From fd5591653d905bc688397ce50c7d2dc94eec5979 Mon Sep 17 00:00:00 2001
From: Kent Overstreet <kent.overstreet@linux.dev>
Date: Sun, 8 Mar 2026 20:07:07 -0400
Subject: [PATCH] remove hardcoded skip lists, prune orphan edges in fsck
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All nodes in the store are memory — none should be excluded from
knowledge extraction, search, or graph algorithms by name. Removed
the MEMORY/where-am-i/work-queue/work-state skip lists entirely.
Deleted where-am-i and work-queue nodes from the store (ephemeral
scratchpads that don't belong). Added orphan edge pruning to fsck
so broken links get cleaned up automatically.

Co-Authored-By: ProofOfConcept <poc@bcachefs.org>
---
 src/knowledge.rs     | 16 ++--------------
 src/llm.rs           |  4 +---
 src/main.rs          | 25 +++++++++++++++++++------
 src/neuro/prompts.rs |  4 +---
 4 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/src/knowledge.rs b/src/knowledge.rs
index ccfd9bc..a66bd39 100644
--- a/src/knowledge.rs
+++ b/src/knowledge.rs
@@ -515,11 +515,7 @@ fn spectral_distance(embedding: &HashMap<String, Vec<f64>>, a: &str, b: &str) ->
 
 fn select_extractor_clusters(_store: &Store, n: usize) -> Vec<Vec<String>> {
     let embedding = load_spectral_embedding();
-    let skip = ["MEMORY", "where-am-i", "work-queue", "work-state"];
-
-    let semantic_keys: Vec<&String> = embedding.keys()
-        .filter(|k| !skip.contains(&k.as_str()))
-        .collect();
+    let semantic_keys: Vec<&String> = embedding.keys().collect();
 
     let cluster_size = 5;
     let mut used = HashSet::new();
@@ -578,12 +574,7 @@ pub fn run_extractor(store: &Store, graph: &Graph, batch_size: usize) -> Result<
 
 fn select_connector_pairs(store: &Store, graph: &Graph, n: usize) -> Vec<(Vec<String>, Vec<String>)> {
     let embedding = load_spectral_embedding();
-    let skip_exact: HashSet<&str> = ["MEMORY", "where-am-i",
-        "work-queue", "work-state"].iter().copied().collect();
-
-    let semantic_keys: Vec<&String> = embedding.keys()
-        .filter(|k| !skip_exact.contains(k.as_str()))
-        .collect();
+    let semantic_keys: Vec<&String> = embedding.keys().collect();
 
     let mut pairs = Vec::new();
     let mut used = HashSet::new();
@@ -651,9 +642,6 @@ pub fn run_challenger(store: &Store, graph: &Graph, batch_size: usize) -> Result
     let topology = get_graph_topology(store, graph);
 
     let mut candidates: Vec<(&String, usize)> = store.nodes.iter()
-        .filter(|(k, _)| {
-            !["MEMORY", "where-am-i", "work-queue", "work-state"].contains(&k.as_str())
-        })
         .map(|(k, _)| (k, graph.degree(k)))
         .collect();
     candidates.sort_by(|a, b| b.1.cmp(&a.1));
diff --git a/src/llm.rs b/src/llm.rs
index fafadb8..2ed31e9 100644
--- a/src/llm.rs
+++ b/src/llm.rs
@@ -133,11 +133,9 @@ pub(crate) fn parse_json_response(response: &str) -> Result<serde_json::Value, S
     Err(format!("no valid JSON in response: {preview}..."))
 }
 
-/// Get non-operational keys for prompt context.
+/// Get all keys for prompt context.
 pub(crate) fn semantic_keys(store: &Store) -> Vec<String> {
-    let skip = ["MEMORY", "where-am-i", "work-queue", "work-state"];
     let mut keys: Vec<String> = store.nodes.keys()
-        .filter(|k| !skip.contains(&k.as_str()))
         .cloned()
         .collect();
     keys.sort();
diff --git a/src/main.rs b/src/main.rs
index b9c577f..4a1f88f 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -416,18 +416,31 @@ fn cmd_fsck() -> Result<(), String> {
     store::fsck()?;
     store::strip_md_keys()?;
 
-    // Check for broken links
-    let store = store::Store::load()?;
-    let mut orphans = 0usize;
+    // Prune broken links (relations referencing deleted/missing nodes)
+    let mut store = store::Store::load()?;
+    let mut to_tombstone = Vec::new();
     for rel in &store.relations {
         if rel.deleted { continue; }
         if !store.nodes.contains_key(&rel.source_key)
             || !store.nodes.contains_key(&rel.target_key) {
-            orphans += 1;
+            let mut tombstone = rel.clone();
+            tombstone.deleted = true;
+            tombstone.version += 1;
+            to_tombstone.push(tombstone);
         }
     }
-    if orphans > 0 {
-        eprintln!("{} broken links (run `health` for details)", orphans);
+    if !to_tombstone.is_empty() {
+        let count = to_tombstone.len();
+        store.append_relations(&to_tombstone)?;
+        for t in &to_tombstone {
+            if let Some(r) = store.relations.iter_mut().find(|r|
+                r.source == t.source && r.target == t.target && !r.deleted) {
+                r.deleted = true;
+                r.version = t.version;
+            }
+        }
+        store.save()?;
+        eprintln!("Pruned {} broken links", count);
     } else {
         eprintln!("No broken links");
     }
diff --git a/src/neuro/prompts.rs b/src/neuro/prompts.rs
index 9f41a83..222d4f2 100644
--- a/src/neuro/prompts.rs
+++ b/src/neuro/prompts.rs
@@ -145,11 +145,9 @@ fn format_nodes_section(store: &Store, items: &[ReplayItem], graph: &Graph) -> S
         // Suggested link targets: text-similar semantic nodes not already neighbors
         let neighbor_keys: std::collections::HashSet<&str> = neighbors.iter()
             .map(|(k, _)| k.as_str()).collect();
-        let skip = ["MEMORY", "where-am-i", "work-queue", "work-state"];
         let mut candidates: Vec<(&str, f32)> = store.nodes.iter()
             .filter(|(k, _)| {
-                !skip.contains(&k.as_str())
-                    && *k != &item.key
+                *k != &item.key
                     && !neighbor_keys.contains(k.as_str())
             })
             .map(|(k, n)| {