Embeddings Setup

Embeddings setup

Open Second Brain ships with two search paths: keyword-only (always on, no credentials) and semantic via embedded vectors (opt-in). This SKILL walks the activation flow for the semantic path. The flow is proactive — when the user mentions semantic search or o2b search check surfaces missing pieces, take the user through this list rather than waiting for explicit instruction.

Step 1 — Always start with o2b search check

o2b search check

The output names every missing piece and ends with a recommendations: block listing the exact commands to fix each. Read both before suggesting next steps. The recommendations field is also present in the --json output for headless callers.

Branch on what the report shows:

• embedding_key: MISSING → go to step 2.
• vec_extension: unavailable on macOS → go to step 3.
• vec_extension: unavailable on Linux → go to step 4.
• Everything OK but semantic_enabled: false (no embeddings yet) → go to step 5.

Step 2 — Provider and API key

Ask the user which provider they want. The default is text-embedding-3-small from OpenAI (about $0.02 per 1M tokens, which covers tens of thousands of vault pages). Any OpenAI-compatible endpoint works — Groq, Together, a local LM Studio server, etc.

Required env vars (write to ~/.hermes/.env or the configured env file, never to a tracked file):

OPEN_SECOND_BRAIN_EMBEDDING_PROVIDER=openai-compat
OPEN_SECOND_BRAIN_EMBEDDING_MODEL=text-embedding-3-small
OPEN_SECOND_BRAIN_EMBEDDING_KEY=<placeholder; user pastes the key>
# Optional — only when not using OpenAI:
# OPEN_SECOND_BRAIN_EMBEDDING_BASE_URL=https://api.together.xyz/v1

Never invent or echo the key. Write a placeholder, then ask the user to paste their key in place of it. Recheck with o2b search check after the user confirms.

Step 3 — macOS: install Homebrew SQLite

Apple ships /usr/lib/libsqlite3.dylib with SQLITE_OMIT_LOAD_EXTENSION, so the optional sqlite-vec extension cannot load against the system SQLite. Homebrew's sqlite formula is built with extension loading enabled.

brew install sqlite

The o2b wrapper auto-detects Homebrew SQLite on Darwin and exports DYLD_LIBRARY_PATH for bun:sqlite on the next invocation. No manual patching of the wrapper script is needed (the v0.10.5 shim scripts/_macos-sqlite.sh handles it). Verify with:

o2b search check

Expect vec_extension: loaded.

Step 4 — Linux: reconfirm the optional dependency

sqlite-vec ships as an optional dependency. If the install path missed it, force a rebuild:

bun pm ls | grep sqlite-vec
bun install --force

If the package is present but still does not load, the Linux build of libsqlite3 may have been compiled without LOAD_EXTENSION. Capture sqlite3 :memory: "PRAGMA compile_options;" and surface it to the user — they will know whether their distro's SQLite is unusual.

Step 5 — Compute the first vectors

o2b search reindex --embeddings

This walks the vault, chunks every Markdown file, and computes embeddings. Cost scales linearly with vault size — a 150-file vault typically lands in a few seconds.

Verify semantic search works:

o2b search "preferences for code review"

The output rows carry (semantic) in the source column when the match came from the vector index.

Step 6 — Offer periodic reindex

The vault keeps changing — other agents add notes, the user edits existing ones. Without periodic refresh the embeddings drift behind the keyword index.

o2b search reindex --cron-template

Prints a watchdog script (a heredoc that, when the operator runs the printed block, lands at ~/.local/bin/osb-reindex.sh), a native crontab line, and a hermes cron create command. Pure stdout — the verb writes nothing on its own; pick the path that matches the host and paste the relevant section into your shell / crontab. Recommended cadence:

• 30 minutes when the vault sees active multi-agent work.
• 6 hours when changes are sporadic.

Override with --interval 6h (or any <N>m|h|d value below 60m / 24h / unlimited days).

Multi-agent note

Only the agent that runs reindex needs OPEN_SECOND_BRAIN_EMBEDDING_KEY. Read-only consumers (sibling Claude Code / Codex / OpenClaw sessions on the same vault) query the already-computed vectors and never see the key. When designating the reindex owner, the canonical choice is Hermes (it carries the cron infrastructure); the others stay credential-free.

What this SKILL does NOT do

• Does not invoke brew install on the user's behalf. The SKILL prints the command; the user runs it.
• Does not paste an API key into the env file silently. Always use a placeholder, then ask the user to substitute.
• Does not commit env files. They live outside the tracked tree.
• Does not launch a long-running watcher inside OSB — the --cron-template recipe is the endorsed automation path.