consciousness/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.
#[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 {
    // ── Core (daily use) ──────────────────────────────────────────────

    /// 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,
        /// Also match key components (e.g. "irc" matches "irc-access")
        #[arg(long)]
        fuzzy: bool,
        /// Also search node content (slow, use when graph search misses)
        #[arg(long)]
        content: bool,
    },
    /// Output a node's content to stdout
    Render {
        /// Node key
        key: Vec<String>,
    },
    /// Upsert node content from stdin
    Write {
        /// Node key
        key: Vec<String>,
    },
    /// Edit a node in $EDITOR
    Edit {
        /// 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>,
    },
    /// Show most recent writes to the node log
    Tail {
        /// Number of entries (default: 20)
        #[arg(default_value_t = 20)]
        n: usize,
        /// Show full content
        #[arg(long)]
        full: bool,
        /// Filter by provenance (substring match, e.g. "surface-observe")
        #[arg(long, short)]
        provenance: Option<String>,
        /// Show all versions (default: dedup to latest per key)
        #[arg(long)]
        all_versions: bool,
    },
    /// Summary of memory state
    Status,
    /// Query the memory graph
    #[command(after_long_help = "\
EXPRESSIONS:
  *                                all nodes
  key ~ 'pattern'                  regex match on node key
  content ~ 'phrase'               regex match on node content
  degree > 15                      numeric comparison on any field
  field = value                    exact match
  field != value                   not equal
  expr AND expr                    boolean AND
  expr OR expr                     boolean OR
  NOT expr                         negation
  neighbors('key')                 nodes linked to key
  neighbors('key') WHERE expr      ... with filter on edges/nodes

FIELDS:
  key, weight, content, degree, node_type, provenance,
  emotion, retrievals, uses, wrongs, created,
  clustering_coefficient (cc), community_id

OPERATORS:
  >  <  >=  <=  =  !=  ~(regex)

PIPE STAGES:
  | sort FIELD [asc]               sort (desc by default)
  | limit N                        cap results
  | select F,F,...                 output fields as TSV
  | count                          just show count
  | connectivity                   show graph structure between results

FUNCTIONS:
  community('key')                 community id of a node
  degree('key')                    degree of a node

EXAMPLES:
  key ~ 'inner-life'                         substring match on keys
  content ~ 'made love'                      full-text search
  content ~ 'made love' | connectivity       find clusters among results
  (content ~ 'A' OR content ~ 'B') | connectivity
  degree > 15 | sort degree | limit 10       high-degree nodes
  key ~ 'journal' AND degree > 10 | count    count matching nodes
  neighbors('identity') WHERE strength > 0.5 | sort strength
  * | sort weight asc | limit 20             lowest-weight nodes
")]
    Query {
        /// Query expression (e.g. "key ~ 'inner-life'")
        expr: Vec<String>,
    },
    /// 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>,
    },
    /// Mark a search result as not relevant (weakens edges that led to it)
    #[command(name = "not-relevant")]
    NotRelevant {
        /// Node key that was not relevant
        key: String,
    },
    /// Mark a node as not useful (weakens node weight, not edges)
    #[command(name = "not-useful")]
    NotUseful {
        /// Node key
        key: String,
    },
    /// Set a node's weight directly
    #[command(name = "weight-set")]
    WeightSet {
        /// Node key
        key: String,
        /// Weight (0.01 to 1.0)
        weight: f32,
    },
    /// Record a gap in memory coverage
    Gap {
        /// Gap description
        description: Vec<String>,
    },

    // ── Node operations ───────────────────────────────────────────────

    /// Node operations (delete, rename, list)
    #[command(subcommand)]
    Node(NodeCmd),

    // ── Journal ───────────────────────────────────────────────────────

    /// Journal operations (write, tail, enrich)
    #[command(subcommand)]
    Journal(JournalCmd),

    // ── Graph ─────────────────────────────────────────────────────────

    /// Graph operations (link, audit, spectral)
    #[command(subcommand, name = "graph")]
    GraphCmd(GraphCmd),

    // ── Cursor (spatial memory) ──────────────────────────────────────

    /// Navigate the memory graph with a persistent cursor
    #[command(subcommand)]
    Cursor(CursorCmd),

    // ── Agents ────────────────────────────────────────────────────────

    /// Agent and daemon operations
    #[command(subcommand)]
    Agent(AgentCmd),

    // ── Admin ─────────────────────────────────────────────────────────

    /// Admin operations (fsck, health, import, export)
    #[command(subcommand)]
    Admin(AdminCmd),
}

#[derive(Subcommand)]
enum NodeCmd {
    /// Soft-delete a node
    Delete {
        /// Node key
        key: Vec<String>,
    },
    /// Rename a node key
    Rename {
        /// Old key
        old_key: String,
        /// New key
        new_key: String,
    },
    /// List all node keys (one per line, optional glob)
    #[command(name = "list")]
    List {
        /// Glob pattern to filter keys
        pattern: Option<String>,
    },
    /// List all edges (tsv: source target strength type)
    Edges,
    /// Dump entire store as JSON
    #[command(name = "dump")]
    Dump,
}

#[derive(Subcommand)]
enum CursorCmd {
    /// Show current cursor position with context
    Show,
    /// Set cursor to a node key
    Set {
        /// Node key
        key: Vec<String>,
    },
    /// Move cursor forward in time
    Forward,
    /// Move cursor backward in time
    Back,
    /// Move up the digest hierarchy (journal→daily→weekly→monthly)
    Up,
    /// Move down the digest hierarchy (to first child)
    Down,
    /// Clear the cursor
    Clear,
}

#[derive(Subcommand)]
enum JournalCmd {
    /// Write a journal entry to the store
    Write {
        /// Entry name (becomes the node key)
        name: String,
        /// Entry text
        text: Vec<String>,
    },
    /// Show recent journal/digest entries
    Tail {
        /// 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,
    },
    /// Enrich journal entry with conversation links
    Enrich {
        /// 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,
    },
}

#[derive(Subcommand)]
enum GraphCmd {
    /// Show neighbors of a node
    Link {
        /// Node key
        key: Vec<String>,
    },
    /// Find related nodes via spreading activation from seed nodes
    Spread {
        /// Seed node keys
        keys: Vec<String>,
        /// Maximum results (default: 20)
        #[arg(short = 'n', default_value_t = 20)]
        max_results: usize,
    },
    /// 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>,
    },
    /// Set strength of an existing link
    #[command(name = "link-set")]
    LinkSet {
        /// Source node key
        source: String,
        /// Target node key
        target: String,
        /// Strength (0.0–1.0)
        strength: f32,
    },
    /// Simulate adding an edge, report topology impact
    #[command(name = "link-impact")]
    LinkImpact {
        /// Source node key
        source: String,
        /// Target node key
        target: String,
    },
    /// Walk every link, send to Sonnet for quality review
    #[command(name = "link-audit")]
    LinkAudit {
        /// Apply changes (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// 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,
    },
    /// 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,
    },
    /// 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,
    },
    /// Set link strengths from neighborhood overlap (Jaccard similarity)
    #[command(name = "normalize-strengths")]
    NormalizeStrengths {
        /// Apply changes (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// 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 temporal links: semantic ↔ episodic ↔ conversation
    Trace {
        /// Node key
        key: Vec<String>,
    },
    /// Detect potentially confusable memory pairs
    Interference {
        /// Similarity threshold (default: 0.4)
        #[arg(long, default_value_t = 0.4)]
        threshold: f32,
    },
    /// Show communities sorted by isolation (most isolated first)
    Communities {
        /// Number of communities to show
        #[arg(default_value_t = 20)]
        top_n: usize,
        /// Minimum community size to show
        #[arg(long, default_value_t = 2)]
        min_size: usize,
    },
    /// Show graph structure overview
    Overview,
    /// 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,
    },
    /// Diagnose duplicate/overlapping nodes for a topic cluster
    Organize {
        /// Search term (matches node keys; also content unless --key-only)
        term: String,
        /// Similarity threshold for pair reporting (default: 0.4)
        #[arg(long, default_value_t = 0.4)]
        threshold: f32,
        /// Only match node keys, not content
        #[arg(long)]
        key_only: bool,
        /// Create anchor node for the search term and link to cluster
        #[arg(long)]
        anchor: bool,
    },
}

#[derive(Subcommand)]
enum DaemonCmd {
    /// Start the daemon (default)
    Start,
    /// Show daemon status
    Status,
    /// Show daemon log
    Log {
        /// Job name to filter by
        job: Option<String>,
        /// Tail a task's log file (drill down from daemon log)
        #[arg(long)]
        task: Option<String>,
        /// Number of lines to show
        #[arg(long, default_value_t = 20)]
        lines: usize,
    },
    /// Install systemd service
    Install,
    /// Trigger consolidation via daemon
    Consolidate,
    /// Run an agent via the daemon
    Run {
        /// Agent name (e.g. organize, replay, linker)
        #[arg(default_value = "replay")]
        agent: String,
        /// Batch size
        #[arg(default_value_t = 1)]
        count: usize,
    },
    /// Interactive TUI
    Tui,
    /// Reload config file without restarting
    ReloadConfig,
}

#[derive(Subcommand)]
enum AgentCmd {
    /// Background job daemon
    #[command(subcommand)]
    Daemon(DaemonCmd),
    /// 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,
    },
    /// 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>,
    },
    /// Analyze metrics, plan agent allocation
    #[command(name = "consolidate-session")]
    ConsolidateSession,
    /// Autonomous: plan → agents → apply → digests → links
    #[command(name = "consolidate-full")]
    ConsolidateFull,
    /// Import pending agent results into the graph
    #[command(name = "apply-agent")]
    ApplyAgent {
        /// Process all files without moving to done/
        #[arg(long)]
        all: bool,
    },
    /// 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>,
    },
    /// 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,
    },
    /// Mine conversation for experiential moments to journal
    #[command(name = "experience-mine")]
    ExperienceMine {
        /// Path to JSONL transcript (default: most recent)
        jsonl_path: Option<String>,
    },
    /// 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,
    },
    /// Run a single agent by name
    Run {
        /// Agent name (e.g. observation, linker, distill)
        agent: String,
        /// Batch size (number of seed nodes/fragments)
        #[arg(long, default_value_t = 5)]
        count: usize,
        /// Target specific node keys (overrides agent's query)
        #[arg(long)]
        target: Vec<String>,
        /// Run agent on each result of a query (e.g. 'key ~ "bcachefs" | limit 10')
        #[arg(long)]
        query: Option<String>,
        /// Dry run — set POC_MEMORY_DRY_RUN=1 so mutations are no-ops
        #[arg(long)]
        dry_run: bool,
        /// Run locally instead of queuing to daemon
        #[arg(long)]
        local: bool,
        /// Directory for agent output/input state (persists across runs)
        #[arg(long)]
        state_dir: Option<String>,
    },
    /// Show spaced repetition replay queue
    #[command(name = "replay-queue")]
    ReplayQueue {
        /// Number of items to show
        #[arg(long, default_value_t = 10)]
        count: usize,
    },
    /// Evaluate agent quality by LLM-sorted ranking
    #[command(name = "evaluate")]
    Evaluate {
        /// Number of pairwise matchups to run
        #[arg(long, default_value_t = 30)]
        matchups: usize,
        /// Model to use for comparison (haiku or sonnet)
        #[arg(long, default_value = "haiku")]
        model: String,
        /// Show example comparison prompt without calling LLM
        #[arg(long)]
        dry_run: bool,
    },
}

#[derive(Subcommand)]
enum AdminCmd {
    /// Scan markdown files, index all memory units
    Init,
    /// Report graph metrics (CC, communities, small-world)
    Health,
    /// Run consistency checks and repair
    Fsck,
    /// Find and merge duplicate nodes (same key, multiple UUIDs)
    Dedup {
        /// Apply the merge (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// Bulk rename: replace a character in all keys
    #[command(name = "bulk-rename")]
    BulkRename {
        /// Character to replace
        from: String,
        /// Replacement character
        to: String,
        /// Apply changes (default: dry run)
        #[arg(long)]
        apply: bool,
    },
    /// Brief metrics check (for cron/notifications)
    #[command(name = "daily-check")]
    DailyCheck,
    /// 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,
    },
    /// Output session-start context from the store
    #[command(name = "load-context")]
    LoadContext {
        /// Show word count statistics instead of content
        #[arg(long)]
        stats: bool,
    },
    /// Show recent retrieval log
    Log,
    /// Show current parameters
    Params,
    /// 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>,
    },
    /// Migrate transcript stub nodes to progress log
    #[command(name = "migrate-transcript-progress")]
    MigrateTranscriptProgress,
}

#[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,
}

/// Print help with subcommands expanded to show nested commands.
fn print_help() {
    use clap::CommandFactory;
    let cmd = Cli::command();

    println!("poc-memory - graph-structured memory store");
    println!("usage: poc-memory <command> [<args>]\n");

    for sub in cmd.get_subcommands() {
        if sub.get_name() == "help" { continue }
        let children: Vec<_> = sub.get_subcommands()
            .filter(|c| c.get_name() != "help")
            .collect();
        if !children.is_empty() {
            for child in &children {
                let about = child.get_about().map(|s| s.to_string()).unwrap_or_default();
                let full = format!("{} {}", sub.get_name(), child.get_name());
                // Recurse one more level for daemon subcommands etc.
                let grandchildren: Vec<_> = child.get_subcommands()
                    .filter(|c| c.get_name() != "help")
                    .collect();
                if !grandchildren.is_empty() {
                    for gc in grandchildren {
                        let gc_about = gc.get_about().map(|s| s.to_string()).unwrap_or_default();
                        let gc_full = format!("{} {}", full, gc.get_name());
                        println!("  {:<34}{gc_about}", gc_full);
                    }
                } else {
                    println!("  {:<34}{about}", full);
                }
            }
        } else {
            let about = sub.get_about().map(|s| s.to_string()).unwrap_or_default();
            println!("  {:<34}{about}", sub.get_name());
        }
    }
}

// ── Dispatch ─────────────────────────────────────────────────────────

trait Run {
    fn run(self) -> Result<(), String>;
}

impl Run for Command {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Search { query, pipeline, expand, full, debug, fuzzy, content }
                => cli::misc::cmd_search(&query, &pipeline, expand, full, debug, fuzzy, content),
            Self::Render { key }        => cli::node::cmd_render(&key),
            Self::Write { key }         => cli::node::cmd_write(&key),
            Self::Edit { key }          => cli::node::cmd_edit(&key),
            Self::History { full, key }  => cli::node::cmd_history(&key, full),
            Self::Tail { n, full, provenance, all_versions }
                => cli::journal::cmd_tail(n, full, provenance.as_deref(), !all_versions),
            Self::Status                 => cli::misc::cmd_status(),
            Self::Query { expr }         => cli::misc::cmd_query(&expr),
            Self::Used { key }           => cli::node::cmd_used(&key),
            Self::Wrong { key, context } => cli::node::cmd_wrong(&key, &context),
            Self::NotRelevant { key }    => cli::node::cmd_not_relevant(&key),
            Self::NotUseful { key }      => cli::node::cmd_not_useful(&key),
            Self::WeightSet { key, weight } => cli::node::cmd_weight_set(&key, weight),
            Self::Gap { description }    => cli::node::cmd_gap(&description),
            Self::Node(sub)              => sub.run(),
            Self::Journal(sub)           => sub.run(),
            Self::GraphCmd(sub)          => sub.run(),
            Self::Cursor(sub)            => sub.run(),
            Self::Agent(sub)             => sub.run(),
            Self::Admin(sub)             => sub.run(),
            // mcp-schema moved to standalone binary src/claude/mcp-schema.rs
        }
    }
}

impl Run for NodeCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Delete { key }            => cli::node::cmd_node_delete(&key),
            Self::Rename { old_key, new_key } => cli::node::cmd_node_rename(&old_key, &new_key),
            Self::List { pattern }          => cli::node::cmd_list_keys(pattern.as_deref()),
            Self::Edges                     => cli::node::cmd_list_edges(),
            Self::Dump                      => cli::node::cmd_dump_json(),
        }
    }
}

impl Run for JournalCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Write { name, text }                    => cli::journal::cmd_journal_write(&name, &text),
            Self::Tail { n, full, level }                => cli::journal::cmd_journal_tail(n, full, level),
            Self::Enrich { jsonl_path, entry_text, grep_line }
                => cli::agent::cmd_journal_enrich(&jsonl_path, &entry_text, grep_line),
        }
    }
}

impl Run for GraphCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Link { key }                  => cli::graph::cmd_link(&key),
            Self::Spread { keys, max_results }  => cli::graph::cmd_spread(&keys, max_results),
            Self::LinkAdd { source, target, reason }
                => cli::graph::cmd_link_add(&source, &target, &reason),
            Self::LinkSet { source, target, strength }
                => cli::graph::cmd_link_set(&source, &target, strength),
            Self::LinkImpact { source, target } => cli::graph::cmd_link_impact(&source, &target),
            Self::LinkAudit { apply }           => cli::graph::cmd_link_audit(apply),
            Self::LinkOrphans { min_degree, links_per, sim_threshold }
                => cli::graph::cmd_link_orphans(min_degree, links_per, sim_threshold),
            Self::TriangleClose { min_degree, sim_threshold, max_per_hub }
                => cli::graph::cmd_triangle_close(min_degree, sim_threshold, max_per_hub),
            Self::CapDegree { max_degree }      => cli::graph::cmd_cap_degree(max_degree),
            Self::NormalizeStrengths { apply }   => cli::graph::cmd_normalize_strengths(apply),
            Self::Differentiate { key, apply }  => cli::graph::cmd_differentiate(key.as_deref(), apply),
            Self::Trace { key }                 => cli::graph::cmd_trace(&key),
            Self::Interference { threshold }    => cli::graph::cmd_interference(threshold),
            Self::Communities { top_n, min_size } => cli::graph::cmd_communities(top_n, min_size),
            Self::Overview                      => cli::graph::cmd_graph(),
            Self::Spectral { k }                => cli::graph::cmd_spectral(k),
            Self::SpectralSave { k }            => cli::graph::cmd_spectral_save(k),
            Self::SpectralNeighbors { key, n }  => cli::graph::cmd_spectral_neighbors(&key, n),
            Self::SpectralPositions { n }       => cli::graph::cmd_spectral_positions(n),
            Self::SpectralSuggest { n }         => cli::graph::cmd_spectral_suggest(n),
            Self::Organize { term, threshold, key_only, anchor }
                => cli::graph::cmd_organize(&term, threshold, key_only, anchor),
        }
    }
}

impl Run for CursorCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Show => {
                let store = store::Store::load()?;
                cursor::show(&store)
            }
            Self::Set { key } => {
                if key.is_empty() { return Err("cursor set requires a key".into()); }
                let key = key.join(" ");
                let store = store::Store::load()?;
                let bare = store::strip_md_suffix(&key);
                if !store.nodes.contains_key(&bare) {
                    return Err(format!("Node not found: {}", bare));
                }
                cursor::set(&bare)?;
                cursor::show(&store)
            }
            Self::Forward => { let s = store::Store::load()?; cursor::move_temporal(&s, true) }
            Self::Back    => { let s = store::Store::load()?; cursor::move_temporal(&s, false) }
            Self::Up      => { let s = store::Store::load()?; cursor::move_up(&s) }
            Self::Down    => { let s = store::Store::load()?; cursor::move_down(&s) }
            Self::Clear   => cursor::clear(),
        }
    }
}

impl Run for DaemonCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Start       => daemon::run_daemon(),
            Self::Status      => daemon::show_status(),
            Self::Log { job, task, lines } => {
                if let Some(ref task_name) = task {
                    daemon::show_task_log(task_name, lines)
                } else {
                    daemon::show_log(job.as_deref(), lines)
                }
            }
            Self::Install     => daemon::install_service(),
            Self::Consolidate => daemon::rpc_consolidate(),
            Self::Run { agent, count } => daemon::rpc_run_agent(&agent, count),
            Self::Tui         => Err("TUI moved to consciousness binary (F4/F5)".into()),
            Self::ReloadConfig => {
                match daemon::send_rpc_pub("reload-config") {
                    Some(resp) => { eprintln!("{}", resp.trim()); Ok(()) }
                    None => Err("daemon not running".into()),
                }
            }
        }
    }
}

impl Run for AgentCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Daemon(sub) => sub.run(),
            Self::KnowledgeLoop { max_cycles, batch_size, window, max_depth }
                => cli::agent::cmd_knowledge_loop(max_cycles, batch_size, window, max_depth),
            Self::ConsolidateBatch { count, auto, agent }
                => cli::agent::cmd_consolidate_batch(count, auto, agent),
            Self::ConsolidateSession => cli::agent::cmd_consolidate_session(),
            Self::ConsolidateFull    => cli::agent::cmd_consolidate_full(),
            Self::ApplyAgent { all } => cmd_apply_agent(all),
            Self::ApplyConsolidation { apply, report }
                => cli::agent::cmd_apply_consolidation(apply, report.as_deref()),
            Self::Digest { level }   => cmd_digest(level),
            Self::DigestLinks { apply } => cli::agent::cmd_digest_links(apply),
            Self::ExperienceMine { .. }
                => Err("experience-mine has been removed — use the observation agent instead.".into()),
            Self::FactMine { path, batch, dry_run, output, min_messages }
                => cli::agent::cmd_fact_mine(&path, batch, dry_run, output.as_deref(), min_messages),
            Self::FactMineStore { path } => cli::agent::cmd_fact_mine_store(&path),
            Self::Run { agent, count, target, query, dry_run, local, state_dir }
                => cli::agent::cmd_run_agent(&agent, count, &target, query.as_deref(), dry_run, local, state_dir.as_deref()),
            Self::ReplayQueue { count } => cli::agent::cmd_replay_queue(count),
            Self::Evaluate { matchups, model, dry_run }
                => cli::agent::cmd_evaluate_agents(matchups, &model, dry_run),
        }
    }
}

impl Run for AdminCmd {
    fn run(self) -> Result<(), String> {
        match self {
            Self::Init          => cli::admin::cmd_init(),
            Self::Health        => cli::admin::cmd_health(),
            Self::Fsck          => cli::admin::cmd_fsck(),
            Self::Dedup { apply } => cli::admin::cmd_dedup(apply),
            Self::BulkRename { from, to, apply } => cli::admin::cmd_bulk_rename(&from, &to, apply),
            Self::DailyCheck    => cli::admin::cmd_daily_check(),
            Self::Import { files } => cli::admin::cmd_import(&files),
            Self::Export { files, all } => cli::admin::cmd_export(&files, all),
            Self::LoadContext { stats } => cli::misc::cmd_load_context(stats),
            Self::Log           => cli::misc::cmd_log(),
            Self::Params        => cli::misc::cmd_params(),
            Self::LookupBump { keys } => cli::node::cmd_lookup_bump(&keys),
            Self::Lookups { date } => cli::node::cmd_lookups(date.as_deref()),
            Self::MigrateTranscriptProgress => {
                let mut store = store::Store::load()?;
                let count = store.migrate_transcript_progress()?;
                println!("Migrated {} transcript segment markers", count);
                Ok(())
            }
        }
    }
}

fn main() {
    // Handle --help ourselves for expanded subcommand display
    let args: Vec<String> = std::env::args().collect();
    if args.len() <= 1 || args.iter().any(|a| a == "--help" || a == "-h") && args.len() == 2 {
        print_help();
        return;
    }

    let cli = Cli::parse();

    if let Err(e) = cli.command.run() {
        eprintln!("Error: {}", e);
        process::exit(1);
    }
}

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

/// 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 = crate::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)
        }
    }
}