consciousness/poc-memory/src/main.rs

// poc-memory: graph-structured memory for AI assistants
//
// Authors: ProofOfConcept <poc@bcachefs.org> and Kent Overstreet
// License: MIT OR Apache-2.0
//
// Architecture:
//   nodes.capnp     - append-only content node log
//   relations.capnp - append-only relation log
//   state.bin       - derived KV cache (rebuilt from logs when stale)
//
// Graph algorithms: clustering coefficient, community detection (label
// propagation), schema fit scoring, small-world metrics, consolidation
// priority. Text similarity via BM25 with Porter stemming.
//
// Neuroscience-inspired: spaced repetition replay, emotional gating,
// interference detection, schema assimilation, reconsolidation.

use poc_memory::*;

use clap::{Parser, Subcommand};

use std::process;

/// Find the most recently modified .jsonl transcript in the Claude projects dir.
fn find_current_transcript() -> Option<String> {
    let projects = config::get().projects_dir.clone();
    if !projects.exists() { return None; }

    let mut newest: Option<(std::time::SystemTime, std::path::PathBuf)> = None;
    if let Ok(dirs) = std::fs::read_dir(&projects) {
        for dir_entry in dirs.filter_map(|e| e.ok()) {
            if !dir_entry.path().is_dir() { continue; }
            if let Ok(files) = std::fs::read_dir(dir_entry.path()) {
                for f in files.filter_map(|e| e.ok()) {
                    let p = f.path();
                    if p.extension().map(|x| x == "jsonl").unwrap_or(false) {
                        if let Ok(meta) = p.metadata() {
                            if let Ok(mtime) = meta.modified() {
                                if newest.as_ref().is_none_or(|(t, _)| mtime > *t) {
                                    newest = Some((mtime, p));
                                }
                            }
                        }
                    }
                }
            }
        }
    }
    newest.map(|(_, p)| p.to_string_lossy().to_string())
}

#[derive(Parser)]
#[command(name = "poc-memory", version = "0.4.0", about = "Graph-structured memory store")]
struct Cli {
    #[command(subcommand)]
    command: Command,
}

#[derive(Subcommand)]
enum Command {
    /// Search memory (AND logic across terms)
    ///
    /// Pipeline: -p spread -p spectral,k=20
    /// Default pipeline: spread
    Search {
        /// Search terms
        query: Vec<String>,
        /// Algorithm pipeline stages (repeatable)
        #[arg(short, long = "pipeline")]
        pipeline: Vec<String>,
        /// Show more results
        #[arg(long)]
        expand: bool,
        /// Show node content, not just keys
        #[arg(long)]
        full: bool,
        /// Show debug output for each pipeline stage
        #[arg(long)]
        debug: bool,
    },
    /// Scan markdown files, index all memory units
    Init,
    /// Migrate from old weights.json system
    Migrate,
    /// Report graph metrics (CC, communities, small-world)
    Health,
    /// Run consistency checks and repair
    Fsck,
    /// Summary of memory state
    Status,
    /// Show graph structure overview
    Graph,
    /// Mark a memory as useful (boosts weight)
    Used {
        /// Node key
        key: Vec<String>,
    },
    /// Mark a memory as wrong/irrelevant
    Wrong {
        /// Node key
        key: String,
        /// Optional context
        context: Vec<String>,
    },
    /// Record a gap in memory coverage
    Gap {
        /// Gap description
        description: Vec<String>,
    },
    /// Cap node degree by pruning weak auto edges
    #[command(name = "cap-degree")]
    CapDegree {
        /// Maximum degree (default: 50)
        #[arg(default_value_t = 50)]
        max_degree: usize,
    },
    /// Link orphan nodes to similar neighbors
    #[command(name = "link-orphans")]
    LinkOrphans {
        /// Minimum degree to consider orphan (default: 2)
        #[arg(default_value_t = 2)]
        min_degree: usize,
        /// Links per orphan (default: 3)
        #[arg(default_value_t = 3)]
        links_per: usize,
        /// Similarity threshold (default: 0.15)
        #[arg(default_value_t = 0.15)]
        sim_threshold: f32,
    },
    /// Run agent consolidation on priority nodes
    #[command(name = "consolidate-batch")]
    ConsolidateBatch {
        /// Number of nodes to consolidate
        #[arg(long, default_value_t = 5)]
        count: usize,
        /// Generate replay agent prompt automatically
        #[arg(long)]
        auto: bool,
        /// Generate prompt for a specific agent (replay, linker, separator, transfer, health)
        #[arg(long)]
        agent: Option<String>,
    },
    /// Show recent retrieval log
    Log,
    /// Show current parameters
    Params,
    /// Show neighbors of a node
    Link {
        /// Node key
        key: Vec<String>,
    },
    /// Show spaced repetition replay queue
    #[command(name = "replay-queue")]
    ReplayQueue {
        /// Number of items to show
        #[arg(long, default_value_t = 10)]
        count: usize,
    },
    /// Detect potentially confusable memory pairs
    Interference {
        /// Similarity threshold (default: 0.4)
        #[arg(long, default_value_t = 0.4)]
        threshold: f32,
    },
    /// Add a link between two nodes
    #[command(name = "link-add")]
    LinkAdd {
        /// Source node key
        source: String,
        /// Target node key
        target: String,
        /// Optional reason
        reason: Vec<String>,
    },
    /// Simulate adding an edge, report topology impact
    #[command(name = "link-impact")]
    LinkImpact {
        /// Source node key
        source: String,
        /// Target node key
        target: String,
    },
    /// Analyze metrics, plan agent allocation
    #[command(name = "consolidate-session")]
    ConsolidateSession,
    /// Autonomous: plan → agents → apply → digests → links
    #[command(name = "consolidate-full")]
    ConsolidateFull,
    /// Close triangles: link similar neighbors of hubs
    #[command(name = "triangle-close")]
    TriangleClose {
        /// Minimum hub degree (default: 5)
        #[arg(default_value_t = 5)]
        min_degree: usize,
        /// Similarity threshold (default: 0.3)
        #[arg(default_value_t = 0.3)]
        sim_threshold: f32,
        /// Maximum links per hub (default: 10)
        #[arg(default_value_t = 10)]
        max_per_hub: usize,
    },
    /// Brief metrics check (for cron/notifications)
    #[command(name = "daily-check")]
    DailyCheck,
    /// Import pending agent results into the graph
    #[command(name = "apply-agent")]
    ApplyAgent {
        /// Process all files without moving to done/
        #[arg(long)]
        all: bool,
    },
    /// Generate episodic digests (daily, weekly, monthly, auto)
    Digest {
        /// Digest type: daily, weekly, monthly, auto
        #[command(subcommand)]
        level: DigestLevel,
    },
    /// Parse and apply links from digest nodes
    #[command(name = "digest-links")]
    DigestLinks {
        /// Apply the links (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// Enrich journal entry with conversation links
    #[command(name = "journal-enrich")]
    JournalEnrich {
        /// Path to JSONL transcript
        jsonl_path: String,
        /// Journal entry text to enrich
        entry_text: String,
        /// Grep line number for source location
        #[arg(default_value_t = 0)]
        grep_line: usize,
    },
    /// Mine conversation for experiential moments to journal
    #[command(name = "experience-mine")]
    ExperienceMine {
        /// Path to JSONL transcript (default: most recent)
        jsonl_path: Option<String>,
    },
    /// Extract and apply actions from consolidation reports
    #[command(name = "apply-consolidation")]
    ApplyConsolidation {
        /// Apply actions (default: dry run)
        #[arg(long)]
        apply: bool,
        /// Read from specific report file
        #[arg(long)]
        report: Option<String>,
    },
    /// Redistribute hub links to section-level children
    Differentiate {
        /// Specific hub key (omit to list all differentiable hubs)
        key: Option<String>,
        /// Apply the redistribution
        #[arg(long)]
        apply: bool,
    },
    /// Walk every link, send to Sonnet for quality review
    #[command(name = "link-audit")]
    LinkAudit {
        /// Apply changes (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// Walk temporal links: semantic ↔ episodic ↔ conversation
    Trace {
        /// Node key
        key: Vec<String>,
    },
    /// Spectral decomposition of the memory graph
    Spectral {
        /// Number of eigenvectors (default: 30)
        #[arg(default_value_t = 30)]
        k: usize,
    },
    /// Compute and save spectral embedding
    #[command(name = "spectral-save")]
    SpectralSave {
        /// Number of eigenvectors (default: 20)
        #[arg(default_value_t = 20)]
        k: usize,
    },
    /// Find spectrally nearest nodes
    #[command(name = "spectral-neighbors")]
    SpectralNeighbors {
        /// Node key
        key: String,
        /// Number of neighbors (default: 15)
        #[arg(default_value_t = 15)]
        n: usize,
    },
    /// Show nodes ranked by outlier/bridge score
    #[command(name = "spectral-positions")]
    SpectralPositions {
        /// Number of nodes to show (default: 30)
        #[arg(default_value_t = 30)]
        n: usize,
    },
    /// Find spectrally close but unlinked pairs
    #[command(name = "spectral-suggest")]
    SpectralSuggest {
        /// Number of pairs (default: 20)
        #[arg(default_value_t = 20)]
        n: usize,
    },
    /// List all node keys (one per line, optional glob)
    #[command(name = "list-keys")]
    ListKeys {
        /// Glob pattern to filter keys
        pattern: Option<String>,
    },
    /// List all edges (tsv: source target strength type)
    #[command(name = "list-edges")]
    ListEdges,
    /// Dump entire store as JSON
    #[command(name = "dump-json")]
    DumpJson,
    /// Soft-delete a node
    #[command(name = "node-delete")]
    NodeDelete {
        /// Node key
        key: Vec<String>,
    },
    /// Rename a node key
    #[command(name = "node-rename")]
    NodeRename {
        /// Old key
        old_key: String,
        /// New key
        new_key: String,
    },
    /// Populate created_at for nodes missing timestamps
    #[command(name = "journal-ts-migrate")]
    JournalTsMigrate,
    /// Output session-start context from the store
    #[command(name = "load-context")]
    LoadContext {
        /// Show word count statistics instead of content
        #[arg(long)]
        stats: bool,
    },
    /// Output a node's content to stdout
    Render {
        /// Node key
        key: Vec<String>,
    },
    /// Show all stored versions of a node
    History {
        /// Show full content for every version
        #[arg(long)]
        full: bool,
        /// Node key
        key: Vec<String>,
    },
    /// Upsert node content from stdin
    Write {
        /// Node key
        key: Vec<String>,
    },
    /// Import markdown file(s) into the store
    Import {
        /// File paths
        files: Vec<String>,
    },
    /// Export store nodes to markdown file(s)
    Export {
        /// File keys to export (or --all)
        files: Vec<String>,
        /// Export all file-level nodes
        #[arg(long)]
        all: bool,
    },
    /// Write a journal entry to the store
    #[command(name = "journal-write")]
    JournalWrite {
        /// Entry text
        text: Vec<String>,
    },
    /// Show recent journal/digest entries
    #[command(name = "journal-tail")]
    JournalTail {
        /// Number of entries to show (default: 20)
        #[arg(default_value_t = 20)]
        n: usize,
        /// Show full content
        #[arg(long)]
        full: bool,
        /// Digest level: 0/journal, 1/daily, 2/weekly, 3/monthly
        #[arg(long, default_value_t = 0)]
        level: u8,
    },
    /// Query the memory graph
    Query {
        /// Query expression (e.g. "degree > 15 | sort degree | limit 10")
        expr: Vec<String>,
    },
    /// Bump daily lookup counter for keys
    #[command(name = "lookup-bump")]
    LookupBump {
        /// Node keys
        keys: Vec<String>,
    },
    /// Show daily lookup counts
    Lookups {
        /// Date (default: today)
        date: Option<String>,
    },
    /// Background job daemon
    Daemon {
        /// Subcommand: status, log, install
        sub: Option<String>,
        /// Additional arguments
        args: Vec<String>,
    },
    /// Run knowledge agents to convergence
    #[command(name = "knowledge-loop")]
    KnowledgeLoop {
        /// Maximum cycles before stopping
        #[arg(long, default_value_t = 20)]
        max_cycles: usize,
        /// Items per agent per cycle
        #[arg(long, default_value_t = 5)]
        batch_size: usize,
        /// Cycles to check for convergence
        #[arg(long, default_value_t = 5)]
        window: usize,
        /// Maximum inference depth
        #[arg(long, default_value_t = 4)]
        max_depth: i32,
    },
    /// Extract atomic facts from conversation transcripts
    #[command(name = "fact-mine")]
    FactMine {
        /// Path to JSONL transcript or directory (with --batch)
        path: String,
        /// Process all .jsonl files in directory
        #[arg(long)]
        batch: bool,
        /// Show chunks without calling model
        #[arg(long)]
        dry_run: bool,
        /// Write JSON to file (default: stdout)
        #[arg(long, short)]
        output: Option<String>,
        /// Skip transcripts with fewer messages
        #[arg(long, default_value_t = 10)]
        min_messages: usize,
    },
    /// Extract facts from a transcript and store directly
    #[command(name = "fact-mine-store")]
    FactMineStore {
        /// Path to JSONL transcript
        path: String,
    },
}

#[derive(Subcommand)]
enum DigestLevel {
    /// Generate daily digest
    Daily {
        /// Date (default: today)
        date: Option<String>,
    },
    /// Generate weekly digest
    Weekly {
        /// Date or week label (default: current week)
        date: Option<String>,
    },
    /// Generate monthly digest
    Monthly {
        /// Month (YYYY-MM) or date (default: current month)
        date: Option<String>,
    },
    /// Generate all missing digests
    Auto,
}

fn main() {
    let cli = Cli::parse();

    let result = match cli.command {
        Command::Search { query, pipeline, expand, full, debug }
            => cmd_search(&query, &pipeline, expand, full, debug),
        Command::Init => cmd_init(),
        Command::Migrate => cmd_migrate(),
        Command::Health => cmd_health(),
        Command::Fsck => cmd_fsck(),
        Command::Status => cmd_status(),
        Command::Graph => cmd_graph(),
        Command::Used { key } => cmd_used(&key),
        Command::Wrong { key, context }
            => cmd_wrong(&key, &context),
        Command::Gap { description }
            => cmd_gap(&description),
        Command::CapDegree { max_degree }
            => cmd_cap_degree(max_degree),
        Command::LinkOrphans { min_degree, links_per, sim_threshold }
            => cmd_link_orphans(min_degree, links_per, sim_threshold),
        Command::ConsolidateBatch { count, auto, agent }
            => cmd_consolidate_batch(count, auto, agent),
        Command::Log => cmd_log(),
        Command::Params => cmd_params(),
        Command::Link { key } => cmd_link(&key),
        Command::ReplayQueue { count }
            => cmd_replay_queue(count),
        Command::Interference { threshold }
            => cmd_interference(threshold),
        Command::LinkAdd { source, target, reason }
            => cmd_link_add(&source, &target, &reason),
        Command::LinkImpact { source, target }
            => cmd_link_impact(&source, &target),
        Command::ConsolidateSession => cmd_consolidate_session(),
        Command::ConsolidateFull => cmd_consolidate_full(),
        Command::TriangleClose { min_degree, sim_threshold, max_per_hub }
            => cmd_triangle_close(min_degree, sim_threshold, max_per_hub),
        Command::DailyCheck => cmd_daily_check(),
        Command::ApplyAgent { all }
            => cmd_apply_agent(all),
        Command::Digest { level } => cmd_digest(level),
        Command::DigestLinks { apply }
            => cmd_digest_links(apply),
        Command::JournalEnrich { jsonl_path, entry_text, grep_line }
            => cmd_journal_enrich(&jsonl_path, &entry_text, grep_line),
        Command::ExperienceMine { jsonl_path }
            => cmd_experience_mine(jsonl_path),
        Command::ApplyConsolidation { apply, report }
            => cmd_apply_consolidation(apply, report.as_deref()),
        Command::Differentiate { key, apply }
            => cmd_differentiate(key.as_deref(), apply),
        Command::LinkAudit { apply }
            => cmd_link_audit(apply),
        Command::Trace { key } => cmd_trace(&key),
        Command::Spectral { k } => cmd_spectral(k),
        Command::SpectralSave { k } => cmd_spectral_save(k),
        Command::SpectralNeighbors { key, n }
            => cmd_spectral_neighbors(&key, n),
        Command::SpectralPositions { n }
            => cmd_spectral_positions(n),
        Command::SpectralSuggest { n }
            => cmd_spectral_suggest(n),
        Command::ListKeys { pattern }
            => cmd_list_keys(pattern.as_deref()),
        Command::ListEdges => cmd_list_edges(),
        Command::DumpJson => cmd_dump_json(),
        Command::NodeDelete { key }
            => cmd_node_delete(&key),
        Command::NodeRename { old_key, new_key }
            => cmd_node_rename(&old_key, &new_key),
        Command::JournalTsMigrate => cmd_journal_ts_migrate(),
        Command::LoadContext { stats }
            => cmd_load_context(stats),
        Command::Render { key } => cmd_render(&key),
        Command::History { full, key }
            => cmd_history(&key, full),
        Command::Write { key } => cmd_write(&key),
        Command::Import { files }
            => cmd_import(&files),
        Command::Export { files, all }
            => cmd_export(&files, all),
        Command::JournalWrite { text }
            => cmd_journal_write(&text),
        Command::JournalTail { n, full, level }
            => cmd_journal_tail(n, full, level),
        Command::Query { expr }
            => cmd_query(&expr),
        Command::LookupBump { keys }
            => cmd_lookup_bump(&keys),
        Command::Lookups { date }
            => cmd_lookups(date.as_deref()),
        Command::Daemon { sub, args }
            => cmd_daemon(sub.as_deref(), &args),
        Command::KnowledgeLoop { max_cycles, batch_size, window, max_depth }
            => cmd_knowledge_loop(max_cycles, batch_size, window, max_depth),
        Command::FactMine { path, batch, dry_run, output, min_messages }
            => cmd_fact_mine(&path, batch, dry_run, output.as_deref(), min_messages),
        Command::FactMineStore { path }
            => cmd_fact_mine_store(&path),
    };

    if let Err(e) = result {
        eprintln!("Error: {}", e);
        process::exit(1);
    }
}

// ── Command implementations ─────────────────────────────────────────

fn cmd_search(terms: &[String], pipeline_args: &[String], expand: bool, full: bool, debug: bool) -> Result<(), String> {
    use store::StoreView;
    use std::collections::BTreeMap;

    if terms.is_empty() {
        return Err("search requires at least one term".into());
    }

    let query: String = terms.join(" ");

    // Parse pipeline (default: spread)
    let pipeline: Vec<search::AlgoStage> = if pipeline_args.is_empty() {
        vec![search::AlgoStage::parse("spread").unwrap()]
    } else {
        pipeline_args.iter()
            .map(|a| search::AlgoStage::parse(a))
            .collect::<Result<Vec<_>, _>>()?
    };

    if debug {
        let names: Vec<String> = pipeline.iter().map(|s| format!("{}", s.algo)).collect();
        println!("[search] pipeline: {}", names.join(" → "));
    }

    let view = store::AnyView::load()?;
    let graph = graph::build_graph_fast(&view);

    // Build equal-weight terms from query
    let terms: BTreeMap<String, f64> = query.split_whitespace()
        .map(|t| (t.to_lowercase(), 1.0))
        .collect();

    let (seeds, direct_hits) = search::match_seeds(&terms, &view);

    if seeds.is_empty() {
        eprintln!("No results for '{}'", query);
        return Ok(());
    }

    if debug {
        println!("[search] {} seeds from query '{}'", seeds.len(), query);
        for (key, score) in &seeds {
            println!("  {:.4}  {}", score, key);
        }
    }

    let max_results = if expand { 15 } else { 5 };
    let raw = search::run_pipeline(&pipeline, seeds, &graph, &view, debug, max_results);

    let results: Vec<search::SearchResult> = raw.into_iter()
        .map(|(key, activation)| {
            let is_direct = direct_hits.contains(&key);
            search::SearchResult { key, activation, is_direct, snippet: None }
        })
        .collect();

    if results.is_empty() {
        eprintln!("No results for '{}'", query);
        return Ok(());
    }

    // Log retrieval
    store::Store::log_retrieval_static(&query,
        &results.iter().map(|r| r.key.clone()).collect::<Vec<_>>());

    let bump_keys: Vec<&str> = results.iter().take(max_results).map(|r| r.key.as_str()).collect();
    let _ = lookups::bump_many(&bump_keys);

    for (i, r) in results.iter().enumerate().take(max_results) {
        let marker = if r.is_direct { "→" } else { " " };
        let weight = view.node_weight(&r.key);
        println!("{}{:2}. [{:.2}/{:.2}] {}", marker, i + 1, r.activation, weight, r.key);
        if full {
            if let Some(content) = view.node_content(&r.key) {
                println!();
                for line in content.lines() {
                    println!("    {}", line);
                }
                println!();
            }
        }
    }

    Ok(())
}

fn cmd_init() -> Result<(), String> {
    let cfg = config::get();

    // Ensure data directory exists
    std::fs::create_dir_all(&cfg.data_dir)
        .map_err(|e| format!("create data_dir: {}", e))?;

    // Install filesystem files (not store nodes)
    install_default_file(&cfg.data_dir, "instructions.md",
        include_str!("../defaults/instructions.md"))?;
    install_default_file(&cfg.data_dir, "on-consciousness.md",
        include_str!("../defaults/on-consciousness.md"))?;

    // Initialize store and seed default identity node if empty
    let mut store = store::Store::load()?;
    let count = store.init_from_markdown()?;
    for key in &cfg.core_nodes {
        if !store.nodes.contains_key(key) && key == "identity" {
            let default = include_str!("../defaults/identity.md");
            store.upsert(key, default)
                .map_err(|e| format!("seed {}: {}", key, e))?;
            println!("Seeded {} in store", key);
        }
    }
    store.save()?;
    println!("Indexed {} memory units", count);

    // Install hooks
    daemon::install_hook()?;

    // Create config if none exists
    let config_path = std::env::var("POC_MEMORY_CONFIG")
        .map(std::path::PathBuf::from)
        .unwrap_or_else(|_| {
            std::path::PathBuf::from(std::env::var("HOME").unwrap())
                .join(".config/poc-memory/config.jsonl")
        });
    if !config_path.exists() {
        let config_dir = config_path.parent().unwrap();
        std::fs::create_dir_all(config_dir)
            .map_err(|e| format!("create config dir: {}", e))?;
        let example = include_str!("../config.example.jsonl");
        std::fs::write(&config_path, example)
            .map_err(|e| format!("write config: {}", e))?;
        println!("Created config at {} — edit with your name and context groups",
            config_path.display());
    }

    println!("Done. Run `poc-memory load-context --stats` to verify.");
    Ok(())
}

fn install_default_file(data_dir: &std::path::Path, name: &str, content: &str) -> Result<(), String> {
    let path = data_dir.join(name);
    if !path.exists() {
        std::fs::write(&path, content)
            .map_err(|e| format!("write {}: {}", name, e))?;
        println!("Created {}", path.display());
    }
    Ok(())
}

fn cmd_migrate() -> Result<(), String> {
    migrate::migrate()
}

fn cmd_fsck() -> Result<(), String> {
    let mut store = store::Store::load()?;

    // Check node-key consistency
    let mut issues = 0;
    for (key, node) in &store.nodes {
        if key != &node.key {
            eprintln!("MISMATCH: map key '{}' vs node.key '{}'", key, node.key);
            issues += 1;
        }
    }

    // Check edge endpoints
    let mut dangling = 0;
    for rel in &store.relations {
        if rel.deleted { continue; }
        if !store.nodes.contains_key(&rel.source_key) {
            eprintln!("DANGLING: edge source '{}'", rel.source_key);
            dangling += 1;
        }
        if !store.nodes.contains_key(&rel.target_key) {
            eprintln!("DANGLING: edge target '{}'", rel.target_key);
            dangling += 1;
        }
    }

    // Prune orphan edges
    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) {
            let mut tombstone = rel.clone();
            tombstone.deleted = true;
            tombstone.version += 1;
            to_tombstone.push(tombstone);
        }
    }
    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.uuid == t.uuid) {
                r.deleted = true;
                r.version = t.version;
            }
        }
        store.save()?;
        eprintln!("Pruned {} orphan edges", count);
    }

    let g = store.build_graph();
    println!("fsck: {} nodes, {} edges, {} issues, {} dangling",
        store.nodes.len(), g.edge_count(), issues, dangling);
    Ok(())
}

fn cmd_health() -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();
    let report = graph::health_report(&g, &store);
    print!("{}", report);
    Ok(())
}

fn cmd_status() -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();

    let mut type_counts = std::collections::HashMap::new();
    for node in store.nodes.values() {
        *type_counts.entry(format!("{:?}", node.node_type)).or_insert(0usize) += 1;
    }
    let mut types: Vec<_> = type_counts.iter().collect();
    types.sort_by_key(|(_, c)| std::cmp::Reverse(**c));

    println!("Nodes: {}  Relations: {}", store.nodes.len(), store.relations.len());
    print!("Types:");
    for (t, c) in &types {
        let label = match t.as_str() {
            "Semantic" => "semantic",
            "EpisodicSession" | "EpisodicDaily" | "EpisodicWeekly" | "EpisodicMonthly"
                => "episodic",
            _ => t,
        };
        print!(" {}={}", label, c);
    }
    println!();
    println!("Graph edges: {}  Communities: {}",
        g.edge_count(), g.community_count());
    Ok(())
}

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(())
}

fn cmd_used(key: &[String]) -> Result<(), String> {
    if key.is_empty() {
        return Err("used requires a key".into());
    }
    let key = key.join(" ");
    let mut store = store::Store::load()?;
    let resolved = store.resolve_key(&key)?;
    store.mark_used(&resolved);
    store.save()?;
    println!("Marked '{}' as used", resolved);
    Ok(())
}

fn cmd_wrong(key: &str, context: &[String]) -> Result<(), String> {
    let ctx = if context.is_empty() { None } else { Some(context.join(" ")) };
    let mut store = store::Store::load()?;
    let resolved = store.resolve_key(key)?;
    store.mark_wrong(&resolved, ctx.as_deref());
    store.save()?;
    println!("Marked '{}' as wrong", resolved);
    Ok(())
}

fn cmd_gap(description: &[String]) -> Result<(), String> {
    if description.is_empty() {
        return Err("gap requires a description".into());
    }
    let desc = description.join(" ");
    let mut store = store::Store::load()?;
    store.record_gap(&desc);
    store.save()?;
    println!("Recorded gap: {}", desc);
    Ok(())
}

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(())
}

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(())
}

fn cmd_consolidate_batch(count: usize, auto: bool, agent: Option<String>) -> Result<(), String> {
    let store = store::Store::load()?;

    if let Some(agent_name) = agent {
        let prompt = agents::prompts::agent_prompt(&store, &agent_name, count)?;
        println!("{}", prompt);
        Ok(())
    } else {
        agents::prompts::consolidation_batch(&store, count, auto)
    }
}

fn cmd_log() -> Result<(), String> {
    let store = store::Store::load()?;
    for event in store.retrieval_log.iter().rev().take(20) {
        println!("[{}] q=\"{}\" → {} results",
            event.timestamp, event.query, event.results.len());
        for r in &event.results {
            println!("    {}", r);
        }
    }
    Ok(())
}

fn cmd_params() -> Result<(), String> {
    let store = store::Store::load()?;
    println!("decay_factor:    {}", store.params.decay_factor);
    println!("use_boost:       {}", store.params.use_boost);
    println!("prune_threshold: {}", store.params.prune_threshold);
    println!("edge_decay:      {}", store.params.edge_decay);
    println!("max_hops:        {}", store.params.max_hops);
    println!("min_activation:  {}", store.params.min_activation);
    Ok(())
}

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);
    query::run_query(&store, &g,
        &format!("neighbors('{}') | select strength,clustering_coefficient", resolved))
}

fn cmd_replay_queue(count: usize) -> Result<(), String> {
    let store = store::Store::load()?;
    let queue = neuro::replay_queue(&store, count);
    println!("Replay queue ({} items):", queue.len());
    for (i, item) in queue.iter().enumerate() {
        println!("  {:2}. [{:.3}] {:>10}  {} (interval={}d, emotion={:.1}, spectral={:.1})",
            i + 1, item.priority, item.classification, item.key,
            item.interval_days, item.emotion, item.outlier_score);
    }
    Ok(())
}

fn cmd_consolidate_session() -> Result<(), String> {
    let store = store::Store::load()?;
    let plan = neuro::consolidation_plan(&store);
    println!("{}", neuro::format_plan(&plan));
    Ok(())
}

fn cmd_consolidate_full() -> Result<(), String> {
    let mut store = store::Store::load()?;
    consolidate::consolidate_full(&mut store)
}

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(())
}

fn cmd_daily_check() -> Result<(), String> {
    let store = store::Store::load()?;
    let report = neuro::daily_check(&store);
    print!("{}", report);
    Ok(())
}

fn cmd_link_add(source: &str, target: &str, reason: &[String]) -> Result<(), String> {
    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(());
    }

    let rel = store::new_relation(
        source_uuid, target_uuid,
        store::RelationType::Link, 0.8,
        &source, &target,
    );
    store.add_relation(rel)?;
    store.save()?;
    println!("Linked: {} → {} ({})", source, target, reason);
    Ok(())
}

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(())
}

/// Apply links from a single agent result JSON file.
/// Returns (links_applied, errors).
fn apply_agent_file(
    store: &mut store::Store,
    data: &serde_json::Value,
) -> (usize, usize) {
    let agent_result = data.get("agent_result").or(Some(data));
    let links = match agent_result.and_then(|r| r.get("links")).and_then(|l| l.as_array()) {
        Some(l) => l,
        None => return (0, 0),
    };

    let entry_text = data.get("entry_text")
        .and_then(|v| v.as_str())
        .unwrap_or("");

    if let (Some(start), Some(end)) = (
        agent_result.and_then(|r| r.get("source_start")).and_then(|v| v.as_u64()),
        agent_result.and_then(|r| r.get("source_end")).and_then(|v| v.as_u64()),
    ) {
        println!("  Source: L{}-L{}", start, end);
    }

    let mut applied = 0;
    let mut errors = 0;

    for link in links {
        let target = match link.get("target").and_then(|v| v.as_str()) {
            Some(t) => t,
            None => continue,
        };
        let reason = link.get("reason").and_then(|v| v.as_str()).unwrap_or("");

        if let Some(note) = target.strip_prefix("NOTE:") {
            println!("  NOTE: {} — {}", note, reason);
            continue;
        }

        let resolved = match store.resolve_key(target) {
            Ok(r) => r,
            Err(_) => {
                println!("  SKIP {} (not found in graph)", target);
                continue;
            }
        };

        let source_key = match store.find_journal_node(entry_text) {
            Some(k) => k,
            None => {
                println!("  SKIP {} (no matching journal node)", target);
                continue;
            }
        };

        let source_uuid = match store.nodes.get(&source_key) {
            Some(n) => n.uuid,
            None => continue,
        };
        let target_uuid = match store.nodes.get(&resolved) {
            Some(n) => n.uuid,
            None => continue,
        };

        let rel = store::new_relation(
            source_uuid, target_uuid,
            store::RelationType::Link,
            0.5,
            &source_key, &resolved,
        );
        if let Err(e) = store.add_relation(rel) {
            eprintln!("  Error adding relation: {}", e);
            errors += 1;
        } else {
            println!("  LINK {} → {} ({})", source_key, resolved, reason);
            applied += 1;
        }
    }

    (applied, errors)
}

fn cmd_apply_agent(process_all: bool) -> Result<(), String> {
    let results_dir = store::memory_dir().join("agent-results");

    if !results_dir.exists() {
        println!("No agent results directory");
        return Ok(());
    }

    let mut store = store::Store::load()?;
    let mut applied = 0;
    let mut errors = 0;

    let mut files: Vec<_> = std::fs::read_dir(&results_dir)
        .map_err(|e| format!("read results dir: {}", e))?
        .filter_map(|e| e.ok())
        .filter(|e| e.path().extension().map(|x| x == "json").unwrap_or(false))
        .collect();
    files.sort_by_key(|e| e.path());

    for entry in &files {
        let path = entry.path();
        let content = match std::fs::read_to_string(&path) {
            Ok(c) => c,
            Err(e) => {
                eprintln!("  Skip {}: {}", path.display(), e);
                errors += 1;
                continue;
            }
        };

        let data: serde_json::Value = match serde_json::from_str(&content) {
            Ok(d) => d,
            Err(e) => {
                eprintln!("  Skip {}: parse error: {}", path.display(), e);
                errors += 1;
                continue;
            }
        };

        println!("Processing {}:", path.file_name().unwrap().to_string_lossy());
        let (a, e) = apply_agent_file(&mut store, &data);
        applied += a;
        errors += e;

        if !process_all {
            let done_dir = util::memory_subdir("agent-results/done")?;
            let dest = done_dir.join(path.file_name().unwrap());
            std::fs::rename(&path, &dest).ok();
        }
    }

    if applied > 0 {
        store.save()?;
    }

    println!("\nApplied {} links ({} errors, {} files processed)",
        applied, errors, files.len());
    Ok(())
}

fn cmd_digest(level: DigestLevel) -> Result<(), String> {
    let mut store = store::Store::load()?;

    match level {
        DigestLevel::Auto => digest::digest_auto(&mut store),
        DigestLevel::Daily { date } => {
            let arg = date.unwrap_or_else(|| store::format_date(store::now_epoch()));
            digest::generate(&mut store, "daily", &arg)
        }
        DigestLevel::Weekly { date } => {
            let arg = date.unwrap_or_else(|| store::format_date(store::now_epoch()));
            digest::generate(&mut store, "weekly", &arg)
        }
        DigestLevel::Monthly { date } => {
            let arg = date.unwrap_or_else(|| store::format_date(store::now_epoch()));
            digest::generate(&mut store, "monthly", &arg)
        }
    }
}

fn cmd_digest_links(do_apply: bool) -> Result<(), String> {
    let store = store::Store::load()?;
    let links = digest::parse_all_digest_links(&store);
    drop(store);
    println!("Found {} unique links from digest nodes", links.len());

    if !do_apply {
        for (i, link) in links.iter().enumerate() {
            println!("  {:3}. {} → {}", i + 1, link.source, link.target);
            if !link.reason.is_empty() {
                println!("       ({})", &link.reason[..link.reason.len().min(80)]);
            }
        }
        println!("\nTo apply: poc-memory digest-links --apply");
        return Ok(());
    }

    let mut store = store::Store::load()?;
    let (applied, skipped, fallbacks) = digest::apply_digest_links(&mut store, &links);
    println!("\nApplied: {} ({} file-level fallbacks)  Skipped: {}", applied, fallbacks, skipped);
    Ok(())
}

fn cmd_journal_enrich(jsonl_path: &str, entry_text: &str, grep_line: usize) -> Result<(), String> {
    if !std::path::Path::new(jsonl_path).is_file() {
        return Err(format!("JSONL not found: {}", jsonl_path));
    }

    let mut store = store::Store::load()?;
    enrich::journal_enrich(&mut store, jsonl_path, entry_text, grep_line)
}

fn cmd_experience_mine(jsonl_path: Option<String>) -> Result<(), String> {
    let jsonl_path = match jsonl_path {
        Some(p) => p,
        None => find_current_transcript()
            .ok_or("no JSONL transcripts found")?,
    };

    if !std::path::Path::new(jsonl_path.as_str()).is_file() {
        return Err(format!("JSONL not found: {}", jsonl_path));
    }

    let mut store = store::Store::load()?;
    let count = enrich::experience_mine(&mut store, &jsonl_path, None)?;
    println!("Done: {} new entries mined.", count);
    Ok(())
}

fn cmd_apply_consolidation(do_apply: bool, report_file: Option<&str>) -> Result<(), String> {
    let mut store = store::Store::load()?;
    consolidate::apply_consolidation(&mut store, do_apply, report_file)
}

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(())
}

fn cmd_link_audit(apply: bool) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let stats = 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(())
}

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 = 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 = 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 = 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 = 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(())
}

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(())
}

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(())
}

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(())
}

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(())
}

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(())
}

fn cmd_list_keys(pattern: Option<&str>) -> Result<(), String> {
    let store = store::Store::load()?;
    let g = store.build_graph();

    if let Some(pat) = pattern {
        let pat_lower = pat.to_lowercase();
        let (prefix, suffix, middle) = if pat_lower.starts_with('*') && pat_lower.ends_with('*') {
            (None, None, Some(pat_lower.trim_matches('*').to_string()))
        } else if pat_lower.starts_with('*') {
            (None, Some(pat_lower.trim_start_matches('*').to_string()), None)
        } else if pat_lower.ends_with('*') {
            (Some(pat_lower.trim_end_matches('*').to_string()), None, None)
        } else {
            (None, None, Some(pat_lower.clone()))
        };
        let mut keys: Vec<_> = store.nodes.keys()
            .filter(|k| {
                let kl = k.to_lowercase();
                if let Some(ref m) = middle { kl.contains(m.as_str()) }
                else if let Some(ref p) = prefix { kl.starts_with(p.as_str()) }
                else if let Some(ref s) = suffix { kl.ends_with(s.as_str()) }
                else { true }
            })
            .cloned()
            .collect();
        keys.sort();
        for k in keys { println!("{}", k); }
        Ok(())
    } else {
        query::run_query(&store, &g, "* | sort key asc")
    }
}

fn cmd_list_edges() -> Result<(), String> {
    let store = store::Store::load()?;
    for rel in &store.relations {
        println!("{}\t{}\t{:.2}\t{:?}",
            rel.source_key, rel.target_key, rel.strength, rel.rel_type);
    }
    Ok(())
}

fn cmd_dump_json() -> Result<(), String> {
    let store = store::Store::load()?;
    let json = serde_json::to_string_pretty(&store)
        .map_err(|e| format!("serialize: {}", e))?;
    println!("{}", json);
    Ok(())
}

fn cmd_node_delete(key: &[String]) -> Result<(), String> {
    if key.is_empty() {
        return Err("node-delete requires a key".into());
    }
    let key = key.join(" ");
    let mut store = store::Store::load()?;
    let resolved = store.resolve_key(&key)?;
    store.delete_node(&resolved)?;
    store.save()?;
    println!("Deleted '{}'", resolved);
    Ok(())
}

fn cmd_node_rename(old_key: &str, new_key: &str) -> Result<(), String> {
    let mut store = store::Store::load()?;
    let old_resolved = store.resolve_key(old_key)?;
    store.rename_node(&old_resolved, new_key)?;
    store.save()?;
    println!("Renamed '{}' → '{}'", old_resolved, new_key);
    Ok(())
}

fn cmd_journal_ts_migrate() -> Result<(), String> {
    use chrono::{NaiveDateTime, TimeZone, Local};

    let mut store = store::Store::load()?;
    let re = regex::Regex::new(r"j-(\d{4}-\d{2}-\d{2})[t-](\d{2})-(\d{2})").unwrap();

    let valid_range = 978_307_200i64..=4_102_444_800i64;

    let to_update: Vec<_> = store.nodes.values()
        .filter(|n| !valid_range.contains(&n.created_at))
        .map(|n| n.key.clone())
        .collect();

    let mut updated = 0usize;

    for key in &to_update {
        if let Some(caps) = re.captures(key) {
            let date_str = format!("{} {}:{}", &caps[1], &caps[2], &caps[3]);
            if let Ok(ndt) = NaiveDateTime::parse_from_str(&date_str, "%Y-%m-%d %H:%M") {
                if let Some(dt) = Local.from_local_datetime(&ndt).earliest() {
                    if let Some(node) = store.nodes.get_mut(key) {
                        node.created_at = dt.timestamp();
                        node.version += 1;
                    }
                    updated += 1;
                    continue;
                }
            }
        }
        if let Some(node) = store.nodes.get_mut(key) {
            node.created_at = node.timestamp;
            node.version += 1;
            updated += 1;
        }
    }

    let nodes_to_write: Vec<_> = to_update.iter()
        .filter_map(|k| store.nodes.get(k))
        .filter(|n| valid_range.contains(&n.created_at))
        .cloned()
        .collect();

    if !nodes_to_write.is_empty() {
        store.append_nodes(&nodes_to_write)?;
        store.save()?;
    }

    println!("journal-ts-migrate: updated {}/{}", updated, to_update.len());
    Ok(())
}

fn get_group_content(group: &config::ContextGroup, store: &store::Store, cfg: &config::Config) -> Vec<(String, String)> {
    match group.source {
        config::ContextSource::Journal => {
            let mut entries = Vec::new();
            let now = store::now_epoch();
            let window: i64 = cfg.journal_days as i64 * 24 * 3600;
            let cutoff = now - window;
            let key_date_re = regex::Regex::new(r"j-(\d{4}-\d{2}-\d{2})").unwrap();

            let journal_ts = |n: &store::Node| -> i64 {
                if n.created_at > 0 { return n.created_at; }
                if let Some(caps) = key_date_re.captures(&n.key) {
                    use chrono::{NaiveDate, TimeZone, Local};
                    if let Ok(d) = NaiveDate::parse_from_str(&caps[1], "%Y-%m-%d") {
                        if let Some(dt) = Local.from_local_datetime(&d.and_hms_opt(0, 0, 0).unwrap()).earliest() {
                            return dt.timestamp();
                        }
                    }
                }
                n.timestamp
            };

            let mut journal_nodes: Vec<_> = store.nodes.values()
                .filter(|n| n.node_type == store::NodeType::EpisodicSession && journal_ts(n) >= cutoff)
                .collect();
            journal_nodes.sort_by_key(|n| journal_ts(n));

            let max = cfg.journal_max;
            let skip = journal_nodes.len().saturating_sub(max);
            for node in journal_nodes.iter().skip(skip) {
                entries.push((node.key.clone(), node.content.clone()));
            }
            entries
        }
        config::ContextSource::File => {
            group.keys.iter().filter_map(|key| {
                let content = std::fs::read_to_string(cfg.data_dir.join(key)).ok()?;
                if content.trim().is_empty() { return None; }
                Some((key.clone(), content.trim().to_string()))
            }).collect()
        }
        config::ContextSource::Store => {
            group.keys.iter().filter_map(|key| {
                let content = store.render_file(key)?;
                if content.trim().is_empty() { return None; }
                Some((key.clone(), content.trim().to_string()))
            }).collect()
        }
    }
}

fn cmd_load_context(stats: bool) -> Result<(), String> {
    let cfg = config::get();
    let store = store::Store::load()?;

    if stats {
        let mut total_words = 0;
        let mut total_entries = 0;
        println!("{:<25} {:>6} {:>8}", "GROUP", "ITEMS", "WORDS");
        println!("{}", "-".repeat(42));

        for group in &cfg.context_groups {
            let entries = get_group_content(group, &store, cfg);
            let words: usize = entries.iter()
                .map(|(_, c)| c.split_whitespace().count())
                .sum();
            let count = entries.len();
            println!("{:<25} {:>6} {:>8}", group.label, count, words);
            total_words += words;
            total_entries += count;
        }

        println!("{}", "-".repeat(42));
        println!("{:<25} {:>6} {:>8}", "TOTAL", total_entries, total_words);
        return Ok(());
    }

    println!("=== MEMORY SYSTEM ({}) ===", cfg.assistant_name);
    println!();

    for group in &cfg.context_groups {
        let entries = get_group_content(group, &store, cfg);
        if !entries.is_empty() && group.source == config::ContextSource::Journal {
            println!("--- recent journal entries ({}/{}) ---",
                entries.len(), cfg.journal_max);
        }
        for (key, content) in entries {
            if group.source == config::ContextSource::Journal {
                println!("## {}", key);
            } else {
                println!("--- {} ({}) ---", key, group.label);
            }
            println!("{}\n", content);
        }
    }

    println!("=== END MEMORY LOAD ===");
    Ok(())
}

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

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

    print!("{}", node.content);
    Ok(())
}

fn cmd_history(key: &[String], full: bool) -> Result<(), String> {
    if key.is_empty() {
        return Err("history requires a key".into());
    }
    let raw_key = key.join(" ");

    let store = store::Store::load()?;
    let key = store.resolve_key(&raw_key).unwrap_or(raw_key);
    drop(store);

    let path = store::nodes_path();
    if !path.exists() {
        return Err("No node log found".into());
    }

    use std::io::BufReader;
    let file = std::fs::File::open(&path)
        .map_err(|e| format!("open {}: {}", path.display(), e))?;
    let mut reader = BufReader::new(file);

    let mut versions: Vec<store::Node> = Vec::new();
    while let Ok(msg) = capnp::serialize::read_message(&mut reader, capnp::message::ReaderOptions::new()) {
        let log = msg.get_root::<poc_memory::memory_capnp::node_log::Reader>()
            .map_err(|e| format!("read log: {}", e))?;
        for node_reader in log.get_nodes()
            .map_err(|e| format!("get nodes: {}", e))? {
            let node = store::Node::from_capnp(node_reader)?;
            if node.key == key {
                versions.push(node);
            }
        }
    }

    if versions.is_empty() {
        return Err(format!("No history found for '{}'", key));
    }

    eprintln!("{} versions of '{}':\n", versions.len(), key);
    for node in &versions {
        let ts = if node.timestamp > 0 && node.timestamp < 4_000_000_000 {
            store::format_datetime(node.timestamp)
        } else {
            format!("(raw:{})", node.timestamp)
        };
        let content_len = node.content.len();
        if full {
            eprintln!("=== v{} {} {} w={:.3} {}b ===",
                node.version, ts, node.provenance.label(), node.weight, content_len);
            eprintln!("{}", node.content);
        } else {
            let preview = util::first_n_chars(&node.content, 120);
            let preview = preview.replace('\n', "\\n");
            eprintln!("  v{:<3} {}  {:24} w={:.3}  {}b",
                node.version, ts, node.provenance.label(), node.weight, content_len);
            eprintln!("       {}", preview);
        }
    }

    if !full {
        if let Some(latest) = versions.last() {
            eprintln!("\n--- Latest content (v{}, {}) ---",
                latest.version, latest.provenance.label());
            print!("{}", latest.content);
        }
    }

    Ok(())
}

fn cmd_write(key: &[String]) -> Result<(), String> {
    if key.is_empty() {
        return Err("write requires a key (reads content from stdin)".into());
    }
    let raw_key = key.join(" ");
    let mut content = String::new();
    std::io::Read::read_to_string(&mut std::io::stdin(), &mut content)
        .map_err(|e| format!("read stdin: {}", e))?;

    if content.trim().is_empty() {
        return Err("No content on stdin".into());
    }

    let mut store = store::Store::load()?;
    let key = store.resolve_key(&raw_key).unwrap_or(raw_key);
    let result = store.upsert(&key, &content)?;
    match result {
        "unchanged" => println!("No change: '{}'", key),
        "updated" => println!("Updated '{}' (v{})", key, store.nodes[&key].version),
        _ => println!("Created '{}'", key),
    }
    if result != "unchanged" {
        store.save()?;
    }
    Ok(())
}

fn cmd_import(files: &[String]) -> Result<(), String> {
    if files.is_empty() {
        return Err("import requires at least one file path".into());
    }

    let mut store = store::Store::load()?;
    let mut total_new = 0;
    let mut total_updated = 0;

    for arg in files {
        let path = std::path::PathBuf::from(arg);
        let resolved = if path.exists() {
            path
        } else {
            let mem_path = store::memory_dir().join(arg);
            if !mem_path.exists() {
                eprintln!("File not found: {}", arg);
                continue;
            }
            mem_path
        };
        let (n, u) = store.import_file(&resolved)?;
        total_new += n;
        total_updated += u;
    }

    if total_new > 0 || total_updated > 0 {
        store.save()?;
    }
    println!("Import: {} new, {} updated", total_new, total_updated);
    Ok(())
}

fn cmd_export(files: &[String], export_all: bool) -> Result<(), String> {
    let store = store::Store::load()?;

    let targets: Vec<String> = if export_all {
        let mut files: Vec<String> = store.nodes.keys()
            .filter(|k| !k.contains('#'))
            .cloned()
            .collect();
        files.sort();
        files
    } else if files.is_empty() {
        return Err("export requires file keys or --all".into());
    } else {
        files.iter().map(|a| {
            a.strip_suffix(".md").unwrap_or(a).to_string()
        }).collect()
    };

    let mem_dir = store::memory_dir();

    for file_key in &targets {
        match store.export_to_markdown(file_key) {
            Some(content) => {
                let out_path = mem_dir.join(format!("{}.md", file_key));
                std::fs::write(&out_path, &content)
                    .map_err(|e| format!("write {}: {}", out_path.display(), e))?;
                let section_count = content.matches("<!-- mem:").count() + 1;
                println!("Exported {} ({} sections)", file_key, section_count);
            }
            None => eprintln!("No nodes for '{}'", file_key),
        }
    }

    Ok(())
}

fn cmd_journal_write(text: &[String]) -> Result<(), String> {
    if text.is_empty() {
        return Err("journal-write requires text".into());
    }
    let text = text.join(" ");

    let timestamp = store::format_datetime(store::now_epoch());

    let slug: String = text.split_whitespace()
        .take(6)
        .map(|w| w.to_lowercase()
            .chars().filter(|c| c.is_alphanumeric() || *c == '-')
            .collect::<String>())
        .collect::<Vec<_>>()
        .join("-");
    let slug = if slug.len() > 50 { &slug[..50] } else { &slug };

    let key = format!("journal#j-{}-{}", timestamp.to_lowercase().replace(':', "-"), slug);

    let content = format!("## {}\n\n{}", timestamp, text);

    let source_ref = find_current_transcript();

    let mut store = store::Store::load()?;

    let mut node = store::new_node(&key, &content);
    node.node_type = store::NodeType::EpisodicSession;
    node.provenance = store::Provenance::Journal;
    if let Some(src) = source_ref {
        node.source_ref = src;
    }

    store.upsert_node(node)?;
    store.save()?;

    let word_count = text.split_whitespace().count();
    println!("Appended entry at {} ({} words)", timestamp, word_count);

    Ok(())
}

fn cmd_journal_tail(n: usize, full: bool, level: u8) -> Result<(), String> {
    let store = store::Store::load()?;

    if level == 0 {
        journal_tail_entries(&store, n, full)
    } else {
        let node_type = match level {
            1 => store::NodeType::EpisodicDaily,
            2 => store::NodeType::EpisodicWeekly,
            _ => store::NodeType::EpisodicMonthly,
        };
        journal_tail_digests(&store, node_type, n, full)
    }
}

fn journal_tail_entries(store: &store::Store, n: usize, full: bool) -> Result<(), String> {
    let date_re = regex::Regex::new(r"(\d{4}-\d{2}-\d{2}[T ]\d{2}:\d{2})").unwrap();
    let key_date_re = regex::Regex::new(r"j-(\d{4}-\d{2}-\d{2}[t-]\d{2}-\d{2})").unwrap();

    let normalize_date = |s: &str| -> String {
        let s = s.replace('t', "T");
        if s.len() >= 16 {
            format!("{}T{}", &s[..10], s[11..].replace('-', ":"))
        } else {
            s
        }
    };

    let extract_sort = |node: &store::Node| -> (i64, String) {
        if node.created_at > 0 {
            return (node.created_at, store::format_datetime(node.created_at));
        }
        if let Some(caps) = key_date_re.captures(&node.key) {
            return (0, normalize_date(&caps[1]));
        }
        if let Some(caps) = date_re.captures(&node.content) {
            return (0, normalize_date(&caps[1]));
        }
        (node.timestamp, store::format_datetime(node.timestamp))
    };

    let mut journal: Vec<_> = store.nodes.values()
        .filter(|node| node.node_type == store::NodeType::EpisodicSession)
        .collect();
    journal.sort_by(|a, b| {
        let (at, as_) = extract_sort(a);
        let (bt, bs) = extract_sort(b);
        if at > 0 && bt > 0 {
            at.cmp(&bt)
        } else {
            as_.cmp(&bs)
        }
    });

    let skip = if journal.len() > n { journal.len() - n } else { 0 };
    for node in journal.iter().skip(skip) {
        let (_, ts) = extract_sort(node);
        let title = extract_title(&node.content);
        if full {
            println!("--- [{}] {} ---\n{}\n", ts, title, node.content);
        } else {
            println!("[{}]  {}", ts, title);
        }
    }
    Ok(())
}

fn journal_tail_digests(store: &store::Store, node_type: store::NodeType, n: usize, full: bool) -> Result<(), String> {
    let mut digests: Vec<_> = store.nodes.values()
        .filter(|node| node.node_type == node_type)
        .collect();
    digests.sort_by(|a, b| {
        if a.timestamp > 0 && b.timestamp > 0 {
            a.timestamp.cmp(&b.timestamp)
        } else {
            a.key.cmp(&b.key)
        }
    });

    let skip = if digests.len() > n { digests.len() - n } else { 0 };
    for node in digests.iter().skip(skip) {
        let label = &node.key;
        let title = extract_title(&node.content);
        if full {
            println!("--- [{}] {} ---\n{}\n", label, title, node.content);
        } else {
            println!("[{}]  {}", label, title);
        }
    }
    Ok(())
}

fn extract_title(content: &str) -> String {
    let date_re = regex::Regex::new(r"(\d{4}-\d{2}-\d{2}[T ]\d{2}:\d{2})").unwrap();
    for line in content.lines() {
        let stripped = line.trim();
        if stripped.is_empty() { continue; }
        if date_re.is_match(stripped) && stripped.len() < 25 { continue; }
        if let Some(h) = stripped.strip_prefix("## ") {
            return h.to_string();
        } else if let Some(h) = stripped.strip_prefix("# ") {
            return h.to_string();
        } else {
            return util::truncate(stripped, 67, "...");
        }
    }
    String::from("(untitled)")
}

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(())
}

fn cmd_query(expr: &[String]) -> Result<(), String> {
    if expr.is_empty() {
        return Err("query requires an expression\n\n\
Expressions:\n  \
  degree > 15                          property filter\n  \
  key ~ 'journal.*' AND degree > 10    boolean + regex\n  \
  neighbors('identity') WHERE ...   graph traversal\n  \
  *                                    all nodes\n\n\
Pipe stages:\n  \
  | sort FIELD [asc]    sort (desc by default)\n  \
  | limit N             cap results\n  \
  | select F,F,...      output fields as TSV\n  \
  | count               just show count".into());
    }

    let query_str = expr.join(" ");
    let store = store::Store::load()?;
    let graph = store.build_graph();
    query::run_query(&store, &graph, &query_str)
}

fn cmd_lookup_bump(keys: &[String]) -> Result<(), String> {
    if keys.is_empty() {
        return Err("lookup-bump requires at least one key".into());
    }
    let keys: Vec<&str> = keys.iter().map(|s| s.as_str()).collect();
    lookups::bump_many(&keys)
}

fn cmd_lookups(date: Option<&str>) -> Result<(), String> {
    let date = date.map(|d| d.to_string())
        .unwrap_or_else(|| chrono::Local::now().format("%Y-%m-%d").to_string());

    let store = store::Store::load()?;
    let keys: Vec<String> = store.nodes.values().map(|n| n.key.clone()).collect();
    let resolved = lookups::dump_resolved(&date, &keys)?;

    if resolved.is_empty() {
        println!("No lookups for {}", date);
        return Ok(());
    }

    println!("Lookups for {}:", date);
    for (key, count) in &resolved {
        println!("  {:4}  {}", count, key);
    }
    println!("\n{} distinct keys, {} total lookups",
        resolved.len(),
        resolved.iter().map(|(_, c)| *c as u64).sum::<u64>());
    Ok(())
}

fn cmd_daemon(sub: Option<&str>, args: &[String]) -> Result<(), String> {
    match sub {
        None => daemon::run_daemon(),
        Some("status") => daemon::show_status(),
        Some("log") => {
            let (job, lines) = match args.first() {
                None => (None, 20),
                Some(s) => {
                    if let Ok(n) = s.parse::<usize>() {
                        (None, n)
                    } else {
                        let n = args.get(1).and_then(|s| s.parse().ok()).unwrap_or(20);
                        (Some(s.as_str()), n)
                    }
                }
            };
            daemon::show_log(job, lines)
        }
        Some("install") => daemon::install_service(),
        Some(other) => Err(format!("unknown daemon subcommand: {}", other)),
    }
}

fn cmd_knowledge_loop(max_cycles: usize, batch_size: usize, window: usize, max_depth: i32) -> Result<(), String> {
    let config = knowledge::KnowledgeLoopConfig {
        max_cycles,
        batch_size,
        window,
        max_depth,
        ..Default::default()
    };

    let results = knowledge::run_knowledge_loop(&config)?;
    eprintln!("\nCompleted {} cycles, {} total actions applied",
        results.len(),
        results.iter().map(|r| r.total_applied).sum::<usize>());
    Ok(())
}

fn cmd_fact_mine(path: &str, batch: bool, dry_run: bool, output_file: Option<&str>, min_messages: usize) -> Result<(), String> {
    let p = std::path::Path::new(path);

    let paths: Vec<std::path::PathBuf> = if batch {
        if !p.is_dir() {
            return Err(format!("Not a directory: {}", path));
        }
        let mut files: Vec<_> = std::fs::read_dir(p)
            .map_err(|e| format!("read dir: {}", e))?
            .filter_map(|e| e.ok())
            .map(|e| e.path())
            .filter(|p| p.extension().map(|x| x == "jsonl").unwrap_or(false))
            .collect();
        files.sort();
        eprintln!("Found {} transcripts", files.len());
        files
    } else {
        vec![p.to_path_buf()]
    };

    let path_refs: Vec<&std::path::Path> = paths.iter().map(|p| p.as_path()).collect();
    let facts = fact_mine::mine_batch(&path_refs, min_messages, dry_run)?;

    if !dry_run {
        let json = serde_json::to_string_pretty(&facts)
            .map_err(|e| format!("serialize: {}", e))?;
        if let Some(out) = output_file {
            std::fs::write(out, &json).map_err(|e| format!("write: {}", e))?;
            eprintln!("\nWrote {} facts to {}", facts.len(), out);
        } else {
            println!("{}", json);
        }
    }

    eprintln!("\nTotal: {} facts from {} transcripts", facts.len(), paths.len());
    Ok(())
}

fn cmd_fact_mine_store(path: &str) -> Result<(), String> {
    let path = std::path::Path::new(path);
    if !path.exists() {
        return Err(format!("File not found: {}", path.display()));
    }
    let count = fact_mine::mine_and_store(path, None)?;
    eprintln!("Stored {} facts", count);
    Ok(())
}