transduce() is now THE single mechanism: one function, no content-type
branch inside it. It never asks whether `source` is prose, JSON, or
raw/opaque bytes (audio, etc.) — it runs one algorithm unconditionally:
split on "\n\n" as a universal boundary-marker check, and if that finds
no boundary, fall back to fixed 4096-char windows. Same node/edge wiring
(root -contains-> chunk, chunk -precedes-> next, "#"-prefixed chunk gets
a heading/section_of link) regardless of what's inside a chunk. Dedup is
the existing find_existing_by_content path via merge_manifold, applied
uniformly. The old transduce_structured JSON dataset/records/feature-node
interpretation is deleted outright, not just unused — a JSON file now
gets chunked and deduped like anything else, with no pre-computed
structure. All five ingest_* entry points still exist unchanged in name
and role; ingest_file/ingest_dir/ingest_url/ingest_llm now call the one
transduce() (ingest_stream builds its own turn-nodes directly and never
called either old function, so it's untouched).
This unlocks raw/opaque content (audio, or anything else with no natural
text/JSON shape) without any DSP, LLM call, or external API: transduce()
chunks it exactly like it chunks anything else. There is zero semantic
understanding of audio (or any payload) claimed or built here — any
meaning is expected to emerge later from Neuron's own existing mechanisms
(embedding, spreading activation, dedup) acting on this real geometry
over time.
Two small C builtins added to el_runtime.c/h (fs_size, fs_read_b64_chunk)
because El strings are NUL-unsafe under strlen-based ops and fs_read()'s
result silently truncates at the first embedded NUL, which is routine in
real binary/audio bytes. ingest_file compares fs_read()'s string length
against a real fs_size() stat() count; on mismatch it rebuilds the
payload as base64-encoded fixed 3072-byte windows read directly off disk
(binary-safe in C, verbatim, no invention), joined with the same "\n\n"
marker transduce()'s boundary scan already looks for. This is a
mechanical fidelity fix, not interpretation of content — transduce()
never learns a fallback happened. Registered both builtins' arity in
codegen.el; did not rebuild the elc compiler binary itself (unrelated,
pre-existing gap: self-hosting elc via el_seed.c fails on this worktree
independent of this change, reproduced with codegen.el reverted) — the
existing elc binary compiles calls to unregistered builtins via its
already-existing arity=-1 passthrough, confirmed by an actual clean
`elc ingest.el` + `cc` build against the modified el_runtime.c.
INGEST_KIND keeps existing only as an acquisition-mechanism selector
(dir/file/url/llm/stream — which RPC to use to fetch bytes), not as a
content-type flag; the redundant "structured" value (an alias for "file"
that hinted the now-deleted JSON branch) is removed. ingest_dir drops its
file-extension filter for the same reason: transduce() takes anything now.
Verification: local manifold construction confirmed correct against a
real captured audio file (will_clean.wav, 304288 bytes, and a 12288-byte
real prefix slice) — exact expected node/edge counts both times
(101 nodes/199 edges full file; 5 nodes/7 edges for the slice, matching
ceil(bytes/3072)+1 nodes and 2n-1 edges), with real, verbatim base64
content confirmed decoding back to the actual WAV header bytes. Compiles
clean via the real elc + the modified el_runtime.c/engram_*.c (built and
booted an actual sandbox engram off this exact source with `nsbx create
--branch`).
NOT verified this session, disclosed rather than papered over: end-to-end
server-confirmed persistence (a real before/after /api/stats delta, and a
fetched node by id) for the audio, prose, and JSON-fixture cases. Every
local nsbx sandbox engram tried tonight (two stock pre-#109 binaries
hitting the known O(N*D) brute-force scan bug, then a fresh #109/HNSW
binary built from current dev) took minutes-to indefinitely long on the
final /api/load-merge write's embedding step and hit the client's 60s
HTTP timeout before responding, even for a 5-node write. This is
confirmed as real (if slow) forward progress, not a hang: the sandbox's
WAL file was observed growing steadily across every attempt. The code's
own pre-existing HONESTY GATE correctly refused to report success in
every case, returning "load-merge failed: ..." with a
"nothing below this manifold was confirmed persisted by the server" note
instead — exactly as designed. This is an environment/infrastructure
limitation, not a defect introduced by this change: the engram server
binary itself is untouched by this commit.
Reconciles PR #105 ("fix: engram search latency — pin embed model, cache
query embeddings, bound activate BFS") with dev's ACTUAL current
engram_activate, rather than the ancient pre-restructure snapshot #105 was
built against.
WHY THIS NEEDED RECONCILIATION, NOT A DIRECT PORT: #105's single commit
(1dc49b1) modifies `lang/el-compiler/runtime/el_runtime.c` — a path that does
not exist on dev (dev has `lang/runtime/el_runtime.c`; the restructure that
renamed it happened after #105's branch point, which traces to a July 22
merge-base, weeks before the M8/M8.1/qgate/fan-effect/adjacency-index work
this file has grown since). #105's own engram_activate is consequently the
PRE-restructure version: no adjacency index (O(E) full edge scan per hop),
no query-aware qgate, no ACT-R fan effect, no eg_edge_eff_weight, and no
awareness of dev's cosq/e_eff embedding-blend semantic layer — it built a
parallel `g_qcache`/`engram_embed_raw` mechanism from scratch against code
that no longer exists at that path. A raw merge/cherry-pick was not possible
and would have been wrong even if it were: taking #105's tree wholesale would
have thrown away everything dev grew in the meantime (qgate, fan effect,
adjacency index, and this session's own M8 HNSW vindex integration).
RECONCILIATION: kept dev's cosq/e_eff mechanism as the semantic layer
entirely intact (unchanged by this commit) and ported #105's three genuinely
additive wins on TOP of it, at their equivalent sites in the CURRENT
eg_embed_fetch/engram_activate:
1. keep_alive:-1 on the Ollama embed request body (eg_embed_fetch) — pins
the embed model resident so a larger generation model loading under
unified-memory pressure can't evict it and force a cold reload on the
next search (#105 measured ~2.2s cold vs ~0.02-0.05s warm).
2. Query-embedding cache upgraded from dev's single-slot (`_eg_qcache_text`,
only ever remembered the LAST query) to a direct-mapped, FNV-1a-keyed,
1024-slot cache (reusing the existing engram_id_hash) — so the
curiosity loop's rotating phrases actually hit the cache instead of
evicting each other every call. Same "pointer owned by the cache, not
freed by caller" contract as before, just per-slot instead of global.
3. Beam cap on the layer-1 spreading-activation BFS (new
engram_activate_beam(), tunable via ENGRAM_ACTIVATE_BEAM, default 128).
The FIFO frontier is processed in hop-level batches (entries sharing
.hops are provably contiguous — see the code comment); when a level
exceeds the beam width, only the top-`beam` by activation actually
EXPAND. Every node in an oversized level still gets reached[]/best_bg[]
recorded (that happens at enqueue time, one level up) and appears in
the reported/promoted set — the cap bounds associative SPREAD width
only, never recall of what was already found. Kept as a genuine
additional bound even though the adjacency index + qgate + fan effect
already mitigate #105's original "hub-node explosion" failure mode for
a different reason: those prune WHICH targets matter; this bounds
worst-case width regardless.
Everything else in dev's engram_activate — cosq/e_eff, the qgate rescale,
the fan effect, eg_edge_eff_weight, the M8 HNSW vindex seed discovery from
the #109 reconciliation earlier this session — is untouched.
VERIFIED (nsbx sandbox only, live :8742/:7770 never touched): cc -std=c11
-O2 clean build; booted in an isolated sandbox against a real cloned
production snapshot (13,424 nodes / 37,656 edges); ran 5 activate() calls
across rotating queries at depth 3, including the same query issued twice
non-consecutively (2nd hit landed at 476ms vs the 1st at 483ms — consistent
with a cache hit once Ollama's own warm-model latency is accounted for; no
crash, correct varied result counts (367-2610 nodes) each call; act-stats
JSON read correctly throughout.
Built on top of the M8/#109 reconciliation (bacaf3d, merged to dev as
#109) — dev's current HEAD at the time of this commit.
Lands feat/reframe-region-setop (PR #109: native set-based reframe_region,
decorator-as-seam @route port, teacher-summon, and the M8.1 activate-latency
work — lazy-memoized cosq via eg_cosq_at + engram_vindex HNSW-accelerated
seed discovery + vindex_harvest_from_store/vindex_bench oracle) onto dev's
actual current HEAD, plus engram-tiered-storage's still-unique test suite.
RECONCILING #109 WITH engram-tiered-storage (M4-M10 HNSW/geometry/reason/
verify work): not a two-way merge. engram_vindex.c's HNSW core (search_layer/
select_neighbors/prune_links/insert) is BYTE-IDENTICAL between the two
branches; #109's copy is a strict superset (adds vindex_harvest_from_store,
used by vindex_bench.c's brute-force-vs-HNSW oracle). engram_reason.c and
engram_verify.c are also byte-identical. #109's own branch point already
carried engram-tiered-storage's M4-M10 lineage forward, so there was nothing
left to merge into #109 for those files. The one thing engram-tiered-storage
had that #109's tree dropped: its full test suite (test_vindex.c,
test_geometry.c, test_reason.c, test_verify.c, test_m7_traversal.c, the
interoception P0-P5 tests, bufpool/compaction tests, and their run_*.sh
harnesses) — ported over here unchanged.
WHY THIS NEEDED HAND RECONCILIATION, NOT A MECHANICAL MERGE: #109's branch
forked from dev on 2026-08-14 15:40 (before restructure-adjacent history
diverged the file's merge-base for `git merge` — it presented as an add/add
conflict). A straight two-dot diff (dev tip -> PR tip) applied cleanly, but
it silently reverted THREE dev fixes landed on 2026-08-14/15, after the
branch point, that the PR's diff had no way to know about:
1. qgate rescale (2026-08-14 self-review): PR's lazy eg_cosq_at rewrite of
the query-aware propagation gate dropped the shift-and-floor rescale
about ENGRAM_EMBED_S0 (measured: unrelated-pair median 0.562->raw gate
0.67, i.e. "a small tax, not a gate"). Restored the rescale, wrapped
around the lazy accessor -- the PR's actual improvement (WHEN cosq[oi]
is computed) is orthogonal to WHAT it gates on and both are kept.
2. Eviction cause decomposition (2026-08-14 self-review): dev decomposes
wm_evicted into evict_floor/evict_cap/evict_bll so WM churn is
diagnosable (identity: evicted == floor+cap+bll+dup_wm+dup_wm_global).
PR's tree predates this and dropped all three counters + their JSON
stats fields. Restored declarations, all 4 direct increment sites, the
eg_wm_carry_over bll increment, and the act-stats JSON fields --
alongside (not instead of) the PR's own P4 afferent / API-reshape
counters already in that same struct/JSON.
3. Hebbian link-formation selection (2026-08-15 self-review, TODAY): dev
selects the STRONGEST qualifying candidate for consolidation each call;
PR's tree predates this and reverted to hash-slot order (arbitrary wrt
association strength) for edge formation -- the one path that writes
PERMANENT structure. Restored the strongest-candidate while-loop,
keeping the PR's own genuine improvement at that site
(engram_adj_on_edge_added incremental-index append instead of a bare
adj_dirty=1 full-rebuild flag).
engram/src/server.el's 3-way conflicts (autoconnect_on/ise_offgraph_on env
flags, /api/nodes connected-count in responses) were pure additive: dev's
side was empty, PR's side added the feature. Took PR's side whole.
VERIFIED (nsbx sandbox only, live :8742/:7770 never touched):
- cc -std=c11 -O2, clean link against the real engram/src/server.el via
elc, zero errors.
- vindex_bench (built standalone, read-only harvest) against the real
production store clone (13,671 embedded nodes, 768-dim nomic-embed-text):
recall@10 = 1.0000 at ef 64/128/200; HNSW search 0.28-0.79ms/query vs
2.03ms/query brute-force oracle (2.6x-7.2x). HNSW build itself: 46.5s
for the full 13,671-node set -- see the flagged risk below.
- Booted the reconciled binary in an isolated nsbx sandbox (:8905, cloned
snapshot of the live store, 13,424 nodes / 37,656 edges) and called
/api/activate for real: first call after boot 41.5s (pays the one-time
HNSW build inline -- matches the standalone bench), second/third calls
356ms/605ms, no crash, correct results, act-stats JSON (including the
restored evict_floor/cap/bll fields) reads correctly.
KNOWN RISK TO FLAG BEFORE ANY LIVE CUTOVER (not fixed here; out of scope for
this dev-only land per instructions not to touch :8742/:7770): eg_vindex_sync
builds the HNSW index synchronously, inline, on the first engram_activate()
call after every process start (or index invalidation). On the real node
count that is a ~46s blocking stall on a single-threaded server -- the first
request after every restart (or its concurrent siblings) waits the full
build. Recommend a background/incremental build (or a bounded per-call build
budget) before this ever reaches the live daemon. See PR description / final
report for the fuller writeup.
Adds an O(1) "seen" bitmap so lazily-embedded older nodes get picked up
incrementally instead of only on a full rebuild (embed-gap #20).
Replaces engram_activate's O(N*D) cosine prescan with a lazy-memoized
cosine cache (eg_cosq_at), proven bit-identical to the old path.
Extracts a clean vindex_harvest_from_store primitive (read-only vector
harvest, careful malloc/ownership/error-path handling) reused by both
index-build and the new vindex_bench.c — a read-only proof harness
comparing brute-force vs HNSW recall/latency on both the real store and
synthetic data.
.nsbx-env intentionally excluded — local sandbox config (ports, paths,
dev-only placeholder key), not checked in.
Cancellation-token control channel checked at every step boundary lets a
coordinator PAUSE/RESUME/REDIRECT/KILL a running worker mid-task instead of
waiting for the whole (possibly wrong) plan to finish. Bounded purviews
mean no half-committed state to unwind on interrupt. Includes a proof
harness (proof.el, run.sh) comparing a broken non-interruptible worker
against the new one under identical kill/redirect/pause timing.
Distinct from the already-preserved swarm-ccr orchestrator (fan-out/
converge dispatch): this is single-worker interruptibility, a
complementary mechanism, not a duplicate.
Will waived diff review -> build it for real. Add engram_boundary_beat() to the
runtime (afferent counter++ + engram_chrono_tick + engram_strengthen(self-anchor)
+ dharma_emit) and two act-stats counters (aff_boundary_ops, dharma_emits).
codegen cg_fn injects ONE engram_boundary_beat(op) at the entry of every
@manager/@accessor fn (fn_has_decorator, so it fires under @route @manager too) —
a decorated op self-reports with ZERO hand-written instrumentation. Rebuilt elc
self-host + the cognition engram in the worktree; ran it as the clone daemon on
:8900. Proof (/api/boundary-proof, @manager, empty body, 5x): aff_boundary_ops
0->5, dharma_emits 0->5, self activation_count 1510->1513, chrono stamp advanced.
Brought in feat/cognitive-architecture engram runtime+server for the build.
strengthen = activation bump (not content/edge write) -> identity protection
intact. Live :8742 untouched; no push, no cutover.
Resolve 3 conflicts:
- lang/el-compiler/runtime/el_runtime.c: keep deletion (deprecated runtime fork;
single-source-of-truth is lang/runtime/, enforced by scripts/check-single-runtime.sh).
- lang/releases/v1.0.0-20260501/el_runtime.h: keep deletion (releases/ is a generated
artifact folder, not a source path; a release is a git tag, not a folder).
- lang/runtime/el_platform_win.h: union of dev's Windows port (#80: setsockopt optval
wrapper + curl-less libcurl stubs) and our fsync(->_commit) shim needed by engram_store WAL.
Nothing in dev's build consumes the deprecated fork or releases/ folder.
- Wire paged store into the ENGRAM SERVICE (server.el, the authoritative durable
owner): boot->engram_store_boot, persist_canonical->engram_store_checkpoint,
gated by ENGRAM_STORE.
- elc (lang/elc.c + src/parser.el + codegen.el + elc-combined.el): OOB guard in
tok_kind/tok_value + parse_block progress backstop — fixes the pre-existing
unbounded-memory fold hang on sessions.el.
- engram_prune_telemetry mirrors ISE prune to the store (store_forget) so store
live-count tracks resident and stale telemetry stays bounded.
- Deployed live 2026-08-12: engram :8742 on neuron.egm+WAL, count reconciled 11552.
Flag-on checkpoint now full-walks the resident graph: store_put_node (WM weight,
activation_count, last_activated, wm_anchor) + store_put_edge (hebb, last_fired)
for every node/edge, then engram_checkpoint. Uses store_put_edge (idempotent
upsert) not store_hebb_batch, because activation FORMS new hebbian-associate edges
that bypass the create hook and delta-only hebb_batch can't create them. Store-on
boot now applies the same WM-halving + floor + cap transforms as engram_load.
This is the hebb-survives-restart fix. Gate: reboot from neuron.egm with
snapshot.json deleted -> edge hebb + activation_count survive unchanged, WM weight
survives with identical boot transform; negative control proves persist is
load-bearing (hebb->0 without it). M1 33/33 + M2 36/36 + M3 parity PASS, ASan/UBSan
clean, flag-off untouched. Engine unchanged (boundary held).
Caller-side shim in el_runtime.c maps EngramNode/Edge <-> StoreNode/Edge; engine
keeps zero soul deps (libengram boundary, design §10). Flag off = today's JSON
path byte-for-byte (proven: no neuron.egm created, graph identical). Flag on =
engram_open (import snapshot.json once into neuron.egm, else WAL-replay) +
resident load; node/edge create + forget dual-write via guarded hooks. Files
renamed engram.store->neuron.egm, engram.wal->neuron.wal.
Gate: M3 parity PASS (graph on==off byte-exact modulo ordering; snapshot round-trip;
reboot-from-egm with snapshot.json deleted; activation set+sequence identical;
ASan/UBSan clean). M1 33/33 + M2 36/36 green post-rename.
Known gap (pre-flip): in-place hebb/WM/activation_count updates during activation
are not yet persisted to the store (create/connect/forget are). Must close before
live flip so learned edges survive restart.
Write-back no-steal buffer pool makes the fsync'd WAL load-bearing (M1 was
write-through). Logical WAL with record-granularity page-LSN redo idempotency.
Checkpoint = flush dirty pages, fsync store, advance last_checkpoint_lsn,
reclaim WAL prefix. One-time snapshot.json import only when store absent;
JSON never read as the ongoing store thereafter.
Gates: 33/33 M1 (no regression) + 36/36 M2 — replay parity, torn-tail fuzz
(every byte offset), checkpoint-crash at all 5 phases, torn-page+WAL redo,
legacy-import parity, hebb-survives-crash.
Establish lang/runtime/ as the ONE canonical el runtime (from the active
runtime that carries hebb/emb persistence + the new WAL); repoint the el CI
publish, engram build, elb default, and in-repo build scripts to it; delete
the el-compiler/runtime + lang/releases/ forks; add scripts/check-single-runtime.sh
drift guard.
Fixes a live prod bug: the el CI published el-runtime-c/-h from the LAGGING
el-compiler fork (0 hebb refs), so the shipped soul never persisted Hebbian
edge weights — learned co-activation was wiped on every restart. Publishing
from canonical ships the stranded 'learning that cannot outlive the process'
fix.
WAL storage engine + integrity fixes (DELETE->tombstone + store-layer
protection, safe data-dir default) ride in behind ENGRAM_WAL (default off =
byte-identical to today). Verified: engram elb per-module build clean, WAL
gate 66/66, native smoke ok, drift-guard green.
handle_api_consolidate writes a "SessionSummary" node, but engram_valid_node_type
omitted it — so once this validation ships, every consolidate() would be silently
REJECTED at the engram boundary. Add SessionSummary to the allowlist.
Found in Will's PR review of neuron #1 / el #52.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The wrapper signature was stale and didn't match the C primitive
__engram_node_full(content, node_type, label, salience, importance, confidence, tier, tags).
Because el_val_t is an untyped machine word, the compiler coerced caller args to the
wrong declared param types and forwarded them BY POSITION — so tier received an int,
importance/confidence received strings, label received a float, etc. (~100 corrupt nodes).
- Correct the wrapper to match the C contract 1:1 (no coercion, no reorder).
- Add engram_valid_node_type / engram_valid_tier allowlists; engram_node and
engram_node_full now reject invalid values with __println + return "" (fail loud,
no silent malformed write).
See neuron repo: HANDOFF-engram-write-corruption.md for the full write-up + deploy runbook.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
will.anderson
bigmerge