Delete similarity module, rewrite module, and all text-similarity code

Text cosine similarity was being used as a crutch for operations
the graph structure should handle: interference detection, orphan
linking, triangle closing, hub differentiation. These are all
graph-structural operations that the agents (linker, extractor)
handle with actual semantic understanding.

Removed: similarity.rs (stemming + cosine), rewrite.rs (orphan
linking, triangle closing, hub differentiation), detect_interference,
and all CLI commands and consolidation steps that used them.

-794 lines.

Co-Authored-By: Proof of Concept <poc@bcachefs.org>

src/subconscious/consolidate.rs

@@ -94,17 +94,8 @@ fn consolidate_full_with_progress(
         agent_num - agent_errors, agent_errors));
     store.save()?;
 
-    // --- Step 3: Link orphans ---
-    log_line(&mut log_buf, "\n--- Step 3: Link orphans ---");
-    on_progress("linking orphans");
-    println!("\n--- Linking orphan nodes ---");
-    *store = Store::load()?;
-
-    let (lo_orphans, lo_added) = neuro::link_orphans(store, 2, 3, 0.15);
-    log_line(&mut log_buf, &format!("  {} orphans, {} links added", lo_orphans, lo_added));
-
-    // --- Step 3b: Cap degree ---
-    log_line(&mut log_buf, "\n--- Step 3b: Cap degree ---");
+    // --- Step 3: Cap degree ---
+    log_line(&mut log_buf, "\n--- Step 3: Cap degree ---");
     on_progress("capping degree");
     println!("\n--- Capping node degree ---");
     *store = Store::load()?;

src/subconscious/defs.rs

@@ -9,7 +9,6 @@
 //   {{nodes}}     — query results formatted as node sections
 //   {{episodes}}  — alias for {{nodes}}
 //   {{health}}    — graph health report
-//   {{pairs}}     — interference pairs from detect_interference
 //   {{rename}}    — rename candidates
 //   {{split}}     — split detail for the first query result
 //
@@ -227,18 +226,6 @@ fn resolve(
             keys: vec![],
         }),
 
-        "pairs" => {
-            let mut pairs = crate::neuro::detect_interference(store, graph, 0.5);
-            pairs.truncate(count);
-            let pair_keys: Vec<String> = pairs.iter()
-                .flat_map(|(a, b, _)| vec![a.clone(), b.clone()])
-                .collect();
-            Some(Resolved {
-                text: super::prompts::format_pairs_section(&pairs, store, graph),
-                keys: pair_keys,
-            })
-        }
-
         "rename" => {
             if !keys.is_empty() {
                 // --target provided: present those keys as candidates

src/subconscious/digest.rs

@@ -7,7 +7,6 @@ use std::sync::Arc;
 // pipeline, parameterized by DigestLevel.
 
 use crate::store::{self, Store, new_relation};
-use crate::neuro;
 
 use chrono::{Datelike, Duration, Local, NaiveDate};
 use regex::Regex;
@@ -549,11 +548,6 @@ pub fn apply_digest_links(store: &mut Store, links: &[DigestLink]) -> (usize, us
             }
         };
 
-        // Refine target to best-matching section if available
-        let source_content = store.nodes.get(&source)
-            .map(|n| n.content.as_str()).unwrap_or("");
-        let target = neuro::refine_target(store, source_content, &target);
-
         if source == target { skipped += 1; continue; }
 
         // Check if link already exists

src/subconscious/prompts.rs

@@ -6,7 +6,7 @@ use crate::graph::Graph;
 
 use crate::neuro::{
     ReplayItem,
-    replay_queue, detect_interference,
+    replay_queue,
 };
 
 /// Result of building an agent prompt — includes both the prompt text
@@ -195,41 +195,6 @@ pub fn format_health_section(store: &Store, graph: &Graph) -> String {
     out
 }
 
-pub(super) fn format_pairs_section(
-    pairs: &[(String, String, f32)],
-    store: &Store,
-    graph: &Graph,
-) -> String {
-    let mut out = String::new();
-    let communities = graph.communities();
-
-    for (a, b, sim) in pairs {
-        out.push_str(&format!("## Pair: similarity={:.3}\n", sim));
-
-        let ca = communities.get(a).map(|c| format!("c{}", c)).unwrap_or_else(|| "?".into());
-        let cb = communities.get(b).map(|c| format!("c{}", c)).unwrap_or_else(|| "?".into());
-
-        // Node A
-        out.push_str(&format!("\n### {} ({})\n", a, ca));
-        if let Some(node) = store.nodes.get(a) {
-            let content = crate::util::truncate(&node.content, 500, "...");
-            out.push_str(&format!("Weight: {:.2}\n{}\n",
-                node.weight, content));
-        }
-
-        // Node B
-        out.push_str(&format!("\n### {} ({})\n", b, cb));
-        if let Some(node) = store.nodes.get(b) {
-            let content = crate::util::truncate(&node.content, 500, "...");
-            out.push_str(&format!("Weight: {:.2}\n{}\n",
-                node.weight, content));
-        }
-
-        out.push_str("\n---\n\n");
-    }
-    out
-}
-
 pub(super) fn format_rename_candidates(store: &Store, count: usize) -> (Vec<String>, String) {
     let mut candidates: Vec<(&str, &crate::store::Node)> = store.nodes.iter()
         .filter(|(key, node)| {
@@ -398,14 +363,6 @@ pub fn consolidation_batch(store: &Store, count: usize, auto: bool) -> Result<()
             item.priority, item.key, item.cc, item.interval_days, node_type);
     }
 
-    let pairs = detect_interference(store, &graph, 0.6);
-    if !pairs.is_empty() {
-        println!("\nInterfering pairs ({}):", pairs.len());
-        for (a, b, sim) in pairs.iter().take(5) {
-            println!("  [{:.3}] {} ↔ {}", sim, a, b);
-        }
-    }
-
     println!("\nAgent prompts:");
     println!("  --auto              Generate replay agent prompt");
     println!("  --agent replay      Replay agent (schema assimilation)");