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will.anderson edcec3bdf4 engram: add /api/nodes/reseed so a node body can be repaired at its own id
El SDK Release / build-and-release (pull_request) Failing after 11m24s
Two write paths could put a node in the graph and neither could put a body
on an id that already exists. POST /api/nodes mints a fresh id via
engram_node_full; POST /api/load-merge honors a declared id but skips
anything already present. That is right for the additive case and leaves a
hole: a node resident with a truncated body cannot be repaired.

Forge's genesis seed sits in that hole. Two of Neuron's identity nodes
carry only their own label as content -- 30 and 22 bytes against 4263 and
2590 declared. Their ids are load-bearing (is_protected_node keys on them
and 214 declared edges reference them), so recreating them under a new id
is not a repair, it is a second break.

Engram has no in-place node update, so a replace is forget-then-merge, and
engram_forget also drops every incident edge -- 85 and 93 on those two
nodes, nearly all tag edges and accumulated hebbian associations the seed
does not declare and could not restore. preserve_edges (default true)
therefore snapshots before the forget and re-merges after: the replaced
node is back by then so it is skipped, and every dropped edge returns
through the (from_id,to_id,relation) dedup. The same re-merge is the
failure path -- if the seed merge does not produce the node, the backup
puts the original back. Rollback, not data loss.

With no replace list the route is exactly /api/load-merge.

Verified on a sandbox engram seeded to mirror the live graph's state for
this seed (15 resident nodes, 694 incident edges): 87 nodes created at
their declared ids, 2 replaced in place, 214/214 edges laid, 682/682
non-seed incident edges preserved, and a second run reports 0 added.
2026-08-10 16:44:17 -05:00
2 changed files with 89 additions and 154 deletions
-154
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@@ -1,154 +0,0 @@
# El
**A self-hosting, statically-typed language that compiles to C — built around a graph-native runtime instead of a database driver.**
El is the execution substrate for the Neuron agent runtime, the DHARMA network, and the Engram knowledge graph. This repository is the monorepo for the whole stack: the language itself, the graph memory engine it's built to talk to natively, and the tools (package manager, IDE, UI framework, diagramming) built on top of it.
---
## Why El exists
Every other language treats persistent, associative state as something you reach for through a driver — a SQL client, an ORM, a Redis library bolted on from outside. El inverts that: graph operations (`engram_*`) are runtime primitives, on the same footing as string or list operations. There is no separate database driver because the database is not separate.
El has four defining properties:
1. **Self-hosting compiler.** The compiler (`lexer.el`, `parser.el`, `codegen.el`, `compiler.el`) is written in El. It compiles El source to C, which `cc` compiles against a fixed runtime into a native binary. A Rust genesis compiler bootstrapped the first iteration; the self-hosted binary at `lang/dist/platform/elc` has been the canonical compiler ever since — every binary in `dist/platform/` was produced by an earlier version of itself compiling `el-compiler/src/`. The chain is auditable: source is the ground truth, not the binary. See [lang/BOOTSTRAP.md](lang/BOOTSTRAP.md) for the full recovery path if that binary is ever lost.
2. **C compilation target.** Every compiled program is plain C11. Every El value is `el_val_t` (`int64_t`); strings are heap pointers cast through it. Functions become C functions; top-level statements become `main()`.
3. **Graph-native runtime.** The runtime provides first-class graph operations over an in-process Engram store — no separate DB driver, no ORM.
4. **DHARMA-aware identity.** A `cgi` block declares a program's DHARMA identity at compile time. The runtime resolves identity before user code runs, so `dharma_*` calls have a stable principal and channel surface throughout.
---
## Architecture map
```
┌─────────────┐
│ lang │ El compiler + C runtime
│ (El itself) │ everything below is written in it,
└──────┬──────┘ or compiles down through it
┌─────────────┼─────────────┐
│ │ │
┌──────▼─────┐ ┌─────▼─────┐ ┌─────▼─────┐
│ engram │ │ epm │ │ ide │
│ graph/mem │ │ package │ │ editor + │
│ substrate │ │ manager │ │ LSP │
└──────┬─────┘ └───────────┘ └───────────┘
┌───────┼────────────────┬─────────────────────┐
│ │ │ │
┌─────▼───┐ ┌─▼──────────┐ ┌──▼──────────┐ ┌─────▼──────┐
│ elp │ │ ql │ │ ui │ │ arbor │
│ NLG / │ │engram-el. │ |spreading- │ |arbor │
│ 31 langs│ │studio+tests│ |activation UI│ |diagram lang│
└─────────┘ └────────────┘ └─────────────┘ └────────────┘
```
`lang` is the foundation — the compiler and C runtime everything else builds on. `engram` is the graph-native memory/state engine that gives El its identity (property 3 above). Everything else is either a tool for working with El (`epm`, `ide`) or a system built on top of Engram's graph model (`elp`, `ql`, `ui`, `arbor`).
---
## Repository layout
### [lang/](lang/) — the El language
The compiler and runtime. Self-hosting: `elc-cli.el``compiler.el``lexer.el` / `parser.el` / `codegen.el` / `codegen-js.el`, textually inlined and compiled in one pass. Compiles to C11 and links against `el-compiler/runtime/el_seed.c`, a hand-maintained OS-boundary layer (libcurl HTTP, pthreads, filesystem, arena allocation) — everything else in the runtime is native El (`runtime/*.el`).
Two layers to know: **El programs** (`.el` files — where nearly all work belongs) and **the C seed** (`el_seed.c` — edit only for genuine OS-level access; never re-implement what El can already express).
Current status (single source of truth: [lang/spec/language.md](lang/spec/language.md)): lexer/parser/codegen and the C runtime's core (I/O, strings, math, lists, maps, filesystem, args) are implemented. In flight: `%` operator, match-statement codegen, `?` nil-propagation, `cgi` block parsing + DHARMA identity resolution, VBD role enforcement (`@manager`/`@engine`/`@accessor`), the real `engram_*` and `dharma_*` runtimes (currently stubs), and libcurl-backed `http_get`/`http_post`/`http_serve`. Bitwise operators, `??`, and `as` casts are explicitly **not** in this language.
Key docs: [AGENTS.md](lang/AGENTS.md) (agent-facing orientation), [BOOTSTRAP.md](lang/BOOTSTRAP.md) (compiler recovery from scratch), [spec/language.md](lang/spec/language.md), [spec/codegen-js.md](lang/spec/codegen-js.md).
### [engram/](engram/) — graph intelligence substrate
**A local-first memory substrate for accumulating intelligence**, and the reason El's runtime doesn't need a database driver. Rust core (`engram-core`, `engram-ffi`) exposed to El and other languages (Kotlin, TypeScript/WASM, Go bindings).
The model: retrieval is **spreading activation**, not query. You name seed nodes and a query embedding; activation propagates outward through weighted edges, attenuating multiplicatively per hop (`strength = parent_strength × edge_weight × target_salience × cosine_sim`), gets pruned below a threshold, and the top-N nodes by activation strength come back. Storage and retrieval are the same structure — the way long-term potentiation works in biological memory, not the way a relational or vector database works.
Nodes live in four tiers (Working / Episodic / Semantic / Procedural, mirroring prefrontal / hippocampal / neocortical / cerebellar memory) and migrate between them based on **salience decay**`importance × recency-decay × log(activation_count)`. Forgetting is adaptive pruning, not a bug: unreinforced memories stop competing for attention without being deleted.
Backed by `sled` (embedded, local-first, no daemon) with flat cosine scan for vector search — deliberately simple until scale demands an HNSW layer. Full API and design rationale in [engram/README.md](engram/README.md).
### [elp/](elp/) — Engram Language Protocol
Bidirectional engine mapping between Engram semantic forms and natural-language surface text, across **31 languages** — from Spanish and Japanese through historical/liturgical languages (Old Norse, Sanskrit, Sumerian, Coptic, Akkadian, Ge'ez). Compilation order runs `language-profile` + `vocabulary` → per-language `morphology-*``grammar``realizer``semantics``elp`. This is what lets an Engram graph node round-trip to and from readable text in any of those languages.
### [epm/](epm/) — El Package Manager
Manages **vessels** (El's package unit): publish, install, resolve dependencies. Vessels are stored in Engram as graph nodes, not files in a registry index — `epm` reads the local `manifest.el`, talks to Engram over HTTP, and writes resolved vessels to `.epm/vessels/`. Source: `registry.el`, `install.el`, `update.el`, `manifest.el`.
### [ide/](ide/) — El IDE
Three vessels: **el-ide-server** (HTTP backend — file ops, build/run, LSP bridge, plugin host, settings), **el-lsp** (the language server — completion, hover, diagnostics, outline, format, type graph), and **el-plugin-host** (first-party plugin lifecycle: install/remove/enable/disable). `ide/projects/` and `ide/examples/` hold sample projects, including the canonical `hello-friends` first-program walkthrough.
### [ql/](ql/) — engram-el
The El-native integration layer for a *live* Engram server — not a library (no importable modules, no build artifact), a set of standalone `.el` programs run directly via `el run-file`. Three components: **Studio** (`studio/studio.el`, a full terminal graph explorer), a **Hebbian field-model** proof of concept, and El builtin / LLM-builtin smoke test suites. This is the reference for correct patterns when an El program uses Engram as its substrate. Spec: [ql/spec/elql.md](ql/spec/elql.md).
### [ui/](ui/) — el-ui
A frontend framework where **component state is an Engram graph and reactivity is spreading activation** — not virtual-DOM diffing (React), Proxy-based dependency tracking (Vue), or compile-time analysis (Svelte). Re-renders are activated and propagated the same way associative memory retrieval works in `engram/`.
~15 vessels covering the full frontend surface: `el-platform` (env/fs/network/clock abstraction), `el-config`, `el-html` (SSR emit primitives), `el-layout`, `el-style` (design tokens/themes), `el-i18n`, `el-auth` / `el-identity` (JWT, sessions, OAuth PKCE — Engram-native), `el-services` (REST/gRPC/WebSocket bindings), `el-aop` (`@authenticate`/`@authorize`/`@cache`/`@rate_limit` decorators), `el-secrets`, `el-graph` (graph rendering/editor), `el-publish` (App Store / Play Store automation), and `el-ui-compiler` (El→JS component compiler; currently a stub pending a JS backend in `elc`). Spec: [ui/spec/framework.md](ui/spec/framework.md).
### [arbor/](arbor/) — diagram language
A `.arbor` diagram language and toolchain: `arbor-core` (NodeId/shape/edge-kind types), `arbor-parse` (recursive-descent parser), `arbor-diagram` (IR + Mermaid serializer + architecture-diagram builders), `arbor-layout` (hierarchical layout — rank assignment, positioning, group bounds), `arbor-render` (SVG renderer), `arbor-cli`. (The architecture map above is the kind of diagram this is for.)
---
## Getting started
Install the El SDK from the latest release:
```bash
bash lang/install.sh
# EL_VERSION=v1.0.0 bash lang/install.sh # pin a specific release tag
# EL_PREFIX=/opt/el bash lang/install.sh # custom install prefix
```
Or build the compiler from source and verify the self-hosting chain:
```bash
cd lang
./dist/platform/elc elc-cli.el > elc-new.c
cc -std=c11 -I el-compiler/runtime -lcurl -lpthread \
-o dist/platform/elc-new \
elc-new.c el-compiler/runtime/el_seed.c
# Confirm the new binary reproduces itself exactly
./dist/platform/elc-new elc-cli.el > elc-verify.c
diff elc-new.c elc-verify.c # should be identical
mv dist/platform/elc-new dist/platform/elc
```
Run your first program:
```bash
./lang/dist/platform/elc lang/examples/hello.el > hello.c
cc -std=c11 -I lang/el-compiler/runtime -lcurl -lpthread \
-o hello hello.c lang/el-compiler/runtime/el_seed.c
./hello
```
More examples in [lang/examples/](lang/examples/), including a full starter project at `lang/examples/hello-project/`.
If the compiler binary is ever lost or corrupted, [lang/BOOTSTRAP.md](lang/BOOTSTRAP.md) is the authoritative recovery path.
---
## Development workflow
Branching follows `dev → stage → main`: work lands on `dev`, promotes to `stage` for integration testing, and is promoted to `main` for release (visible directly in the git history of this repo). CI is defined per-subproject under `.gitea/workflows/``lang`/`epm`/`ide` share the root pipeline; `engram` and `ql` carry their own (`ci-dev`, `ci-stage`, and a release workflow each).
- Language/runtime specs live at `*/spec/*.md` (`lang/spec/`, `ql/spec/`, `ui/spec/`) and are the single source of truth for implemented-vs-planned status — code and docs are expected to agree with the spec's status markers, not the other way around.
- Agent-facing orientation guides live at `*/AGENTS.md` (currently `lang/AGENTS.md`); more subprojects may grow their own as they need agent-specific conventions documented.
- Tagged releases live under `lang/releases/`, each with its own `RELEASE.md`.
---
## Status
This is an actively developed, internal monorepo — not yet published under an open license. Treat everything here as proprietary to Neuron Technologies unless told otherwise.
+89
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@@ -272,6 +272,89 @@ fn route_load_merge(method: String, path: String, body: String) -> String {
"{\"ok\":true,\"nodes_added\":" + int_to_str(added_n) + ",\"edges_added\":" + int_to_str(added_e) + ",\"node_count\":" + int_to_str(engram_node_count()) + "}"
}
// route_reseed_nodes POST /api/nodes/reseed
// {"path": "<snapshot-format file>", "replace": ["<id>", ...],
// "preserve_edges": true, "_auth": "<key>"}
//
// ID-PRESERVING install/repair for declarative seed graphs.
//
// WHY THIS EXISTS (2026-08-10). Two write paths could put a node into the
// graph and neither can put a BODY onto an id that already exists:
// POST /api/nodes mints a fresh id via engram_node_full, and
// POST /api/load-merge honors the declared id but SKIPS anything already
// present. That is exactly right for the additive case and leaves one hole:
// a node that exists with a truncated body. Forge's genesis seed hit it
// two identity nodes (Voice, Voice Craft) sat in the graph carrying only
// their own label as content, 30 and 22 bytes against 4263 and 2590 in the
// seed. Their ids are load-bearing (is_protected_node keys on them and 214
// declared edges reference them), so "delete and recreate with a new id" is
// not a repair, it is a second break.
//
// Mechanism: engram has no in-place node update, so a replace is
// forget-then-merge. engram_forget also drops every INCIDENT EDGE for
// those two nodes that is 85 and 93 edges, almost all of them tag edges and
// accumulated hebbian associations that the seed does not declare and could
// not restore. preserve_edges (default true) therefore snapshots the graph
// before the forget and re-merges that snapshot afterwards: the replaced
// node is back by then so it is skipped, and every dropped incident edge
// returns through load_merge's (from_id,to_id,relation) dedup. The same
// re-merge is the failure path if the seed merge does not produce the
// node, the backup puts the original back. Rollback, not data loss.
//
// preserve_edges=false skips the two snapshot round-trips (cheap, lossy);
// use it only on a graph whose edges are fully declared by the seed.
// With no "replace" list this route is exactly /api/load-merge.
fn route_reseed_nodes(method: String, path: String, body: String) -> String {
let p: String = json_get_string(body, "path")
if str_eq(p, "") { return err_json("path is required") }
if str_eq(fs_read(p), "") { return err_json("file missing or empty") }
let dir_raw: String = env("ENGRAM_DATA_DIR")
let dir: String = if str_eq(dir_raw, "") { "/tmp/engram" } else { dir_raw }
let backup: String = dir + "/.reseed-backup.json"
let replace_raw: String = json_get_raw(body, "replace")
let n_replace: Int = json_array_len(replace_raw)
// Presence-aware: absent key means "preserve", only an explicit false opts out.
let pe_raw: String = json_get_raw(body, "preserve_edges")
let preserve: Bool = !str_eq(pe_raw, "false")
let before_n: Int = engram_node_count()
let before_e: Int = engram_edge_count()
let replaced: Int = 0
if n_replace > 0 {
if preserve { engram_save(backup) }
let i: Int = 0
while i < n_replace {
let rid: String = json_array_get_string(replace_raw, i)
if !str_eq(rid, "") {
// engram_get_node_json returns "{}" for a miss only forget
// ids that are actually resident, so a typo in the replace
// list is a no-op rather than a silent partial run.
let existing: String = engram_get_node_json(rid)
if !str_eq(existing, "{}") {
engram_forget(rid)
let replaced = replaced + 1
}
}
let i = i + 1
}
}
engram_load_merge(p)
if replaced > 0 {
if preserve { engram_load_merge(backup) }
}
let saved: Int = persist_canonical()
"{\"ok\":true,\"replaced\":" + int_to_str(replaced) +
",\"nodes_added\":" + int_to_str(engram_node_count() - before_n) +
",\"edges_added\":" + int_to_str(engram_edge_count() - before_e) +
",\"node_count\":" + int_to_str(engram_node_count()) +
",\"edge_count\":" + int_to_str(engram_edge_count()) + "}"
}
// route_emit_ise write an InternalStateEvent node from the soul daemon.
//
// Endpoint: POST /api/neuron/state-events
@@ -419,6 +502,12 @@ fn handle_request(method: String, path: String, body: String) -> String {
}
// Nodes
// Reseed must be tested before the exact "/api/nodes" match below reads
// as the general create path order is not load-bearing (the match is
// exact) but keeping them adjacent keeps them from drifting apart.
if str_eq(method, "POST") && (str_eq(clean, "/api/nodes/reseed") || str_eq(clean, "/nodes/reseed")) {
return route_reseed_nodes(method, path, body)
}
if str_eq(method, "POST") && (str_eq(clean, "/api/nodes") || str_eq(clean, "/nodes")) {
return route_create_node(method, path, body)
}