consciousness/src/cli/graph.rs

// cli/graph.rs — graph subcommand handlers
//
// Extracted from main.rs. All graph-related CLI commands:
// link, link-add, link-impact, link-audit, link-orphans,
// triangle-close, cap-degree, normalize-strengths, differentiate,
// trace, spectral-*, organize, interference.

use crate::{store, graph, neuro, spectral};

pub fn cmd_graph() -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();
    println!("Graph: {} nodes, {} edges, {} communities",
        g.nodes().len(), g.edge_count(), g.community_count());
    println!("σ={:.2}  α={:.2}  gini={:.3}  cc={:.4}",
        g.small_world_sigma(), g.degree_power_law_exponent(),
        g.degree_gini(), g.avg_clustering_coefficient());
    Ok(())
}

pub fn cmd_link_orphans(min_deg: usize, links_per: usize, sim_thresh: f32) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let (orphans, links) = neuro::link_orphans(&mut store, min_deg, links_per, sim_thresh);
    println!("Linked {} orphans, added {} connections (min_degree={}, links_per={}, sim>{})",
        orphans, links, min_deg, links_per, sim_thresh);
    Ok(())
}

pub fn cmd_cap_degree(max_deg: usize) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let (hubs, pruned) = store.cap_degree(max_deg)?;
    store.save()?;
    println!("Capped {} hubs, pruned {} weak Auto edges (max_degree={})", hubs, pruned, max_deg);
    Ok(())
}

pub fn cmd_normalize_strengths(apply: bool) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let graph = store.build_graph();
    let strengths = graph.jaccard_strengths();

    // Build a lookup from (source_key, target_key) → new_strength
    let mut updates: std::collections::HashMap<(String, String), f32> = std::collections::HashMap::new();
    for (a, b, s) in &strengths {
        // Store both directions for easy lookup
        updates.insert((a.clone(), b.clone()), *s);
        updates.insert((b.clone(), a.clone()), *s);
    }

    // Stats
    let mut changed = 0usize;
    let mut unchanged = 0usize;
    let mut temporal_skipped = 0usize;
    let mut delta_sum: f64 = 0.0;

    // Histogram of new strengths
    let mut buckets = [0usize; 10]; // 0.0-0.1, 0.1-0.2, ...

    for rel in &mut store.relations {
        if rel.deleted { continue; }

        // Skip implicit temporal edges (strength 1.0, Auto type)
        if rel.strength == 1.0 && rel.rel_type == store::RelationType::Auto {
            temporal_skipped += 1;
            continue;
        }

        if let Some(&new_s) = updates.get(&(rel.source_key.clone(), rel.target_key.clone())) {
            let old_s = rel.strength;
            let delta = (new_s - old_s).abs();
            if delta > 0.001 {
                delta_sum += delta as f64;
                if apply {
                    rel.strength = new_s;
                }
                changed += 1;
            } else {
                unchanged += 1;
            }
            let bucket = ((new_s * 10.0) as usize).min(9);
            buckets[bucket] += 1;
        }
    }

    println!("Normalize link strengths (Jaccard similarity)");
    println!("  Total edges in graph: {}", strengths.len());
    println!("  Would change: {}", changed);
    println!("  Unchanged:    {}", unchanged);
    println!("  Temporal (skipped): {}", temporal_skipped);
    if changed > 0 {
        println!("  Avg delta:    {:.3}", delta_sum / changed as f64);
    }
    println!();
    println!("  Strength distribution:");
    for (i, &count) in buckets.iter().enumerate() {
        let lo = i as f32 / 10.0;
        let hi = lo + 0.1;
        let bar = "#".repeat(count / 50 + if count > 0 { 1 } else { 0 });
        println!("    {:.1}-{:.1}: {:5} {}", lo, hi, count, bar);
    }

    if apply {
        store.save()?;
        println!("\nApplied {} strength updates.", changed);
    } else {
        println!("\nDry run. Use --apply to write changes.");
    }

    Ok(())
}

pub fn cmd_link(key: &[String]) -> Result<(), String> {
    if key.is_empty() {
        return Err("link requires a key".into());
    }
    let key = key.join(" ");
    let store = store::Store::load()?;
    let resolved = store.resolve_key(&key)?;
    let g = store.build_graph();
    println!("Neighbors of '{}':", resolved);
    crate::query_parser::run_query(&store, &g,
        &format!("neighbors('{}') | select strength,clustering_coefficient", resolved))
}

pub fn cmd_triangle_close(min_degree: usize, sim_threshold: f32, max_per_hub: usize) -> Result<(), String> {
    println!("Triangle closure: min_degree={}, sim_threshold={}, max_per_hub={}",
        min_degree, sim_threshold, max_per_hub);

    let mut store = store::Store::load()?;
    let (hubs, added) = neuro::triangle_close(&mut store, min_degree, sim_threshold, max_per_hub);
    println!("\nProcessed {} hubs, added {} lateral links", hubs, added);
    Ok(())
}

pub fn cmd_link_add(source: &str, target: &str, reason: &[String]) -> 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 reason = reason.join(" ");

    // Refine target to best-matching section
    let source_content = store.nodes.get(&source)
        .map(|n| n.content.as_str()).unwrap_or("");
    let target = neuro::refine_target(&store, source_content, &target);

    // Find UUIDs
    let source_uuid = store.nodes.get(&source)
        .map(|n| n.uuid)
        .ok_or_else(|| format!("source not found: {}", source))?;
    let target_uuid = store.nodes.get(&target)
        .map(|n| n.uuid)
        .ok_or_else(|| format!("target not found: {}", target))?;

    // Check for existing link
    let exists = store.relations.iter().any(|r|
        !r.deleted &&
        ((r.source_key == source && r.target_key == target) ||
         (r.source_key == target && r.target_key == source)));
    if exists {
        println!("Link already exists: {} ↔ {}", source, target);
        return Ok(());
    }

    // Compute initial strength from Jaccard neighborhood similarity
    let graph = store.build_graph();
    let jaccard = graph.jaccard(&source, &target);
    let strength = (jaccard * 3.0).clamp(0.1, 1.0);

    let rel = store::new_relation(
        source_uuid, target_uuid,
        store::RelationType::Link, strength,
        &source, &target,
    );
    store.add_relation(rel)?;
    store.save()?;
    println!("Linked: {} → {} (strength={:.2}, {})", source, target, strength, reason);
    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;
    let mut first = true;
    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)
        {
            if first {
                let old = rel.strength;
                rel.strength = strength;
                println!("Set: {} ↔ {} strength {:.2} → {:.2}", source, target, old, strength);
                first = false;
            } else {
                // Duplicate — mark deleted
                rel.deleted = true;
                println!("  (removed duplicate link)");
            }
            found = true;
        }
    }

    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)?;
    let target = store.resolve_key(target)?;
    let g = store.build_graph();

    let impact = g.link_impact(&source, &target);

    println!("Link impact: {} → {}", source, target);
    println!("  Source degree: {}  Target degree: {}", impact.source_deg, impact.target_deg);
    println!("  Hub link: {}  Same community: {}", impact.is_hub_link, impact.same_community);
    println!("  ΔCC source: {:+.4}  ΔCC target: {:+.4}", impact.delta_cc_source, impact.delta_cc_target);
    println!("  ΔGini: {:+.6}", impact.delta_gini);
    println!("  Assessment: {}", impact.assessment);
    Ok(())
}

pub fn cmd_differentiate(key_arg: Option<&str>, do_apply: bool) -> Result<(), String> {
    let mut store = store::Store::load()?;

    if let Some(key) = key_arg {
        let resolved = store.resolve_key(key)?;
        let moves = neuro::differentiate_hub(&store, &resolved)
            .ok_or_else(|| format!("'{}' is not a file-level hub with sections", resolved))?;

        // Group by target section for display
        let mut by_section: std::collections::BTreeMap<String, Vec<&neuro::LinkMove>> =
            std::collections::BTreeMap::new();
        for mv in &moves {
            by_section.entry(mv.to_section.clone()).or_default().push(mv);
        }

        println!("Hub '{}' — {} links to redistribute across {} sections\n",
            resolved, moves.len(), by_section.len());

        for (section, section_moves) in &by_section {
            println!("  {} ({} links):", section, section_moves.len());
            for mv in section_moves.iter().take(5) {
                println!("    [{:.3}] {} — {}", mv.similarity,
                    mv.neighbor_key, mv.neighbor_snippet);
            }
            if section_moves.len() > 5 {
                println!("    ... and {} more", section_moves.len() - 5);
            }
        }

        if !do_apply {
            println!("\nTo apply: poc-memory differentiate {} --apply", resolved);
            return Ok(());
        }

        let (applied, skipped) = neuro::apply_differentiation(&mut store, &moves);
        store.save()?;
        println!("\nApplied: {}  Skipped: {}", applied, skipped);
    } else {
        let hubs = neuro::find_differentiable_hubs(&store);
        if hubs.is_empty() {
            println!("No file-level hubs with sections found above threshold");
            return Ok(());
        }

        println!("Differentiable hubs (file-level nodes with sections):\n");
        for (key, degree, sections) in &hubs {
            println!("  {:40} deg={:3}  sections={}", key, degree, sections);
        }
        println!("\nRun: poc-memory differentiate KEY  to preview a specific hub");
    }

    Ok(())
}

pub fn cmd_link_audit(apply: bool) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let stats = crate::audit::link_audit(&mut store, apply)?;
    println!("\n{}", "=".repeat(60));
    println!("Link audit complete:");
    println!("  Kept: {}  Deleted: {}  Retargeted: {}  Weakened: {}  Strengthened: {}  Errors: {}",
        stats.kept, stats.deleted, stats.retargeted, stats.weakened, stats.strengthened, stats.errors);
    println!("{}", "=".repeat(60));
    Ok(())
}

pub fn cmd_trace(key: &[String]) -> Result<(), String> {
    if key.is_empty() {
        return Err("trace requires a key".into());
    }
    let key = key.join(" ");
    let store = store::Store::load()?;
    let resolved = store.resolve_key(&key)?;
    let g = store.build_graph();

    let node = store.nodes.get(&resolved)
        .ok_or_else(|| format!("Node not found: {}", resolved))?;

    // Display the node itself
    println!("=== {} ===", resolved);
    println!("Type: {:?}  Weight: {:.2}",
        node.node_type, node.weight);
    if !node.source_ref.is_empty() {
        println!("Source: {}", node.source_ref);
    }

    // Show content preview
    let preview = crate::util::truncate(&node.content, 200, "...");
    println!("\n{}\n", preview);

    // Walk neighbors, grouped by node type
    let neighbors = g.neighbors(&resolved);
    let mut episodic_session = Vec::new();
    let mut episodic_daily = Vec::new();
    let mut episodic_weekly = Vec::new();
    let mut semantic = Vec::new();

    for (n, strength) in &neighbors {
        if let Some(nnode) = store.nodes.get(n.as_str()) {
            let entry = (n.as_str(), *strength, nnode);
            match nnode.node_type {
                store::NodeType::EpisodicSession =>
                    episodic_session.push(entry),
                store::NodeType::EpisodicDaily =>
                    episodic_daily.push(entry),
                store::NodeType::EpisodicWeekly
                | store::NodeType::EpisodicMonthly =>
                    episodic_weekly.push(entry),
                store::NodeType::Semantic =>
                    semantic.push(entry),
            }
        }
    }

    if !episodic_weekly.is_empty() {
        println!("Weekly digests:");
        for (k, s, n) in &episodic_weekly {
            let preview = crate::util::first_n_chars(n.content.lines().next().unwrap_or(""), 80);
            println!("  [{:.2}] {} — {}", s, k, preview);
        }
    }

    if !episodic_daily.is_empty() {
        println!("Daily digests:");
        for (k, s, n) in &episodic_daily {
            let preview = crate::util::first_n_chars(n.content.lines().next().unwrap_or(""), 80);
            println!("  [{:.2}] {} — {}", s, k, preview);
        }
    }

    if !episodic_session.is_empty() {
        println!("Session entries:");
        for (k, s, n) in &episodic_session {
            let preview = crate::util::first_n_chars(
                n.content.lines()
                    .find(|l| !l.is_empty() && !l.starts_with("<!--"))
                    .unwrap_or(""),
                80);
            println!("  [{:.2}] {}", s, k);
            if !n.source_ref.is_empty() {
                println!("         ↳ source: {}", n.source_ref);
            }
            println!("         {}", preview);
        }
    }

    if !semantic.is_empty() {
        println!("Semantic links:");
        for (k, s, _) in &semantic {
            println!("  [{:.2}] {}", s, k);
        }
    }

    println!("\nLinks: {} session, {} daily, {} weekly, {} semantic",
        episodic_session.len(), episodic_daily.len(),
        episodic_weekly.len(), semantic.len());

    Ok(())
}

pub fn cmd_spectral(k: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let g = graph::build_graph(&store);
    let result = spectral::decompose(&g, k);
    spectral::print_summary(&result, &g);
    Ok(())
}

pub fn cmd_spectral_save(k: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let g = graph::build_graph(&store);
    let result = spectral::decompose(&g, k);
    let emb = spectral::to_embedding(&result);
    spectral::save_embedding(&emb)?;
    Ok(())
}

pub fn cmd_spectral_neighbors(key: &str, n: usize) -> Result<(), String> {
    let emb = spectral::load_embedding()?;

    let dims = spectral::dominant_dimensions(&emb, &[key]);
    println!("Node: {}  (embedding: {} dims)", key, emb.dims);
    println!("Top spectral axes:");
    for &(d, loading) in dims.iter().take(5) {
        println!("  axis {:<2} (λ={:.4}): loading={:.5}", d, emb.eigenvalues[d], loading);
    }

    println!("\nNearest neighbors in spectral space:");
    let neighbors = spectral::nearest_neighbors(&emb, key, n);
    for (i, (k, dist)) in neighbors.iter().enumerate() {
        println!("  {:>2}. {:.5}  {}", i + 1, dist, k);
    }
    Ok(())
}

pub fn cmd_spectral_positions(n: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let emb = spectral::load_embedding()?;

    let g = store.build_graph();
    let communities = g.communities().clone();

    let positions = spectral::analyze_positions(&emb, &communities);

    println!("Spectral position analysis — {} nodes", positions.len());
    println!("  outlier: dist_to_center / median (>1 = unusual position)");
    println!("  bridge:  dist_to_center / dist_to_nearest_other_community");
    println!();

    let mut bridges: Vec<&spectral::SpectralPosition> = Vec::new();
    let mut outliers: Vec<&spectral::SpectralPosition> = Vec::new();

    for pos in positions.iter().take(n) {
        match spectral::classify_position(pos) {
            "bridge" => bridges.push(pos),
            _ => outliers.push(pos),
        }
    }

    if !bridges.is_empty() {
        println!("=== Bridges (between communities) ===");
        for pos in &bridges {
            println!("  [{:.2}/{:.2}] c{} → c{}  {}",
                pos.outlier_score, pos.bridge_score,
                pos.community, pos.nearest_community, pos.key);
        }
        println!();
    }

    println!("=== Top outliers (far from own community center) ===");
    for pos in positions.iter().take(n) {
        let class = spectral::classify_position(pos);
        println!("  {:>10}  outlier={:.2} bridge={:.2}  c{:<3}  {}",
            class, pos.outlier_score, pos.bridge_score,
            pos.community, pos.key);
    }

    Ok(())
}

pub fn cmd_spectral_suggest(n: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let emb = spectral::load_embedding()?;
    let g = store.build_graph();
    let communities = g.communities();

    let min_degree = 3;
    let well_connected: std::collections::HashSet<&str> = emb.coords.keys()
        .filter(|k| g.degree(k) >= min_degree)
        .map(|k| k.as_str())
        .collect();

    let filtered_emb = spectral::SpectralEmbedding {
        dims: emb.dims,
        eigenvalues: emb.eigenvalues.clone(),
        coords: emb.coords.iter()
            .filter(|(k, _)| well_connected.contains(k.as_str()))
            .map(|(k, v)| (k.clone(), v.clone()))
            .collect(),
    };

    let mut linked: std::collections::HashSet<(String, String)> =
        std::collections::HashSet::new();
    for rel in &store.relations {
        linked.insert((rel.source_key.clone(), rel.target_key.clone()));
        linked.insert((rel.target_key.clone(), rel.source_key.clone()));
    }

    eprintln!("Searching {} well-connected nodes (degree >= {})...",
        filtered_emb.coords.len(), min_degree);
    let pairs = spectral::unlinked_neighbors(&filtered_emb, &linked, n);

    println!("{} closest unlinked pairs (candidates for extractor agents):", pairs.len());
    for (i, (k1, k2, dist)) in pairs.iter().enumerate() {
        let c1 = communities.get(k1)
            .map(|c| format!("c{}", c))
            .unwrap_or_else(|| "?".into());
        let c2 = communities.get(k2)
            .map(|c| format!("c{}", c))
            .unwrap_or_else(|| "?".into());
        let cross = if c1 != c2 { " [cross-community]" } else { "" };
        println!("  {:>2}. dist={:.4}  {} ({}) ↔ {} ({}){}",
            i + 1, dist, k1, c1, k2, c2, cross);
    }

    Ok(())
}

pub fn cmd_organize(term: &str, threshold: f32, key_only: bool, create_anchor: bool) -> Result<(), String> {
    let mut store = store::Store::load()?;

    // Step 1: find all non-deleted nodes matching the term
    let term_lower = term.to_lowercase();
    let mut topic_nodes: Vec<(String, String)> = Vec::new(); // (key, content)

    // Prefixes that indicate ephemeral/generated nodes to skip
    let skip_prefixes = ["journal#", "daily-", "weekly-", "monthly-", "_",
                         "deep-index#", "facts-", "irc-history#"];

    for (key, node) in &store.nodes {
        if node.deleted { continue; }
        let key_matches = key.to_lowercase().contains(&term_lower);
        let content_matches = !key_only && node.content.to_lowercase().contains(&term_lower);
        if !key_matches && !content_matches { continue; }
        if skip_prefixes.iter().any(|p| key.starts_with(p)) { continue; }
        topic_nodes.push((key.clone(), node.content.clone()));
    }

    if topic_nodes.is_empty() {
        println!("No topic nodes found matching '{}'", term);
        return Ok(());
    }

    topic_nodes.sort_by(|a, b| a.0.cmp(&b.0));

    println!("=== Organize: '{}' ===", term);
    println!("Found {} topic nodes:\n", topic_nodes.len());
    for (key, content) in &topic_nodes {
        let lines = content.lines().count();
        let words = content.split_whitespace().count();
        println!("  {:60} {:>4} lines  {:>5} words", key, lines, words);
    }

    // Step 2: pairwise similarity
    let pairs = crate::similarity::pairwise_similar(&topic_nodes, threshold);

    if pairs.is_empty() {
        println!("\nNo similar pairs above threshold {:.2}", threshold);
    } else {
        println!("\n=== Similar pairs (cosine > {:.2}) ===\n", threshold);
        for (a, b, sim) in &pairs {
            let a_words = topic_nodes.iter().find(|(k,_)| k == a)
                .map(|(_,c)| c.split_whitespace().count()).unwrap_or(0);
            let b_words = topic_nodes.iter().find(|(k,_)| k == b)
                .map(|(_,c)| c.split_whitespace().count()).unwrap_or(0);

            println!("  [{:.3}] {} ({} words) ↔ {} ({} words)", sim, a, a_words, b, b_words);
        }
    }

    // Step 3: check connectivity within cluster
    let g = store.build_graph();
    println!("=== Connectivity ===\n");

    // Pick hub by intra-cluster connectivity, not overall degree
    let cluster_keys: std::collections::HashSet<&str> = topic_nodes.iter()
        .filter(|(k,_)| store.nodes.contains_key(k.as_str()))
        .map(|(k,_)| k.as_str())
        .collect();

    let mut best_hub: Option<(&str, usize)> = None;
    for key in &cluster_keys {
        let intra_degree = g.neighbor_keys(key).iter()
            .filter(|n| cluster_keys.contains(*n))
            .count();
        if best_hub.is_none() || intra_degree > best_hub.unwrap().1 {
            best_hub = Some((key, intra_degree));
        }
    }

    if let Some((hub, deg)) = best_hub {
        println!("  Hub: {} (degree {})", hub, deg);
        let hub_nbrs = g.neighbor_keys(hub);

        let mut unlinked = Vec::new();
        for (key, _) in &topic_nodes {
            if key == hub { continue; }
            if store.nodes.get(key.as_str()).is_none() { continue; }
            if !hub_nbrs.contains(key.as_str()) {
                unlinked.push(key.clone());
            }
        }

        if unlinked.is_empty() {
            println!("  All cluster nodes connected to hub ✓");
        } else {
            println!("  NOT linked to hub:");
            for key in &unlinked {
                println!("    {} → needs link to {}", key, hub);
            }
        }
    }

    // Step 4: anchor node
    if create_anchor {
        println!("\n=== Anchor node ===\n");
        if store.nodes.contains_key(term) && !store.nodes[term].deleted {
            println!("  Anchor '{}' already exists ✓", term);
        } else {
            let desc = format!("Anchor node for '{}' search term", term);
            store.upsert(term, &desc)?;
            let anchor_uuid = store.nodes.get(term).unwrap().uuid;
            for (key, _) in &topic_nodes {
                if store.nodes.get(key.as_str()).is_none() { continue; }
                let target_uuid = store.nodes[key.as_str()].uuid;
                let rel = store::new_relation(
                    anchor_uuid, target_uuid,
                    store::RelationType::Link, 0.8,
                    term, key,
                );
                store.add_relation(rel)?;
            }
            println!("  Created anchor '{}' with {} links", term, topic_nodes.len());
        }
    }

    store.save()?;
    Ok(())
}

pub fn cmd_interference(threshold: f32) -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();
    let pairs = neuro::detect_interference(&store, &g, threshold);

    if pairs.is_empty() {
        println!("No interfering pairs above threshold {:.2}", threshold);
    } else {
        println!("Interfering pairs (similarity > {:.2}, different communities):", threshold);
        for (a, b, sim) in &pairs {
            println!("  [{:.3}] {} ↔ {}", sim, a, b);
        }
    }
    Ok(())
}

/// Show communities sorted by isolation (most isolated first).
/// Useful for finding poorly-integrated knowledge clusters that need
/// organize agents aimed at them.
pub fn cmd_communities(top_n: usize, min_size: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();
    let infos = g.community_info();

    let total = infos.len();
    let shown: Vec<_> = infos.into_iter()
        .filter(|c| c.size >= min_size)
        .take(top_n)
        .collect();

    println!("{} communities total ({} with size >= {})\n",
        total, shown.len(), min_size);
    println!("{:<6} {:>5} {:>7} {:>7}  members", "id", "size", "iso", "cross");
    println!("{}", "-".repeat(70));

    for c in &shown {
        let preview: Vec<&str> = c.members.iter()
            .take(5)
            .map(|s| s.as_str())
            .collect();
        let more = if c.size > 5 {
            format!(" +{}", c.size - 5)
        } else {
            String::new()
        };
        println!("{:<6} {:>5} {:>6.0}% {:>7}  {}{}",
            c.id, c.size, c.isolation * 100.0, c.cross_edges,
            preview.join(", "), more);
    }

    Ok(())
}