Add calibrate agent, link-set command, and dominating-set query stage

calibrate.agent: Haiku-based agent that reads a node and all its
neighbors, then assigns appropriate link strengths relative to each
other. Designed for high-volume runs across the whole graph.

graph link-set: Set strength of an existing link (0.0-1.0).

dominating-set query stage: Greedy 3-covering dominating set — finds
the minimum set of nodes such that every node in the input is within
1 hop of at least 3 selected nodes. Use with calibrate agent to
ensure every link gets assessed from multiple perspectives.

Usage: poc-memory query "content ~ 'bcachefs' | dominating-set"

poc-memory/agents/calibrate.agent

@@ -0,0 +1,56 @@
+{"agent":"calibrate","query":"all | not-visited:calibrate,7d | sort:degree desc | limit:1","model":"haiku","schedule":"daily","tools":["Bash(poc-memory:*)"]}
+
+# Calibrate Agent — Link Strength Assessment
+
+{{node:core-personality}}
+
+{{node:memory-instructions-core}}
+
+You calibrate link strengths in the knowledge graph. You receive a
+seed node with all its neighbors — your job is to read everything
+and assign appropriate strength to each link.
+
+## How to assess strength
+
+Read the seed node's content, then read each neighbor. For each link,
+judge how strongly related they actually are:
+
+- **0.8–1.0** — core relationship. One defines or is essential to the other.
+  Parent-child, same concept different depth, direct dependency.
+- **0.5–0.7** — strong relationship. Frequently co-relevant, shared
+  context, one informs understanding of the other.
+- **0.2–0.4** — moderate relationship. Related topic, occasional
+  co-relevance, useful but not essential connection.
+- **0.05–0.15** — weak relationship. Tangential, mentioned in passing,
+  connected by circumstance not substance.
+
+## How to work
+
+For the seed node, read it and all its neighbors. Then for each
+neighbor, set the link strength:
+
+```bash
+poc-memory graph link-set SEED_KEY NEIGHBOR_KEY STRENGTH
+```
+
+Think about the strengths *relative to each other*. If node A has
+10 neighbors, they can't all be 0.8 — rank them and spread the
+strengths accordingly.
+
+## Guidelines
+
+- **Read before judging.** Don't guess from key names alone.
+- **Calibrate relatively.** The strongest link from this node should
+  be stronger than the weakest. Use the full range.
+- **Journal→topic links are usually weak (0.1–0.3).** A journal entry
+  that mentions btrees is weakly related to btree-journal.
+- **Topic→subtopic links are strong (0.6–0.9).** btree-journal and
+  btree-journal-txn-restart are tightly related.
+- **Hub→leaf links vary.** bcachefs→kernel-patterns is moderate (0.4),
+  bcachefs→some-random-journal is weak (0.1).
+- **Don't remove links.** Only adjust strength. If a link shouldn't
+  exist at all, set it to 0.05.
+
+## Seed node
+
+{{organize}}

poc-memory/src/cli/graph.rs

@@ -178,6 +178,35 @@ pub fn cmd_link_add(source: &str, target: &str, reason: &[String]) -> Result<(),
     Ok(())
 }
 
+pub fn cmd_link_set(source: &str, target: &str, strength: f32) -> Result<(), String> {
+    super::check_dry_run();
+    let mut store = store::Store::load()?;
+    let source = store.resolve_key(source)?;
+    let target = store.resolve_key(target)?;
+    let strength = strength.clamp(0.01, 1.0);
+
+    let mut found = false;
+    for rel in &mut store.relations {
+        if rel.deleted { continue; }
+        if (rel.source_key == source && rel.target_key == target)
+            || (rel.source_key == target && rel.target_key == source)
+        {
+            let old = rel.strength;
+            rel.strength = strength;
+            println!("Set: {} ↔ {} strength {:.2} → {:.2}", source, target, old, strength);
+            found = true;
+            break;
+        }
+    }
+
+    if !found {
+        return Err(format!("No link found between {} and {}", source, target));
+    }
+
+    store.save()?;
+    Ok(())
+}
+
 pub fn cmd_link_impact(source: &str, target: &str) -> Result<(), String> {
     let store = store::Store::load()?;
     let source = store.resolve_key(source)?;

poc-memory/src/main.rs

@@ -299,6 +299,16 @@ enum GraphCmd {
         /// Optional reason
         reason: Vec<String>,
     },
+    /// Set strength of an existing link
+    #[command(name = "link-set")]
+    LinkSet {
+        /// Source node key
+        source: String,
+        /// Target node key
+        target: String,
+        /// Strength (0.0–1.0)
+        strength: f32,
+    },
     /// Simulate adding an edge, report topology impact
     #[command(name = "link-impact")]
     LinkImpact {
@@ -775,6 +785,8 @@ fn main() {
             GraphCmd::Link { key } => cli::graph::cmd_link(&key),
             GraphCmd::LinkAdd { source, target, reason }
                 => cli::graph::cmd_link_add(&source, &target, &reason),
+            GraphCmd::LinkSet { source, target, strength }
+                => cli::graph::cmd_link_set(&source, &target, strength),
             GraphCmd::LinkImpact { source, target }
                 => cli::graph::cmd_link_impact(&source, &target),
             GraphCmd::LinkAudit { apply } => cli::graph::cmd_link_audit(apply),

poc-memory/src/query/engine.rs

@@ -157,6 +157,7 @@ pub enum Filter {
 pub enum Transform {
     Sort(SortField),
     Limit(usize),
+    DominatingSet,
 }
 
 #[derive(Clone, Debug)]
@@ -257,6 +258,11 @@ impl Stage {
             return Ok(Stage::Generator(Generator::All));
         }
 
+        // Transform: "dominating-set"
+        if s == "dominating-set" {
+            return Ok(Stage::Transform(Transform::DominatingSet));
+        }
+
         // Try algorithm parse first (bare words, no colon)
         if !s.contains(':') {
             if let Ok(algo) = AlgoStage::parse(s) {
@@ -348,6 +354,7 @@ impl fmt::Display for Stage {
             Stage::Filter(filt) => write!(f, "{}", filt),
             Stage::Transform(Transform::Sort(field)) => write!(f, "sort:{:?}", field),
             Stage::Transform(Transform::Limit(n)) => write!(f, "limit:{}", n),
+            Stage::Transform(Transform::DominatingSet) => write!(f, "dominating-set"),
             Stage::Algorithm(a) => write!(f, "{}", a.algo),
         }
     }
@@ -508,7 +515,7 @@ fn eval_filter(filt: &Filter, key: &str, store: &Store, now: i64) -> bool {
     }
 }
 
-fn run_transform(
+pub fn run_transform(
     xform: &Transform,
     mut items: Vec<(String, f64)>,
     store: &Store,
@@ -564,6 +571,56 @@ fn run_transform(
             items.truncate(*n);
             items
         }
+        Transform::DominatingSet => {
+            // Greedy 3-covering dominating set: pick the node that covers
+            // the most under-covered neighbors, repeat until every node
+            // has been covered 3 times (by 3 different selected seeds).
+            use std::collections::HashMap as HMap;
+            let input_keys: std::collections::HashSet<String> = items.iter().map(|(k, _)| k.clone()).collect();
+            let mut cover_count: HMap<String, usize> = items.iter().map(|(k, _)| (k.clone(), 0)).collect();
+            let mut selected: Vec<(String, f64)> = Vec::new();
+            let mut selected_set: std::collections::HashSet<String> = std::collections::HashSet::new();
+            const REQUIRED_COVERAGE: usize = 3;
+
+            loop {
+                // Find the unselected node that covers the most under-covered nodes
+                let best = items.iter()
+                    .filter(|(k, _)| !selected_set.contains(k.as_str()))
+                    .map(|(k, _)| {
+                        let mut value = 0usize;
+                        // Count self if under-covered
+                        if cover_count.get(k).copied().unwrap_or(0) < REQUIRED_COVERAGE {
+                            value += 1;
+                        }
+                        for (nbr, _) in graph.neighbors(k) {
+                            if input_keys.contains(nbr.as_str()) {
+                                if cover_count.get(nbr.as_str()).copied().unwrap_or(0) < REQUIRED_COVERAGE {
+                                    value += 1;
+                                }
+                            }
+                        }
+                        (k.clone(), value)
+                    })
+                    .max_by_key(|(_, v)| *v);
+
+                let Some((key, value)) = best else { break };
+                if value == 0 { break; } // everything covered 3x
+
+                // Mark coverage
+                *cover_count.entry(key.clone()).or_default() += 1;
+                for (nbr, _) in graph.neighbors(&key) {
+                    if let Some(c) = cover_count.get_mut(nbr.as_str()) {
+                        *c += 1;
+                    }
+                }
+
+                let score = items.iter().find(|(k, _)| k == &key).map(|(_, s)| *s).unwrap_or(1.0);
+                selected.push((key.clone(), score));
+                selected_set.insert(key);
+            }
+
+            selected
+        }
     }
 }
 

poc-memory/src/query/parser.rs

@@ -64,6 +64,7 @@ pub enum Stage {
     Select(Vec<String>),
     Count,
     Connectivity,
+    DominatingSet,
 }
 
 #[derive(Debug, Clone)]
@@ -90,6 +91,7 @@ peg::parser! {
             / "select" _ f:field_list() { Stage::Select(f) }
             / "count" { Stage::Count }
             / "connectivity" { Stage::Connectivity }
+            / "dominating-set" { Stage::DominatingSet }
 
         rule asc_desc() -> bool
             = "asc" { true }
@@ -425,6 +427,15 @@ fn execute_parsed(
             }
             Stage::Connectivity => {} // handled in output
             Stage::Select(_) | Stage::Count => {} // handled in output
+            Stage::DominatingSet => {
+                let mut items: Vec<(String, f64)> = results.iter()
+                    .map(|r| (r.key.clone(), graph.degree(&r.key) as f64))
+                    .collect();
+                let xform = super::engine::Transform::DominatingSet;
+                items = super::engine::run_transform(&xform, items, store, &graph);
+                let keep: std::collections::HashSet<String> = items.into_iter().map(|(k, _)| k).collect();
+                results.retain(|r| keep.contains(&r.key));
+            }
         }
     }