move LLM-dependent modules into agents/ subdir

Separate the agent layer (everything that calls external LLMs or
orchestrates sequences of such calls) from core graph infrastructure.

agents/: llm, prompts, audit, consolidate, knowledge, enrich,
         fact_mine, digest, daemon

Root: store/, graph, spectral, search, similarity, lookups, query,
      config, util, migrate, neuro/ (scoring + rewrite)

Re-exports at crate root preserve backwards compatibility so
`crate::llm`, `crate::digest` etc. continue to work.

poc-memory/src/agents/audit.rs

@@ -3,7 +3,7 @@
 // Each batch of links gets reviewed by Sonnet, which returns per-link actions:
 // KEEP, DELETE, RETARGET, WEAKEN, STRENGTHEN. Batches run in parallel via rayon.
 
-use crate::llm::call_sonnet;
+use super::llm::call_sonnet;
 use crate::store::{self, Store, new_relation};
 
 use std::collections::HashSet;

poc-memory/src/agents/consolidate.rs

@@ -10,8 +10,8 @@
 //
 // apply_consolidation() processes consolidation reports independently.
 
-use crate::digest;
-use crate::llm::{call_sonnet, parse_json_response};
+use super::digest;
+use super::llm::{call_sonnet, parse_json_response};
 use crate::neuro;
 use crate::store::{self, Store, new_relation};
 
@@ -98,7 +98,7 @@ pub fn consolidate_full_with_progress(
             *store = Store::load()?;
         }
 
-        let prompt = match neuro::agent_prompt(store, agent_type, *count) {
+        let prompt = match super::prompts::agent_prompt(store, agent_type, *count) {
             Ok(p) => p,
             Err(e) => {
                 let msg = format!("  ERROR building prompt: {}", e);
@@ -266,7 +266,7 @@ fn build_consolidation_prompt(store: &Store, report_keys: &[String]) -> Result<S
             "=".repeat(60), key, content));
     }
 
-    neuro::load_prompt("consolidation", &[("{{REPORTS}}", &report_text)])
+    super::prompts::load_prompt("consolidation", &[("{{REPORTS}}", &report_text)])
 }
 
 /// Run the full apply-consolidation pipeline.

poc-memory/src/agents/daemon.rs

@@ -103,7 +103,7 @@ fn job_experience_mine(ctx: &ExecutionContext, path: &str, segment: Option<usize
         ctx.log_line("loading store");
         let mut store = crate::store::Store::load()?;
         ctx.log_line("mining");
-        let count = crate::enrich::experience_mine(&mut store, &path, segment)?;
+        let count = super::enrich::experience_mine(&mut store, &path, segment)?;
         ctx.log_line(format!("{count} entries mined"));
         Ok(())
     })
@@ -115,7 +115,7 @@ fn job_fact_mine(ctx: &ExecutionContext, path: &str) -> Result<(), TaskError> {
         ctx.log_line("mining facts");
         let p = std::path::Path::new(&path);
         let progress = |msg: &str| { ctx.set_progress(msg); };
-        let count = crate::fact_mine::mine_and_store(p, Some(&progress))?;
+        let count = super::fact_mine::mine_and_store(p, Some(&progress))?;
         ctx.log_line(format!("{count} facts stored"));
         Ok(())
     })
@@ -125,7 +125,7 @@ fn job_consolidate(ctx: &ExecutionContext) -> Result<(), TaskError> {
     run_job(ctx, "consolidate", || {
         ctx.log_line("loading store");
         let mut store = crate::store::Store::load()?;
-        crate::consolidate::consolidate_full_with_progress(&mut store, &|msg| {
+        super::consolidate::consolidate_full_with_progress(&mut store, &|msg| {
             ctx.log_line(msg);
         })
     })
@@ -133,13 +133,13 @@ fn job_consolidate(ctx: &ExecutionContext) -> Result<(), TaskError> {
 
 fn job_knowledge_loop(ctx: &ExecutionContext) -> Result<(), TaskError> {
     run_job(ctx, "knowledge-loop", || {
-        let config = crate::knowledge::KnowledgeLoopConfig {
+        let config = super::knowledge::KnowledgeLoopConfig {
             max_cycles: 100,
             batch_size: 5,
             ..Default::default()
         };
         ctx.log_line("running agents");
-        let results = crate::knowledge::run_knowledge_loop(&config)?;
+        let results = super::knowledge::run_knowledge_loop(&config)?;
         ctx.log_line(format!("{} cycles, {} actions",
             results.len(),
             results.iter().map(|r| r.total_applied).sum::<usize>()));
@@ -329,7 +329,7 @@ pub fn run_daemon() -> Result<(), String> {
             let stale = find_stale_sessions();
 
             // Load mined transcript keys once for this tick
-            let mined = crate::enrich::mined_transcript_keys();
+            let mined = super::enrich::mined_transcript_keys();
 
             // Limit new tasks per tick — the resource pool gates execution,
             // but we don't need thousands of task objects in the registry.
@@ -372,7 +372,7 @@ pub fn run_daemon() -> Result<(), String> {
                 let path_str = session.to_string_lossy().to_string();
 
                 // Check for old-style whole-file mined key
-                let experience_done = crate::enrich::is_transcript_mined_with_keys(&mined, &path_str);
+                let experience_done = super::enrich::is_transcript_mined_with_keys(&mined, &path_str);
 
                 if !experience_done {
                     if is_file_open(&session) {
@@ -384,11 +384,11 @@ pub fn run_daemon() -> Result<(), String> {
                     let seg_count = if let Some(&cached) = seg_cache.get(&path_str) {
                         cached
                     } else {
-                        let messages = match crate::enrich::extract_conversation(&path_str) {
+                        let messages = match super::enrich::extract_conversation(&path_str) {
                             Ok(m) => m,
                             Err(_) => continue,
                         };
-                        let count = crate::enrich::split_on_compaction(messages).len();
+                        let count = super::enrich::split_on_compaction(messages).len();
                         seg_cache.insert(path_str.clone(), count);
                         count
                     };
@@ -400,7 +400,7 @@ pub fn run_daemon() -> Result<(), String> {
                         }
                     } else {
                         // Multi-segment — find unmined segments
-                        let fname_key = crate::enrich::transcript_filename_key(&path_str);
+                        let fname_key = super::enrich::transcript_filename_key(&path_str);
                         let mut unmined = 0;
                         for i in 0..seg_count {
                             let seg_key = format!("{}.{}", fname_key, i);

poc-memory/src/agents/digest.rs

@@ -5,7 +5,7 @@
 // summarize weeklies. All three share the same generate/auto-detect
 // pipeline, parameterized by DigestLevel.
 
-use crate::llm::{call_sonnet, semantic_keys};
+use super::llm::{call_sonnet, semantic_keys};
 use crate::store::{self, Store, new_relation};
 use crate::neuro;
 
@@ -209,7 +209,7 @@ fn generate_digest(
         .collect::<Vec<_>>()
         .join(", ");
 
-    let prompt = neuro::load_prompt("digest", &[
+    let prompt = super::prompts::load_prompt("digest", &[
         ("{{LEVEL}}", level.title),
         ("{{PERIOD}}", level.period),
         ("{{INPUT_TITLE}}", level.input_title),

poc-memory/src/agents/enrich.rs

@@ -7,7 +7,7 @@
 // Both extract conversation from JSONL transcripts, build prompts, call Sonnet,
 // and apply results to the store.
 
-use crate::llm::{call_sonnet, parse_json_response, semantic_keys};
+use super::llm::{call_sonnet, parse_json_response, semantic_keys};
 use crate::neuro;
 use crate::store::{self, Store, new_node, new_relation};
 
@@ -174,7 +174,7 @@ fn build_journal_prompt(
         .collect::<Vec<_>>()
         .join("\n");
 
-    neuro::load_prompt("journal-enrich", &[
+    super::prompts::load_prompt("journal-enrich", &[
         ("{{GREP_LINE}}", &grep_line.to_string()),
         ("{{ENTRY_TEXT}}", entry_text),
         ("{{KEYS}}", &keys_text),
@@ -334,7 +334,7 @@ pub fn experience_mine(
         .collect::<Vec<_>>()
         .join("\n");
 
-    let prompt = neuro::load_prompt("experience", &[
+    let prompt = super::prompts::load_prompt("experience", &[
         ("{{IDENTITY}}", &identity),
         ("{{RECENT_JOURNAL}}", &recent),
         ("{{KEYS}}", &keys_text),

poc-memory/src/agents/fact_mine.rs

@@ -6,7 +6,7 @@
 // Uses Haiku (not Sonnet) for cost efficiency on high-volume extraction.
 
 use crate::config;
-use crate::llm;
+use super::llm;
 use crate::store::{self, Provenance};
 
 use serde::{Deserialize, Serialize};

poc-memory/src/agents/knowledge.rs

@@ -11,7 +11,7 @@
 // convergence via graph-structural metrics (sigma, CC, communities).
 
 use crate::graph::Graph;
-use crate::llm;
+use super::llm;
 use crate::spectral;
 use crate::store::{self, Store, new_relation, RelationType};
 
@@ -329,7 +329,7 @@ fn agent_provenance(agent: &str) -> store::Provenance {
 // ---------------------------------------------------------------------------
 
 fn load_prompt(name: &str) -> Result<String, String> {
-    crate::neuro::load_prompt(name, &[])
+    super::prompts::load_prompt(name, &[])
 }
 
 fn get_graph_topology(store: &Store, graph: &Graph) -> String {

poc-memory/src/agents/mod.rs

@@ -0,0 +1,25 @@
+// Agent layer: LLM-powered operations on the memory graph
+//
+// Everything here calls external models (Sonnet, Haiku) or orchestrates
+// sequences of such calls. The core graph infrastructure (store, graph,
+// spectral, search, similarity) lives at the crate root.
+//
+//   llm          — model invocation, response parsing
+//   prompts      — prompt generation from store data
+//   audit        — link quality review via Sonnet
+//   consolidate  — full consolidation pipeline
+//   knowledge    — knowledge production agents + convergence loop
+//   enrich       — journal enrichment, experience mining
+//   fact_mine    — fact extraction from transcripts
+//   digest       — episodic digest generation (daily/weekly/monthly)
+//   daemon       — background job scheduler
+
+pub mod llm;
+pub mod prompts;
+pub mod audit;
+pub mod consolidate;
+pub mod knowledge;
+pub mod enrich;
+pub mod fact_mine;
+pub mod digest;
+pub mod daemon;

poc-memory/src/agents/prompts.rs

@@ -6,7 +6,7 @@ use crate::graph::Graph;
 use crate::similarity;
 use crate::spectral;
 
-use super::scoring::{
+use crate::neuro::{
     ReplayItem, consolidation_priority,
     replay_queue, replay_queue_with_graph, detect_interference,
 };

poc-memory/src/lib.rs

@@ -3,25 +3,27 @@
 // Re-exports modules so that memory-search and other binaries
 // can call library functions directly instead of shelling out.
 
+// Core infrastructure
 pub mod config;
 pub mod store;
 pub mod util;
-pub mod llm;
-pub mod digest;
-pub mod audit;
-pub mod enrich;
-pub mod consolidate;
 pub mod graph;
 pub mod search;
 pub mod similarity;
-pub mod migrate;
-pub mod neuro;
-pub mod query;
 pub mod spectral;
 pub mod lookups;
-pub mod daemon;
-pub mod fact_mine;
-pub mod knowledge;
+pub mod query;
+pub mod migrate;
+pub mod neuro;
+
+// Agent layer (LLM-powered operations)
+pub mod agents;
+
+// Re-export agent submodules at crate root for backwards compatibility
+pub use agents::{
+    llm, audit, consolidate, knowledge,
+    enrich, fact_mine, digest, daemon,
+};
 
 pub mod memory_capnp {
     include!(concat!(env!("OUT_DIR"), "/schema/memory_capnp.rs"));

poc-memory/src/main.rs

@@ -878,11 +878,11 @@ fn cmd_consolidate_batch(count: usize, auto: bool, agent: Option<String>) -> Res
     let store = store::Store::load()?;
 
     if let Some(agent_name) = agent {
-        let prompt = neuro::agent_prompt(&store, &agent_name, count)?;
+        let prompt = agents::prompts::agent_prompt(&store, &agent_name, count)?;
         println!("{}", prompt);
         Ok(())
     } else {
-        neuro::consolidation_batch(&store, count, auto)
+        agents::prompts::consolidation_batch(&store, count, auto)
     }
 }
 

poc-memory/src/neuro/mod.rs

@@ -5,22 +5,17 @@
 //   rewrite  — graph topology mutations: differentiation, closure, linking
 
 mod scoring;
-mod prompts;
 mod rewrite;
 
-// Re-export public API so `neuro::` paths continue to work.
-
 pub use scoring::{
-    replay_queue, detect_interference,
+    ReplayItem,
+    consolidation_priority,
+    replay_queue, replay_queue_with_graph,
+    detect_interference,
     consolidation_plan, format_plan,
     daily_check,
 };
 
-pub use prompts::{
-    load_prompt,
-    consolidation_batch, agent_prompt,
-};
-
 pub use rewrite::{
     refine_target, LinkMove,
     differentiate_hub,