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Architecture Decision Records

A running log of decisions and why. Format per entry: Context · Decision · Rationale · Alternatives rejected · Status. Newest decisions extend the log; supersede rather than delete.

ADR-001 — Two memory types, kept as separate systems

Context: Earlier attempts to make one tool serve both "what happened" and "how do we do X" felt forced (e.g. trying to make memsearch filter knowledge by tags).
Decision: Model episodic memory and semantic/knowledge memory as two separate systems with different tools.
Rationale: They have different lifecycles (episodic accretes and decays; knowledge is deliberately maintained), different write paths (auto-captured vs curated with guardrails), and different query patterns ("when did we…" vs "how do we…"). Separation dissolves the earlier integration tension entirely.
Alternatives rejected: One unified store (memsearch-for-everything, or OpenBrain's single thoughts table) — conflates the two and forces awkward filtering.
Status: Accepted.

ADR-002 — memsearch for the episodic layer

Context: Need timeline/"what happened" memory (Goal 3) that's NL-queryable and lazy.
Decision: Adopt memsearch (Zilliz) off-the-shelf for episodic memory.
Rationale: It already implements the OpenClaw daily-notes + "dreaming" pattern and the markdown-as-truth / disposable-shadow-index philosophy we'd otherwise build. Embedded Milvus Lite (single file), hybrid BM25+vector+RRF search, local ONNX embeddings (no API key/cost), a FileWatcher that handles deletions — no Docker, no server. Two-line install.
Alternatives rejected: claude-mem (MCP-based — Claude must actively call search; opaque blobs vs readable markdown; overkill features). Hand-building daily notes + dreaming ourselves (reinventing a solved tool).
Status: Accepted.

ADR-003 — Flat vault with namespaced tags, not folders

Context: Connelly/Huryn organize by folders (tools/, domain/). User wants a flat Obsidian vault with tags as virtual indexes, and cross-cutting filters (client × tool × convention).
Decision: One flat markdown vault; organize via namespaced, nested tags (tool/, client/, domain/, convention/, scope/). Slashes are valid Obsidian nested tags, so #tool matches all children.
Rationale: A note can carry several namespaces at once (tool/semrush + client/sesame3g + convention/react-ts) — folders can't express that. Enables "filter by client+tool to narrow the index." Enumerable virtual indexes ("what clients/tools exist").
Alternatives rejected: Folder hierarchy (single-axis; can't do cross-cutting filters). Pure-prefix path filtering via memsearch source_prefix (would force directories back in).
Trade-off accepted: Tags give the human/Obsidian free filtering, but the AI gets nothing for free from tags — we must materialize them into a queryable index (see ADR-004).
Status: Refined by ADR-011 (type/ and project/ namespaces added; hierarchy-vs-facets clarified). Core decision — flat vault, namespaced tags — stands.

ADR-004 — SQLite + Sequel (Ruby) tag index as the knowledge-layer cache

Context: The AI can't use Obsidian tags directly; tag filtering needs a machine-queryable index. A previous ~/Documents/SecondBrain/ tag database was lost track of.
Decision: A small Ruby program using the Sequel ORM over SQLite, exposed as a CLI. Schema: files(path, mtime, summary, scope), tags(name), files_tags join (many_to_many). The summary is a column on files (an attribute), not a join.
Rationale: Normalized tags table makes enumerating the vocabulary a first-class cheap query (the "virtual index" goal). The summary column is what turns the index from a finder into a router — the AI sees enough to pick a file without opening it (progressive disclosure, low tokens). Ruby + Sequel + CLI keeps the contract clean and the DB swappable; the AI never touches SQLite directly.
Failure-mode guard (the lost-SecondBrain lesson): markdown is always authoritative; the SQLite file is a disposable cache that is never synced and can be rebuilt from frontmatter anytime (index update --rebuild).
Alternatives rejected: Plain-markdown generated INDEX.md (must regenerate; grep-at-scale is token-heavy). Frontmatter grep on demand (scales badly). Milvus/Postgres for knowledge (overkill; QMD/memsearch prove SQLite is enough — see ADR-006/008).
Query output: returns path + summary + matched tags (option C) — tags are cheap and show why a result matched, useful for cross-client queries.
Status: Superseded by ADR-010 (Graphify replaces the Ruby/SQLite tag index). The summary + namespaced-tag frontmatter this ADR introduced is retained as note metadata; only the bespoke Ruby/SQLite index and its CLI are dropped.

ADR-005 — Structured-first; semantic search over the vault deferred

Context: Tag filtering ("client/sesame3g + tool/semrush") may miss notes whose wording doesn't match the query ("how do we use semrush" vs a note titled "search analytics integration").
Decision: Ship the knowledge layer structured-only (tags + summaries). Defer meaning-based search over the vault until it demonstrably bites.
Rationale: Structured tagging is the lightweight/fast thing the user wants, and the summary+tag design is built to make it work. Follow the video's "only level up when it bites."
Status: Superseded by ADR-010. The premise (ship structured-only, bolt on semantics later) no longer holds: Graphify makes the knowledge layer a graph from day one, giving structured and connection-based recall together. The "only level up when it bites" instinct carries forward to whether a vector layer is ever needed on top of the graph.

ADR-006 — QMD as the (deferred) semantic-over-knowledge layer

Context: When ADR-005's structured-only proves insufficient, we want a set-and-forget semantic layer over the vault, local and Docker-free.
Decision: Earmark QMD (github.com/tobi/qmd) for that role; do not install yet.
Rationale: Local markdown search using SQLite + FTS5/BM25 + local vector embeddings (EmbeddingGemma-300M GGUF) + LLM rerank; CLI + optional MCP server; no Docker, no API keys. Validates that SQLite + a local vector model suffices (no Milvus/Postgres for knowledge). Complements the tag index (QMD filters by path/collection context, not first-class frontmatter tags), so it adds semantic recall without replacing structured filtering.
Alternatives rejected: Pointing memsearch at the vault (mixes episodic and knowledge corpora; its filtering is path-prefix not tags). A bespoke embedding index (reinvents QMD).
Status: Superseded by ADR-010. Graphify's knowledge graph fills the semantic-recall role (traversal/explain over connections) without a separate vector system, so QMD is no longer earmarked. Revisit a vector layer only if graph traversal demonstrably misses cases where embedding similarity would win.

ADR-007 — Lazy freshness: write-hook + session-start reconcile, no daemon/cron

Context: The cache must reflect new/edited/deleted/renamed notes without becoming a resource hog or going stale on renames.
Decision: Option A (lazy). A PostToolUse hook updates the index on AI writes (single-file, prunes on delete). Manual edits are caught by a session-start reconcile (index update --since + prune of vanished paths). No daemon, no cron.
Rationale: The AI is the primary writer, so write-time hooks give event-driven freshness with no polling. The user rarely edits the vault by hand, so a session-start reconcile is enough; a continuous inotify daemon (the listen gem) would add an always-on process to manage/sync for negligible benefit. Matches the user's "lazy sync is fine" stance.
Alternatives rejected: inotify/listen daemon (live freshness, but always-on process to manage — unnecessary). Cron reconcile ("seems silly" per user; session-start covers it).
Status: Accepted.

ADR-008 — Markdown-as-truth; sync the vault, not the indexes

Context: Must be accessible on a VPS / multiple machines but run local-fast (Goal 4).
Decision: Sync the markdown vault to the VPS via git or Syncthing (choice deferred to build time). Graphs/indexes (Milvus Lite, Graphify graphify-out/) are rebuilt per machine and never synced.
Rationale: Markdown is plain text — git/Syncthing sync it trivially; lazy (hourly or continuous-async) is enough. Indexes are disposable caches; syncing binary DBs invites conflicts for no gain. Local reads stay fast; ownership and portability stay with the user.
Alternatives rejected: OpenBrain / Mem0 hosted DBs — always-remote, adds per-query latency and monthly cost, conflicts with local-fast; ownership weaker (Mem0 especially). Only worth it for real-time cross-tool memory, which the user called overkill.
Status: Accepted.

ADR-009 — Package as a global Claude Code plugin with skills

Context: Every project, on every machine, should know how to use the vault — write conventions, query patterns, the hooks, and the CLI — without per-project setup.
Decision: Ship hooks + scripts + CRUD know-how as a global Claude Code plugin with skills, installed at the user level.
Rationale: Skills carry the "when to write / what conventions / how & when to query" guidance to the model; the plugin registers the session-start / session-end / PostToolUse hooks and wires up Graphify (extraction/update/query + MCP server). Global install = consistent behavior everywhere; single source of truth for the conventions themselves.
Status: Accepted (to be built — see 04-build-plan.md).

ADR-010 — 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.
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).
Status: Accepted (to be built — see 04-build-plan.md and 06-graphify-evaluation.md).

ADR-011 — Faceted tag taxonomy: six independent namespaces (refines ADR-003)

Date: 2026-06-04

Context: ADR-003 introduced five namespaces (tool/, client/, domain/, convention/, scope/). During vault-reuse assessment (ADR-012) it became clear that (1) the existing SecondBrain vault uses a de-facto first-tag convention for note kind (research/plan/log/adr/howto) that should be made explicit and machine-queryable, and (2) for a freelancer working many projects per client, project identity deserves a first-class namespace rather than being implied by client/ or domain/.
Decision: Knowledge-vault notes are classified by six independent, flat tag facets that sit side-by-side, never nested into one another:
- type/ — note kind: research, howto, adr, hub, plan, log, clip, etc.
- client/ — which client
- project/ — which project (first-class; a freelancer's projects are the primary unit of work)
- domain/ — knowledge domain / topic area
- tool/ — tool-specific knowledge
- convention/ — conventions
- …plus scope/global or scope/project (retained from ADR-003)
Hierarchy and relationships are expressed via hub notes (type/hub), wikilinks, and Graphify knowledge-graph edges — NOT via nested tag paths.

By convention type/ is listed first in frontmatter, preserving the SecondBrain vault's existing type-first ordering habit and making the note kind immediately visible.
Rationale: The vault is flat — hierarchy is not expressed through folder paths or tag nesting. The user's reality is many-to-many (many projects per client, knowledge domains spanning clients), which a single-parent tree models badly and forces false hierarchy. A project hub note links out to both its client/ and relevant domain/ tags rather than being buried under either. Per-type _templates will be provided for core types only (research, howto, adr, hub); the long tail stays freeform until a pattern earns a template. Consistent per-type structure also improves Graphify's local-SLM extraction reliability.
Alternatives rejected: Hierarchical nesting in the style of John Conneely's domain/{product}/{project}.md folder structure (from the youngleaders.tech article "How I finally sorted my Claude Code memory" — secondary/interview-grade source, not verified against primary implementation). Rejected because: (1) the vault is flat — hierarchy is not expressed through folder paths; (2) the user's many-to-many reality maps badly onto a single-parent folder tree and forces false hierarchy; (3) nesting one facet through another (e.g. domain/client/project) creates Law-of-Demeter-style traversal coupling. Conneely's structure was the inspiration but diverges here on hierarchy-vs-facets. Faceted parallel tags are the flat-vault analogue of what the Graphify graph already does with edges, so they compose naturally with the chosen knowledge layer.
Status: Accepted (supersedes the namespace list in ADR-003; core flat-vault + namespaced-tags decision stands).

ADR-012 — Reuse the existing SecondBrain vault as the knowledge vault