). See
  `06-graphify-evaluation.md`.

## Decision

Use **Graphify as the knowledge-layer engine** over the vault, with a **local
  Ollama** backend for doc extraction and free AST for per-project code graphs. **Drop** the
  Ruby/SQLite tag-index CLI (ADR-004) and the earmarked QMD layer (ADR-006); **retain** the
  `summary` + namespaced-tag frontmatter from ADR-003/004 as note metadata.
- **Rationale**: One off-the-shelf tool delivers both what the tag index was for (structured
  retrieval) and what QMD was deferred for (connection/meaning-based recall via graph
  traversal + `explain`) — without writing or maintaining a bespoke index, and without a vector
  store. Code graphs come free. Keeps the markdown-as-truth, no-Docker, no-API-key, local-first
  properties (extraction runs against local Ollama). Net scope reduction: the entire Ruby build
  (old critical-path Step 2) and the QMD layer are removed.
- **What's retained / changed**: `summary` stays the human-written router hint Graphify does not
  generate; namespaced tags stay useful for Obsidian filtering and as node attributes. How
  tightly metadata should feed graph queries is a **build-time refinement**, not settled here.
- **Trade-off accepted**: Graphify's `--update` doesn't prune deleted nodes (stale-node drift) —
  mitigated by a periodic `--force` rebuild on the session-start staleness check (ADR-007's lazy
  model still applies). Graphify also moves fast (flags are version-dependent; anchored to
  v0.8.30) and its headline token-savings numbers are corpus-dependent — benchmark our own.

## Consequences

Graphify becomes the knowledge-layer engine over the vault (local Ollama backend for docs, free tree-sitter AST for code), replacing the planned Ruby/SQLite tag index (ADR-004) and the earmarked QMD semantic layer (ADR-006), while retaining the summary + namespaced-tag frontmatter as note metadata. This reduces the scope of what must be built and maintained, but introduces reliance on Graphify's behavior, including a known trade-off that `--update` doesn't prune deleted nodes (mitigated by periodic `--force` rebuilds) and that its flags/behavior are version-dependent.

## Alternatives rejected

Building the Ruby/SQLite index as originally planned (more code to
  own; no semantic recall); adding QMD as a second system on top (two stores where one graph
  suffices).