Round 2 of the PR #147 review forged origin: static for yaml.v3 with an
alias key plus a "..." document-end line: per-line judgement cannot see
context-dependent YAML. It also found REST ingest writing pages with no
provenance (stampPages lived only in the MCP server).
- New package internal/provenance. Apply keeps only top-level groups
`key: value` with a bare-identifier key whose group decodes on its own
to exactly that key, drops reserved and duplicate keys and everything
else (aliases, anchors as keys, document markers, complex/merge keys,
flow maps, tags, quoted keys), appends the stamp, then decodes the
whole result with yaml.v3 and refuses the write unless it reads back
exactly the stamp. api.StampProvenance wraps it and now returns an
error, which every caller propagates.
- The ingest pipeline stamps every page it writes or merges, from
provenance.FromContext(ctx); MCP attaches the caller's stamp, REST and
the watcher stamp unknown. RunRaw takes a ctx.
- brain_edit snapshots the note and rolls the edit back if the stamp
cannot be verified.
Tests: R1/R2 payloads join the write/update variant table, plus
brain_edit with the alias payload; REST /ingest-raw (title newline
checked with the line-oriented reader) and REST /ingest (stub LLM) stamp
unknown. Two existing byte-exact tests updated for the stamp line.
Refs #145#144
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
The PR #147 review forged origin: static as a JWT principal through
three tools the first version never touched (brain_edit, brain_ingest_raw,
ingest_raw + brain_promote), and through YAML spellings a key-name match
missed (quoted, escaped, tagged, flow-mapped, merge keys, lone CR).
- api.StampProvenance removes every spelling of origin/written_by from
the frontmatter and appends the real values. A line is dropped if
EITHER yaml.v3 (decoding quotes, escapes, tags, flow maps) or the
brain's line-oriented readers would read it as provenance; complex
keys, orphan values and merge keys are dropped outright. Lone CRs in
frontmatter become LF. Principal values that are not bare words are
quoted.
- Applied as the last step of writeHallNote, UpdateNote, PromoteNote
(re-attributed to the promoter), brain_edit (re-attributed to the
editor) and both ingests (every page written or merged). REST
/write and /promote carry no principal and stamp unknown.
- Ingest: newlines in scalar fields fold to spaces; a page type must be
a plain lower-case name (../raw wrote outside wiki/, pre-existing).
- Audit: outcome is ok|error, never the error text, which echoed
argument values.
Tests: every escape from the review is a table case asserting the
invariant on the file (parses as YAML, yaml.v3 and brain_get agree,
exactly the stamped lines). Plus REST /write, REST capture AuthPath,
body-line provenance in search, and quoted principals; two of the
review's surviving flips now go red. Three tests renamed so names claim
only what they assert.
Refs #145#144
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
brain_write was an ungated, durable prompt-injection path: a session that
just read an untrusted page could write an entry every later session
retrieves as trusted guidance (OWASP MCP06). Decision (#145): tag
provenance rather than stage writes.
Every write and update stamps origin (static | jwt | unknown) and
written_by (the authenticated principal) into frontmatter. Server-owned:
origin/written_by in caller content or an update fragment are discarded,
so a caller cannot claim a more trusted origin. No principal stamps
origin: unknown, never silence. brain_update re-stamps to the last
writer. capture (the claude.ai connector door) stamps too, via a new
server-derived CaptureContext.AuthPath set by both capture doors after
decode. REST POST /write carries no principal and stamps unknown.
brain_query results carry origin/written_by when the note has them;
older notes omit them rather than fabricate. brain_get already returns
frontmatter.
Refs #145
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Adds brain_reject (RejectNote + MCP tool) and fixes the watcher to skip raw/rejected/, preventing declined notes from being silently re-ingested and republished.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
Removes brain_write legacy domain/type/knowledge-path params (ADR-0012) and migrates the previously-missed cmd/hyperguild CLI caller (hyperguild brain write) from <type> <slug> to <wing> <hall> <slug>, fixing a 100%% regression the first review round caught. Adds TestWrite_CLIPayloadRoundTrips exercising the real Handler.Write over HTTP to pin the wire contract.
Closes#79.
Co-authored-by: Mathias <mthbqv@gmail.com>
Every brain write accepted [[targets]] that resolve to nothing — skill
names, repo names, agent-local memory-file slugs — and each one became a
permanent [high] broken-link finding. The brain-audit digest grew 19 -> 63
high findings between 2026-08-26 and 2026-09-16; 53 of the 63 were exactly
this, and none are fixable by brain-gardener's BrokenLinkFixer, which only
repoints edit-distance-1 renames. There is no target to repoint to.
StripUnresolvedLinks resolves each link against knowledge/ + wiki/ using
brain-gardener's own resolver semantics (bare slug or wing/hall/slug path
form, code spans excluded) and unwraps the misses to plain text, reporting
them as Ref.Unlinked / the MCP `unlinked` field.
Unwrap rather than reject: a refused write on claudewatcher's unattended
ingest path is a lost learning, and the author's words are worth keeping
even when the link is not. An empty corpus is a no-op, so a misconfigured
brainDir cannot strip every link in a note.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
brain_read returns a note verbatim; brain_edit is str_replace with an
exactly-once match, operating on the tree brain-sync commits from.
An adversarial design review before implementation changed three things:
1. Governance files are not in the model-facing tool. Brain content is
ingested from the outside world and reaches a model's context, and that
model would hold the editor — one poisoned page could rewrite the
CLAUDE.md a .dispatch-allow agent later loads as instructions. And
brain-sync merges with --strategy-option=ours, so the live tree beats a
human's corrective push on the conflicting lines. CLAUDE.md now goes
through brain_edit_root: de-surfaced from tools/list and gated on the
local static principal. The scopes are disjoint — the privileged door
has the smaller reach.
2. Reads needed the same allowlist, and brain_get already lacked it: it
returned verbatim session transcripts under archive/ by path. A test
proved the exposure live before the fix.
3. Canonicalise before allowlisting — knowledge/../.git/hooks/post-commit
would otherwise reach a hook that brain-sync executes in a pod holding
the Gitea push credentials.
Plus overlapping match counting, UTF-8 validation both ways, refusal while
git is mid-operation, flock with the read inside the lock, atomic
same-dir rename, and reindex only when frontmatter is touched.
Refs brain#4.
Co-authored-by: Mathias <mthbqv@gmail.com>
brain_index is auto-called after every write, and its own description
said so. A verb surfaced to callers that callers should never call is
cognitive load with no decision behind it — ADR-0012 rule 4.
Removed from tools/list only. The dispatch case stays, so maintenance
can still rebuild a Map of Content by hand: de-surfacing hides the verb,
not the operation. A test pins both halves, since removing the descriptor
and removing the capability look identical from the tool list.
Nothing called it directly — grepped the skills, specs and docs.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BeAp5LTscnz2W7Ubt4eJ6m
Wires the curation primitives into the MCP surface (all three sites:
tools() descriptors, handleCall dispatch, package doc) and registers the
GET /pending + POST /promote REST routes. brain_promote additionally
re-indexes the promoted note into the graph (best-effort), matching the
other write paths. brain_pending is the human-review-queue complement to
the agent-facing brain_write.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Adds the `capture` MCP tool: the #55 relay for harnesses that cannot run
the use-case in-process (claude.ai Chat/Cowork/Design, Crush, Pi, LLM
Council). They reach it through the existing /mcp OAuth connector.
- Thin: forwards to the SAME CaptureService as POST /capture; holds no
state and retains nothing beyond the I5 audit record. The containment
properties accepted in infra security-baseline (I2 ledger) hold by
construction.
- Per-principal: ServeHTTP re-derives the caller's principal from the
Bearer header (the chassis middleware gates but discards it) and stashes
it in context; the tool resolves the trust-zone origin from it. A
caller-asserted harness/origin in the body is ignored — origin is
server-derived, so the I1 confidential refusal still fires for us-nexus
callers (claude.ai), and sovereign-allowlisted JWT principals pass.
- Registered only when WithCapture is wired (all three sites: tools(),
handleCall, package doc); main wires REST + MCP from the same service,
resolver, and credentials.
Tests: listed-only-when-wired, forwards-via-static-principal,
confidential-via-us-nexus-refused, confidential-via-sovereign-allowed,
unauthenticated-rejected, caller-cannot-forge-origin.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Extracts the #45 write/update/get logic + the wiki upkeep that must
accompany a write (wing _index rebuild, cross-wing auto-tunnel, graph
re-index) into a single concrete brainstore.Store implementing
capture.BrainStore. The MCP brain_write/brain_update/brain_get handlers
are re-pointed at it, so there is one implementation, not two — the DRY
payoff #51 is named for. capture and MCP now share the exact same brain
write path and read-after-write contract.
The Server gains a *brainstore.Store, constructed in NewServer and given
the graph store in WithGraph. Embedding refresh stays out-of-band
(mtime-driven vectorstore.Sync), unchanged. Existing MCP brain_update/
brain_get/brain_write tests pass unmodified — behaviour and the
{id, path, content_hash} response contract are preserved.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Wires the #45 verbs into the MCP surface (all three sites: tools()
descriptors, handleCall dispatch, package doc comment).
- brain_update: supersede-by-slug or full path; rebuilds wing _index and
re-tunnels cross-wing matches against the new body (idempotent,
best-effort), re-indexes the graph, returns {id, path, content_hash,
superseded}.
- brain_get: fetch by id or path (both are the brain-relative handle);
returns {id, path, content_hash, frontmatter, body}.
- brain_write: return contract extended from {path} to {id, path,
content_hash} — path kept for backward compat — so the create path
also yields a stable handle.
id == relPath; content_hash == sha256 of the file bytes. Tests cover the
supersede happy path, missing-target error + no-create, get by id/path,
write handle, and an end-to-end re-embed test that drives the real
vectorstore.Sync re-index after an update.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Returns top-N relevant brain entries for a project context. Combines
BM25 hits on project name with 2-hop graph expansion via Track A's
graphstore (when BRAIN_GRAPH_ENABLED). Closes hyperguild#28.
Notes on implementation choices that deviate slightly from the spec:
- Excerpt length: 200 chars per spec (vs the 300 used by search.Result).
truncateExcerpt clamps the already-stripped BM25 excerpt; graph-only
neighbours load their excerpt from disk via a private readExcerpt
helper (search.hydrate is unexported).
- Graph scoring: 0.6 / max(1, distance) per neighbour, so distance-1
contributes 0.6 and distance-2 contributes 0.3. BM25 hits decay
linearly from 3.0 (rank-0) to 1.0 (rank-2), giving BM25 hits a
natural ceiling above pure-graph hits while still letting a doc
surfaced via both edge types outrank a BM25-only one.
- Test placement: package mcp (internal) rather than mcp_test, because
graphReader is unexported and WithGraph only accepts *PGStore; an
internal test can install a dual-interface fake directly on s.graph
without spinning up postgres.
Bump-Type: minor
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Commit 3 of Track A. The MCP server now publishes a new tool that
opens the brain knowledge graph (entities + wikilink edges) for
external consumers (claude.ai connectors, gitea-mcp, agentsquad).
- tools_graph.go: brain_graph handler dispatches by op:
neighbors — 1-hop outgoing from slug, optional edge_type filter
subgraph — every reachable slug within depth hops (≤6)
path — shortest directed path src→dst within depth (≤8)
Returns slug + entity metadata + edge_type + hop distance.
- server.go: handleCall routes "brain_graph" to brainGraph.
- handlers.go: tool descriptor with the op enum + per-op required
fields documented in the description.
- server_test.go: TestServerToolsList expects brain_graph in the
listing.
The tool returns an error when BRAIN_GRAPH_ENABLED is unset — same
shape as brain_answer when the answer LLM is unconfigured.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Commit 2 of Track A. Service stays a no-op until BRAIN_GRAPH_ENABLED=
true; flipping it on creates the schema (idempotent), starts indexing
every successful write, and optionally backfills the existing brain
dir.
- internal/graphsync: best-effort wrapper around graph.Extract +
graphstore. IndexDoc reads docPath under brainDir, parses, upserts
entity + replaces edges. BackfillFromBrainDir walks wiki/ +
knowledge/. Both are no-ops on nil store so callers wire
unconditionally.
- mcp.Server gains WithGraph builder + graphsync.Store field.
brain_write, brain_ingest, brain_ingest_raw, brain_tunnel call
indexInGraph after success — failures slog.Warn but never
propagate (graph is augmentation, not correctness).
- cmd/server gates the wiring on BRAIN_GRAPH_ENABLED=true (default
off so first rollout doesn't surprise). BRAIN_GRAPH_BACKFILL=true
triggers a one-shot walk of the brain dir on boot.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Wires nomic-embed-text (iguana ollama) + pgvector on the shared
postgres18 into brain_query / brain_answer via Reciprocal Rank Fusion.
Pure BM25 stays the default; setting BRAIN_PG_DSN and BRAIN_EMBED_URL
together opts in. Setting one without the other is misconfiguration →
exit 1.
New packages:
- internal/embed
Client.Embed(ctx, text) → []float32 via POST {URL}/api/embed.
Defaults to nomic-embed-text:latest (768 dim). nil-on-empty-URL so
callers gate on a single nil check.
- internal/vectorstore
PGStore wraps a pgxpool against postgres18. Init creates
brain_embeddings(path PK, vector(768), updated_at) + HNSW cosine
index idempotently. Upsert / Delete / Search / KnownPaths.
Sync(brainDir, store, embedder) diffs brain/wiki/ against the store
and upserts new files / deletes removed ones; StartSync runs it on
a ticker (default 300s). Integration tests gated by BRAIN_PG_TEST_DSN.
- scripts/brain-embeddings-init.sql
One-time DBA setup: brain DB, brain_app role, vector extension,
GRANTs. Idempotent.
Search layer:
- search.QueryOptions gains Vector + Embedder fields.
- QueryContext is the cancellable variant; Query stays for callers.
- When both are set, BM25 (top-N) and pgvector (top-4N) candidates
merge via Reciprocal Rank Fusion (k=60, Cormack et al. 2009 — no
tuning knob, robust to scale differences between rankers).
- Vector-only hits are hydrated from disk so callers see uniform
Result records (path, title, excerpt, wing, hall, score).
- Wing/hall filters still apply to vector candidates via path-prefix.
- On embedder/vector errors the search falls back to BM25 — embedding
outage degrades quality but doesn't take the brain offline.
MCP wiring:
- mcp.Server.WithHybridRetrieval(v, e) opt-in setter, same shape as
WithReranker.
- brainQuery and brainAnswer pass the wired vector/embedder through
to search.QueryContext.
REST:
- POST /backfill-embeddings drives Sync synchronously. Returns
{added, deleted, errors[]}. 503 when feature is unconfigured.
cmd/server/main.go:
- BRAIN_PG_DSN + BRAIN_EMBED_URL together enable hybrid; one alone
→ exit 1.
- vectorAdapter bridges *PGStore (returns []Hit) to
search.VectorSearcher (which takes []VectorHit) without either
package importing the other.
- BRAIN_EMBED_SYNC_INTERVAL (default 300s) controls the background
Sync ticker.
Backend pivot from Qdrant to pgvector recorded in DECISIONS.md
2026-05-18 (supersedes 2026-04-08): postgres18 already runs in
databases/ ns, Qdrant was never deployed, one engine beats two.
Dependency: github.com/jackc/pgx/v5 — modern, native pgvector via
parametric vector literals.
Tests:
- embed.Client: empty-URL nil, request shape, dimension, upstream
error propagation, empty-text rejection.
- vectorstore.PGStore: dimension validation (unit); upsert/search/
KnownPaths (integration, BRAIN_PG_TEST_DSN-gated).
- vectorstore.Sync: adds new files, skips known, deletes
disappeared, skips _index.md, no-op when nil, collects embedder
errors.
- search.Query: hybrid promotes vector-only hits via RRF; falls
back to BM25 on embedder error.
Closes hyperguild#8.
Adds the `brain_tunnel` MCP tool and auto-tunnel behaviour for
`brain_write`, so concepts that appear in multiple wings become
navigable from any of them.
New surface in package brain:
- WriteTunnel(brainDir, src, tgt) — appends a `## See also` bidirectional
wikilink between two notes in different wings. Idempotent (link not
duplicated on re-call) and reuses an existing See also section.
- DetectTunnels(brainDir, content) — walks brain/wiki/, returns
TunnelCandidates for notes whose title appears in content. Tags
whole-word case-insensitive hits as Exact=true and substring-only hits
as Exact=false.
- AutoTunnel(brainDir, src, content) — wraps DetectTunnels: writes
cross-wing exact matches, stages fuzzy matches into
brain/raw/tunnel-candidates-<YYYY-MM-DD>.md for human review.
MCP wiring:
- `brain_tunnel` tool: explicit manual link (source, target).
- `brain_write` with wing+hall now triggers AutoTunnel on the new
content. Failures are logged and never abort the primary write.
readTitleAndCreated also humanises the slug fallback (hyphens → spaces)
so titleless notes participate in content matching.
Closes hyperguild#16.
Tests: idempotency, same-wing rejection, missing-note rejection,
See-also reuse, exact/fuzzy detection, slug fallback, MCP tool happy
path, auto-tunnel hook (cross-wing exact → linked; same-wing → skipped;
fuzzy → candidates file).
Adds a two-dimensional address (wing, hall) to brain notes. A wing is a
topic domain (e.g. jepa-fx, hyperguild); a hall is one of a closed
vocabulary of memory types (facts, decisions, failures, hypotheses,
sources). Notes route to brain/wiki/<wing>/<hall>/<slug>.md with
wing/hall/created_at YAML frontmatter, making the directory a valid
Obsidian vault.
Changes:
- new package ingestion/internal/brain (NotePath, ValidHalls, Sanitise,
BuildWingIndex, BuildAllWingIndexes)
- api.WriteNote refactored to WriteNoteOptions; wing+hall routes to
brain/wiki/, otherwise falls back to brain/knowledge/ (legacy)
- search.Query → QueryOptions with optional Wing/Hall filtering; Result
carries wing/hall extracted from frontmatter or path segments
- MCP tools brain_write and brain_query gain optional wing/hall params
(hall enum-validated); new brain_index tool regenerates _index.md MOC
- POST /index REST endpoint mirrors brain_index
- brain_write auto-rebuilds the wing's _index.md after a wing+hall write
- scripts/migrate-brain-halls.sh migrates flat brain/wiki/{concepts,entities}/
into the new layout (dry-run by default, --commit applies)
All existing tests pass; new tests cover wing/hall write routing, scope
filtering, invalid hall rejection, _index.md generation, and migration
script paths.
Closes hyperguild#1.
Adds two new LLM-backed MCP tools to the ingestion service:
- brain_answer(query): BM25 retrieval + LLM synthesis → answer + sources
- brain_classify(text): classifies doc into type/title/tags via LLM
Adds llm.Router for primary→fallback routing (berget.ai → iguana).
Wired via BRAIN_LLM_PRIMARY_URL/BRAIN_LLM_FALLBACK_URL env vars;
no-op when unset so existing deployments are unaffected.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds pass-rate to the CLI README's subcommand block. Updates CLAUDE.md
to note the new /pass-rate endpoint alongside the existing brain
HTTP REST API surface. Updates the session_log MCP tool's
final_status description to reflect the new pass|fail|skip vocabulary
introduced by Plan 5's SKILL.md instrumentation; the aggregator
still accepts legacy ok|error|skipped values for backwards compat.
Appends a JSON line to brainDir/sessions/<session_id>.jsonl using the
session package copied in Task 2. Required for upcoming pass-rate
logging.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Wraps pipeline.Run with the existing LLM client. Mirrors the HTTP
/ingest and /ingest-path semantics — accepts either path or
content+source, validates mutual exclusion, surfaces an explicit error
when the LLM client is not configured (test-mode).
ctx is threaded through to pipeline.Run for cancellation.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Wraps pipeline.RunRaw directly. Same dry-run semantics as the HTTP
/ingest-raw endpoint. Test exercises a single concept page; asserts
returned path and that no file is written under dry_run.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
api.WriteNote captures the file-write logic that was previously inline
in Handler.Write. The existing HTTP endpoint now delegates to it; the
new MCP brain_write tool reuses the same function. Path-traversal
guard is strengthened to explicitly reject filenames containing path
separators or "..", so the rejection is surfaced before filepath.Base
strips the suspicious component (the previous defense-in-depth prefix
check became unreachable for these inputs after Base normalisation).
HTTP error code for caller-input errors shifts from 500 to 400, which
is semantically correct and not exercised by any existing test.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Wraps the existing search.Query function. Same BM25 over
brain/knowledge/ and brain/wiki/ that the HTTP /query endpoint serves.
Plan note: handleCall switch replaces the single-line stub from Task 1
— no unknownToolError type to remove since Task 1 inlined the error.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds an MCP HTTP handler under ingestion/internal/mcp. Implements
initialize, tools/list, and the JSON-RPC notification skip from prior
work. Tool dispatch is stubbed (returns unknown-tool error) and will be
filled in by subsequent tasks.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
mathiasandClaude Opus 5.5