feat(engram): ML-KEM-1024 PQC encryption, nomic embeddings, MCP routes, checkpoint-per-write

- Add ML-KEM-1024 + AES-256-GCM binary persistence to el_runtime.c with
  two-key scheme (Neuron master + user key); SHAKE-256 key derivation
- Add nomic-embed-text 768-dim float32 embeddings on every node write
  via Ollama; graceful fallback when Ollama is not running
- Wire all /api/neuron/* MCP routes directly into Engram (server.el),
  eliminating the Kotlin server as the MCP backend
- Set ENGRAM_CHECKPOINT_INTERVAL = 1 (write binary on every node write,
  not every 50)
- Add el_runtime.h declarations for engram_write_binary_el and
  engram_load_binary_el builtins

lang/releases/v1.0.0-20260501/el_runtime.h

@@ -589,6 +589,10 @@ el_val_t  engram_edge_count(void);
 el_val_t  engram_activate(el_val_t query, el_val_t depth);
 el_val_t  engram_save(el_val_t path);
 el_val_t  engram_load(el_val_t path);
+el_val_t  engram_load_dir(el_val_t data_dir);
+el_val_t  engram_reindex_json(void);
+el_val_t  engram_write_binary_el(el_val_t path);
+el_val_t  engram_load_binary_el(el_val_t path);
 
 /* JSON-string accessors — return pre-serialized JSON so HTTP handlers
  * can pass results straight through without round-tripping ElList/ElMap
@@ -600,6 +604,7 @@ el_val_t  engram_scan_nodes_by_type_json(el_val_t node_type, el_val_t limit, el_
 el_val_t  engram_neighbors_json(el_val_t node_id, el_val_t max_depth, el_val_t direction);
 el_val_t  engram_activate_json(el_val_t query, el_val_t depth);
 el_val_t  engram_stats_json(void);
+el_val_t  engram_apply_decay_json(void);
 el_val_t  engram_list_layers_json(void);
 /* engram_compile_layered_json — produce a prompt-ready text block split
  * into "[LAYER 0 — STRUCTURAL]" (non-suppressible layers, sacred fire)