New brainfs PutRegular (create or replace), CreateRegular (create only), AppendRegular, Remove and RealParent: missing parents created one component at a time through the root, every existing component a real directory, new files created with O_EXCL and confirmed before writing. brain_write, promote/reject (O_EXCL create, source kept on refusal), StampProvenanceFile, BuildWingIndex, RebuildIndex, AppendLog and the tunnel candidate log use them; provenance.ApplyFile removed.
Fixes#188. Refs #158. Adversarial review: BLOCKED, BLOCKED, PASS.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
StripUnresolvedLinks logs a warning and returns the content unchanged when the link index cannot be built (e.g. an unreadable subdirectory), instead of failing every brain_write/brain_update and losing the learning. Nothing is unwrapped on a partial index.
Fixes#178.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
ReadRegular, ReadRegularMax and WriteRegular require a clean, local path and a real directory at every level above the file, so an in-brain directory symlink (or a ".." after one) can no longer redirect brain_update, brain_tunnel, brain_read/get or the other readers elsewhere in the brain. session.Append opens through an os.Root on the brain dir, refuses a non-directory sessions dir, and writes only after confirming the log path is the regular file it opened.
Fixes#173. Adversarial review: BLOCKED, PASS. Follow-up: #188 (brain_write create path).
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
DetectTunnels (inside every brain_write/brain_update via AutoTunnel) walks with brainfs.WalkRegular and reads titles with ReadRegular: a FIFO under wiki/ no longer hangs the write, and a symlinked note's title no longer becomes a tunnel candidate. A wiki/ that is not a real directory yields no candidates; other walk errors still abort.
Fixes#174. Refs #157 (last reader slice). Adversarial review: BLOCKED, PASS.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
brain_tunnel accepts only clean wiki/.../*.md paths and reads/rewrites both notes through brainfs; new brainfs.WriteRegular never creates, never writes through a final symlink (Lstat + O_NOFOLLOW|O_NONBLOCK + os.SameFile on the handle, since os.Root follows in-root final symlinks even with O_NOFOLLOW). brain_update resolves like brain_edit (knowledge/ and wiki/ notes only) and reads/rewrites through brainfs. session_log requires a plain-name session id and opens with O_NOFOLLOW|O_NONBLOCK.
Fixes#169. Adversarial review: BLOCKED, BLOCKED, PASS (round 3 by the estate session's reviewer). Follow-ups: #173, #174.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
BuildWingIndex/BuildAllWingIndexes list wings and halls with the new brainfs.ReadDirDirs and ReadDirRegular and read titles with ReadRegular: a symlinked note no longer reaches _index.md, a symlinked wing is refused (nothing written into its target), a symlinked hall is skipped. linkcheck entryIndex walks with WalkRegular, so a symlinked .md cannot make a link resolve, and a linked tree that is not a real directory is skipped with a warning (brain_write still lands).
Refs #157. Adversarial review: BLOCKED, PASS. Follow-up: #178.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-authored-by: Mathias <mthbqv@gmail.com>
AutoTunnel matched note titles case-insensitively, so a one-word title linked
every entry that happened to use that word. Measured on the live corpus: 185
entries carry an auto-written See-also link to wiki/telos/decisions/wrong.md
(title "WRONG") and 136 to .../status.md — the two most-linked nodes in the
whole graph, and both of them artifacts of the English language rather than
references. telos's projects/problems/strategies/goals/beliefs entries account
for another ~60 between them.
That pollution is not cosmetic: inbound-link count is what the duplicate
Fixer picks survivors by, what orphan detection reads, and what brain_graph
shows.
One-word titles now need the title's own casing in the prose ("WRONG", "BERT",
"NLP" — an entity name in a sentence still links). Multi-word titles keep the
case-insensitive match: "risk tier middleware" is a real mention however it is
capitalised, and a three-word collision is not an accident.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.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>
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.
mathiasandClaude Opus 5.5