14 Commits

Author	SHA1	Message	Date
will.anderson	ee39aa5f17	Merge pull request 'ingest: unify transduce_prose/transduce_structured into one transduce()' (#117) from feat/transduce-unify into dev	2026-08-15 22:36:12 +00:00
bigmerge	e29fe4fd0b	ingest: unify transduce_prose/transduce_structured into one transduce() ... 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.	2026-08-15 17:28:19 -05:00
bigmerge	1bb1edc851	engram: port PR #105's 3 genuine wins onto dev's existing cosq/e_eff semantic layer ... 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.	2026-08-15 16:55:32 -05:00
bigmerge	bacaf3d39c	engram: reconcile M8 HNSW vindex (#109) onto current dev, restore 3 fixes the branch predated ... 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.	2026-08-15 16:46:44 -05:00
will.anderson	e34ebd4b3d	Merge pull request 'nsbx + cognitive architecture design + engram self-review series' (#113) from feat/neuron-sandbox into dev	2026-08-15 19:59:07 +00:00
will.anderson	09ae14a970	Merge pull request 'fix: float arithmetic codegen (segfault/garbage) and math_log aliasing' (#104) from worktree-agent-a456e0cf8cd2ee361 into dev	2026-08-15 19:54:46 +00:00
will.anderson	fdf0d6cb64	Merge pull request 'nsbx: one-command dev onboarding (branch + worktree + isolated engram)' (#99) from feat/nsbx-dev-env into dev	2026-08-15 19:52:35 +00:00
bigmerge	08cbcef5d9	engram: fix lazy-embed index gap (#20) and make activate's cosine scan lazy; extract vindex harvest primitive with a bench/oracle harness ... 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.	2026-08-15 14:26:16 -05:00
bigmerge	01826421c4	seam: implement decorated-fn boundary auto-emit; prove on clone ... 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.	2026-08-14 21:20:18 -05:00
will.anderson	7aa847e32a	Merge origin/dev into engram-tiered-storage ... 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.	2026-08-12 15:23:02 -05:00
will.anderson	bb64a236ed	engram tiered storage: engram-service wiring + elc fold-hang fix + prune-store mirror ... - 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.	2026-08-12 14:14:20 -05:00
will.anderson	9a0266cbf9	engram tiered storage M3.5: persist activation field updates (pre-flip gate) ... 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).	2026-08-11 23:37:52 -05:00
will.anderson	a72145b44e	engram tiered storage M3: wire store behind ENGRAM_STORE (default off) + .egm rename ... 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.	2026-08-11 23:21:21 -05:00
will.anderson	0a72fced28	engram: WAL persistence + integrity hardening + single canonical runtime ... 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.	2026-08-11 21:31:37 -05:00