wiki-retrieve: Hybrid Retrieval over the Vault

The v1.6 query path was Read(hot.md) → Read(index.md) → Read(3-5 pages) → synthesize. It worked, but page-level granularity loses to chunk-level granularity any time the answer lives in a specific passage rather than a whole page. The v1.7 wiki-retrieve skill is the chunk-level upgrade — opt-in, feature-gated, and replaces nothing if you don't run the setup.

Origin: This skill came from the vault's MIT-licensed upstream foundation; there is no kepano equivalent. The technique is from Anthropic's Sept 2024 Contextual Retrieval research and is implemented here as agent-skill plumbing.

Data privacy (v1.7.1+)

Tier 1 (Anthropic API) and tier 2 (claude CLI subprocess) of the contextual-prefix generator send wiki page bodies off-machine. As of v1.7.1, both tiers are GATED behind explicit user consent at two layers:

• scripts/contextual-prefix.py --allow-egress (default off). Without the flag, pick_prefix_tier() returns "synthetic" regardless of ANTHROPIC_API_KEY or claude binary presence.
• bin/setup-retrieve.sh prompts before any non-synthetic Stage 1 run; default is abort.

To run fully on-machine (tier 3 synthetic prefix + local ollama rerank), use bash bin/setup-retrieve.sh --no-llm. This is also the effective behavior if you decline the consent prompt or omit --allow-egress.

The guard mirrors scripts/tiling-check.py:351 --allow-remote-ollama. v1.6 vaults that never provisioned this skill see zero behavior change.

Architecture

INGEST (one-time, then incremental):

  wiki/<page>.md
       │
       ▼
  scripts/contextual-prefix.py
       │   ├─ chunk on paragraph boundaries (~500 token target, 200 char overlap)
       │   ├─ generate 1-2 sentence prefix per chunk
       │   │     tier 1: ANTHROPIC_API_KEY → Anthropic API (Haiku, prompt-cached
       │   │                                 when body ≥ ~16 KB / Haiku 4.5 floor)
       │   │     tier 2: `claude` on PATH  → claude -p subprocess
       │   │     tier 3: synthetic         → frontmatter title + first paragraph
       │   └─ write .vault-meta/chunks/<address>/chunk-NNN.json
       │
       ▼
  scripts/bm25-index.py build
       └─ inverted index over chunks' contextualized_text → .vault-meta/bm25/index.json

QUERY:

  query string
       │
       ▼
  scripts/retrieve.py "<query>" --top 5
       ├─ bm25-index.py query "<query>" --top 20    (sparse candidate set)
       ├─ rerank.py "<query>" --candidates -        (dense rerank via ollama cosine)
       │     cosine(query_embedding, chunk_embedding)
       │     embeddings cached in .vault-meta/embed-cache.json keyed by body_hash
       └─ dedupe by page-address, return top-N candidates with absolute_path
       │
       ▼
  caller (wiki-query / autoresearch) reads the cited pages and synthesizes

Feature gating

Other skills must detect this skill before using it. The canonical detection:

[ -x scripts/retrieve.py ] && [ -d .vault-meta/chunks ] && \
  [ -f .vault-meta/bm25/index.json ] && \
  echo "wiki-retrieve installed" || echo "fallback: legacy hot→index→drill"

If detection fails, callers MUST fall back to the v1.6 read order. This skill never breaks the base plugin.

Setup

bash bin/setup-retrieve.sh

What it does, in order:

1. Sanity-checks the 4 scripts are present and executable.
2. Creates .vault-meta/chunks/ and .vault-meta/bm25/.
3. Probes ollama at http://127.0.0.1:11434 for nomic-embed-text (rerank prerequisite). Reports status; does not install.
4. Reports which contextual-prefix tier will be used (Anthropic API / claude CLI / synthetic).
5. Runs contextual-prefix.py --all to chunk + contextualize every wiki page.
6. Runs bm25-index.py build.
7. Smoke-tests retrieve.py against the query "wiki".

Flags:

• --check — diagnostics only, no provisioning.
• --no-llm — force tier-3 synthetic prefix (cheapest, zero LLM dependency).
• --rebuild — re-chunk every page even if body_hash matches.

Cost ceiling

Per Anthropic's published research, contextual-prefix generation costs approximately $12 per 1,000 documents with Haiku + prompt caching. For a 100-page vault with ~3 chunks per page, that's ~$3.60 one-time, with incremental updates much cheaper (only changed pages re-process).

If you want to validate cost before running on a large vault:

bash bin/setup-retrieve.sh --no-llm   # provision with tier-3 synthetic prefix
# inspect retrieval quality manually; if insufficient, re-run without --no-llm

The claude-cli subprocess tier (no API key) is free in $ terms but slower (~3-10s per chunk depending on Haiku availability).

Skill commands (recipe)

These are the commands wiki-query and autoresearch will execute when wiki-retrieve is feature-detected. Other skills should mirror this pattern.

Standard retrieve

python3 scripts/retrieve.py "your question here" --top 5

Output: JSON with candidates array. Each candidate has absolute_path to the source page; caller reads that page (using the v1.7 transport selector) and synthesizes.

BM25-only (skip rerank)

python3 scripts/retrieve.py "query" --top 5 --no-rerank

Faster (no ollama call); lower quality.

Explain mode (debugging)

python3 scripts/retrieve.py "query" --top 5 --explain

Adds an explain block with per-stage diagnostics (BM25 candidate count, dedupe size, etc.).

Direct BM25 inspection

python3 scripts/bm25-index.py query "query" --top 10
python3 scripts/bm25-index.py stats

Rerank strategy probe

python3 scripts/rerank.py "query" --peek

Reports which strategy will run (cosine via ollama / no-op).

Integration with wiki-query

After this skill is installed, skills/wiki-query/SKILL.md standard and deep modes will:

1. Read wiki/hot.md (always — quick context).
2. Call python3 scripts/retrieve.py "<query>" --top 5.
3. Read the candidate pages from the result's absolute_path field (using the v1.7 transport selector — obsidian-cli read or Read tool).
4. Synthesize with chunk-level citation.

Quick mode is unchanged (hot.md only — never invokes retrieval).

If retrieve.py exits 10 (feature not provisioned), wiki-query falls back to the legacy v1.6 Read(index.md) → Read(N pages) order. No user-visible breakage.

Index maintenance

The index is NOT auto-refreshed when wiki pages change. Re-run after substantive ingest sessions:

python3 scripts/contextual-prefix.py --all      # incremental: only re-processes changed pages
python3 scripts/bm25-index.py build             # always full rebuild (cheap; pure Python)

A future v1.7.x patch will add an opt-in PostToolUse hook that triggers contextual-prefix + BM25 rebuild after every N writes. For v1.7.0, refresh is manual.

To wipe and start over:

rm -rf .vault-meta/chunks/ .vault-meta/bm25/ .vault-meta/embed-cache.json
bash bin/setup-retrieve.sh

Future tiers (v1.7.x roadmap)

Documented for transparency; not implemented in v1.7.0:

Cross-reference

• Decision tree for transports: wiki/references/transport-fallback.md
• Concurrency policy: skills/wiki-ingest/SKILL.md §Concurrency
• DragonScale Memory: wiki/concepts/DragonScale Memory.md
• Anthropic Contextual Retrieval research: https://www.anthropic.com/news/contextual-retrieval

How to think (10-principle mapping)

When working on this skill, apply the 10-principle loop. See skills/think/SKILL.md for the canonical framework.