feat: implement complete MCP tool suite (53 tools, 190+ tests)

AGENTS.md

@@ -76,3 +76,10 @@ internal/
 
 Go rewrite of [cyborg-swarm](https://github.com/unbound-force/cyborg-swarm),
 originally by [Joel Hooks](https://github.com/joelhooks).
+
+## Active Technologies
+- Go 1.25+ + `cobra` (CLI), `modernc.org/sqlite` (pure Go SQLite), stdlib `encoding/json` (MCP JSON-RPC), stdlib `os/exec` (git operations) (001-go-rewrite-phases)
+- SQLite at `~/.config/swarm-tools/swarm.db` (WAL mode, compatible with cyborg-swarm) (001-go-rewrite-phases)
+
+## Recent Changes
+- 001-go-rewrite-phases: Added Go 1.25+ + `cobra` (CLI), `modernc.org/sqlite` (pure Go SQLite), stdlib `encoding/json` (MCP JSON-RPC), stdlib `os/exec` (git operations)

cmd/replicator/doctor.go

@@ -0,0 +1,58 @@
+package main
+
+import (
+	"fmt"
+	"time"
+
+	"github.com/unbound-force/replicator/internal/config"
+	"github.com/unbound-force/replicator/internal/db"
+	"github.com/unbound-force/replicator/internal/doctor"
+)
+
+// runDoctor executes health checks and prints results as a table.
+func runDoctor(cfg *config.Config) error {
+	store, err := db.Open(cfg.DatabasePath)
+	if err != nil {
+		return fmt.Errorf("open database: %w", err)
+	}
+	defer store.Close()
+
+	results, err := doctor.Run(store, cfg)
+	if err != nil {
+		return fmt.Errorf("run checks: %w", err)
+	}
+
+	// Print header.
+	fmt.Printf("%-12s %-6s %s\n", "CHECK", "STATUS", "MESSAGE")
+	fmt.Printf("%-12s %-6s %s\n", "-----", "------", "-------")
+
+	hasFailure := false
+	for _, r := range results {
+		icon := statusIcon(r.Status)
+		fmt.Printf("%-12s %s %-4s %s (%s)\n", r.Name, icon, r.Status, r.Message, r.Duration.Round(time.Millisecond))
+		if r.Status == "fail" {
+			hasFailure = true
+		}
+	}
+
+	if hasFailure {
+		fmt.Println("\nSome checks failed. Run 'replicator setup' to fix common issues.")
+	} else {
+		fmt.Println("\nAll checks passed.")
+	}
+
+	return nil
+}
+
+func statusIcon(status string) string {
+	switch status {
+	case "pass":
+		return "\u2713" // checkmark
+	case "fail":
+		return "\u2717" // X mark
+	case "warn":
+		return "!" // warning
+	default:
+		return "?"
+	}
+}

cmd/replicator/main.go

@@ -34,6 +34,10 @@ via Dewey).`,
 	root.AddCommand(serveCmd())
 	root.AddCommand(cellsCmd())
 	root.AddCommand(versionCmd())
+	root.AddCommand(doctorCmd())
+	root.AddCommand(statsCmd())
+	root.AddCommand(queryCmd())
+	root.AddCommand(setupCmd())
 
 	if err := root.Execute(); err != nil {
 		fmt.Fprintln(os.Stderr, err)
@@ -73,3 +77,59 @@ func versionCmd() *cobra.Command {
 		},
 	}
 }
+
+func doctorCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "doctor",
+		Short: "Run health checks on the replicator environment",
+		Long:  "Checks git, database, Dewey connectivity, and config directory.",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			cfg := config.Load()
+			return runDoctor(cfg)
+		},
+	}
+}
+
+func statsCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "stats",
+		Short: "Show database statistics",
+		Long:  "Displays event counts, recent activity, and cell status summary.",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			cfg := config.Load()
+			return runStats(cfg)
+		},
+	}
+}
+
+func queryCmd() *cobra.Command {
+	var listFlag bool
+
+	cmd := &cobra.Command{
+		Use:   "query [preset]",
+		Short: "Run a preset database query",
+		Long:  "Executes a named preset query against the database. Use --list to see available presets.",
+		Args:  cobra.MaximumNArgs(1),
+		RunE: func(cmd *cobra.Command, args []string) error {
+			if listFlag || len(args) == 0 {
+				listQueryPresets()
+				return nil
+			}
+			cfg := config.Load()
+			return runQuery(cfg, args[0])
+		},
+	}
+	cmd.Flags().BoolVar(&listFlag, "list", false, "List available query presets")
+	return cmd
+}
+
+func setupCmd() *cobra.Command {
+	return &cobra.Command{
+		Use:   "setup",
+		Short: "Initialize replicator environment",
+		Long:  "Creates config directory, initializes database, and verifies git.",
+		RunE: func(cmd *cobra.Command, args []string) error {
+			return runSetup()
+		},
+	}
+}

cmd/replicator/query.go

@@ -0,0 +1,33 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/unbound-force/replicator/internal/config"
+	"github.com/unbound-force/replicator/internal/db"
+	"github.com/unbound-force/replicator/internal/query"
+)
+
+// runQuery executes a preset query and prints results.
+func runQuery(cfg *config.Config, presetName string) error {
+	store, err := db.Open(cfg.DatabasePath)
+	if err != nil {
+		return fmt.Errorf("open database: %w", err)
+	}
+	defer store.Close()
+
+	return query.Run(store, presetName, os.Stdout)
+}
+
+// listQueryPresets prints available preset names.
+func listQueryPresets() {
+	fmt.Println("Available query presets:")
+	for _, p := range query.ListPresets() {
+		fmt.Printf("  %s\n", p)
+	}
+	fmt.Println()
+	fmt.Println("Usage: replicator query <preset>")
+	fmt.Printf("Example: replicator query %s\n", strings.Join(query.ListPresets()[:1], ""))
+}

cmd/replicator/serve.go

@@ -4,8 +4,12 @@ import (
 	"github.com/unbound-force/replicator/internal/config"
 	"github.com/unbound-force/replicator/internal/db"
 	"github.com/unbound-force/replicator/internal/mcp"
+	"github.com/unbound-force/replicator/internal/memory"
 	"github.com/unbound-force/replicator/internal/tools/hive"
+	memorytools "github.com/unbound-force/replicator/internal/tools/memory"
 	"github.com/unbound-force/replicator/internal/tools/registry"
+	swarmtools "github.com/unbound-force/replicator/internal/tools/swarm"
+	swarmmailtools "github.com/unbound-force/replicator/internal/tools/swarmmail"
 )
 
 // serveMCP starts the MCP JSON-RPC server on stdio.
@@ -20,7 +24,13 @@ func serveMCP() error {
 
 	reg := registry.New()
 	hive.Register(reg, store)
+	swarmmailtools.Register(reg, store)
+	swarmtools.Register(reg, store)
 
-	server := mcp.NewServer(reg)
+	// Memory tools proxy to Dewey for semantic search.
+	memClient := memory.NewClient(cfg.DeweyURL)
+	memorytools.Register(reg, memClient)
+
+	server := mcp.NewServer(reg, Version)
 	return server.ServeStdio()
 }

cmd/replicator/setup.go

@@ -0,0 +1,51 @@
+package main
+
+import (
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+
+	"github.com/unbound-force/replicator/internal/config"
+	"github.com/unbound-force/replicator/internal/db"
+)
+
+// runSetup creates the config directory, initializes the database, and
+// verifies git is available.
+func runSetup() error {
+	// 1. Create config directory.
+	home, err := os.UserHomeDir()
+	if err != nil {
+		return fmt.Errorf("determine home directory: %w", err)
+	}
+
+	configDir := filepath.Join(home, ".config", "swarm-tools")
+	if err := os.MkdirAll(configDir, 0o755); err != nil {
+		return fmt.Errorf("create config directory: %w", err)
+	}
+	fmt.Printf("\u2713 Config directory: %s\n", configDir)
+
+	// 2. Initialize database.
+	cfg := config.Load()
+	store, err := db.Open(cfg.DatabasePath)
+	if err != nil {
+		return fmt.Errorf("initialize database: %w", err)
+	}
+	store.Close()
+	fmt.Printf("\u2713 Database: %s\n", cfg.DatabasePath)
+
+	// 3. Verify git.
+	cmd := exec.Command("git", "--version")
+	out, err := cmd.Output()
+	if err != nil {
+		fmt.Printf("\u2717 Git: not found (%v)\n", err)
+		fmt.Println("  Install git: https://git-scm.com/downloads")
+	} else {
+		fmt.Printf("\u2713 Git: %s\n", strings.TrimSpace(string(out)))
+	}
+
+	fmt.Println()
+	fmt.Println("Setup complete. Run 'replicator doctor' to verify all checks pass.")
+	return nil
+}

cmd/replicator/stats.go

@@ -0,0 +1,21 @@
+package main
+
+import (
+	"fmt"
+	"os"
+
+	"github.com/unbound-force/replicator/internal/config"
+	"github.com/unbound-force/replicator/internal/db"
+	"github.com/unbound-force/replicator/internal/stats"
+)
+
+// runStats queries the database and prints statistics.
+func runStats(cfg *config.Config) error {
+	store, err := db.Open(cfg.DatabasePath)
+	if err != nil {
+		return fmt.Errorf("open database: %w", err)
+	}
+	defer store.Close()
+
+	return stats.Run(store, os.Stdout)
+}

internal/db/db.go

@@ -78,4 +78,7 @@ var migrations = []string{
 	migrationAgents,
 	migrationCells,
 	migrationCellEvents,
+	migrationSessions,
+	migrationMessages,
+	migrationReservations,
 }

internal/db/db_test.go

@@ -10,7 +10,7 @@ func TestOpenMemory(t *testing.T) {
 	defer store.Close()
 
 	// Verify tables exist.
-	tables := []string{"events", "agents", "beads", "cell_events"}
+	tables := []string{"events", "agents", "beads", "cell_events", "sessions", "messages", "reservations"}
 	for _, table := range tables {
 		var name string
 		err := store.DB.QueryRow(

internal/db/migrations.go

@@ -71,3 +71,50 @@ CREATE TABLE IF NOT EXISTS cell_events (
 
 CREATE INDEX IF NOT EXISTS idx_cell_events_cell ON cell_events(cell_id);
 `
+
+const migrationSessions = `
+CREATE TABLE IF NOT EXISTS sessions (
+    session_id TEXT PRIMARY KEY,
+    agent_name TEXT,
+    project_path TEXT,
+    started_at TEXT,
+    ended_at TEXT,
+    handoff_notes TEXT,
+    active_cell_id TEXT
+);
+`
+
+const migrationMessages = `
+CREATE TABLE IF NOT EXISTS messages (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    from_agent TEXT,
+    to_agents TEXT,
+    subject TEXT,
+    body TEXT,
+    importance TEXT DEFAULT 'normal',
+    thread_id TEXT,
+    ack_required INTEGER DEFAULT 0,
+    acknowledged INTEGER DEFAULT 0,
+    created_at TEXT DEFAULT (datetime('now'))
+);
+
+CREATE INDEX IF NOT EXISTS idx_messages_from_agent ON messages(from_agent);
+CREATE INDEX IF NOT EXISTS idx_messages_created ON messages(created_at);
+`
+
+const migrationReservations = `
+CREATE TABLE IF NOT EXISTS reservations (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    agent_name TEXT,
+    project_path TEXT,
+    path TEXT,
+    exclusive INTEGER DEFAULT 1,
+    reason TEXT,
+    ttl_seconds INTEGER DEFAULT 300,
+    created_at TEXT DEFAULT (datetime('now')),
+    expires_at TEXT
+);
+
+CREATE INDEX IF NOT EXISTS idx_reservations_path ON reservations(path);
+CREATE INDEX IF NOT EXISTS idx_reservations_agent ON reservations(agent_name);
+`