@codified/cli 0.3.5 → 0.3.6

package/dist/commands/reset.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"reset.d.ts","sourceRoot":"","sources":["../../src/commands/reset.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AASpC,eAAO,MAAM,YAAY,SAmKrB,CAAC"}

package/dist/commands/reset.js

@@ -0,0 +1,157 @@
+// codify reset — drop graph data and re-run migrations
+//
+// Default: TRUNCATE all data tables, re-run migrations. Docker stays running.
+// --hard:  Stop Docker, remove volumes, rebuild everything from scratch.
+import { Command } from "commander";
+import { resolve } from "node:path";
+import { spawnSync } from "node:child_process";
+import { existsSync } from "node:fs";
+import { loadProjectConfig } from "../lib/config.js";
+import { confirm } from "../lib/prompt.js";
+import { getMigrationsDir } from "../lib/paths.js";
+import { runMigrations } from "../lib/migrate.js";
+export const resetCommand = new Command("reset")
+    .description("Reset the context graph (drop data, re-run migrations)")
+    .option("--hard", "Full reset: stop Docker, remove volumes, rebuild")
+    .option("--yes", "Skip confirmation prompt")
+    .action(async (opts) => {
+    try {
+        const cwd = process.cwd();
+        const configDir = resolve(cwd, ".codify");
+        const dockerDir = resolve(configDir, "docker");
+        const isHard = !!opts.hard;
+        const mode = isHard ? "HARD" : "SOFT";
+        console.log(`\n  Codify Reset (${mode})\n`);
+        if (isHard) {
+            console.log("  This will:");
+            console.log("    - Stop all Docker services");
+            console.log("    - Remove all Docker volumes (all data permanently deleted)");
+            console.log("    - Rebuild and restart containers");
+            console.log("    - Re-run all migrations\n");
+        }
+        else {
+            console.log("  This will:");
+            console.log("    - Truncate all data tables (nodes, edges, etc.)");
+            console.log("    - Clear migration tracking");
+            console.log("    - Re-run all migrations");
+            console.log("    - Docker services remain running\n");
+        }
+        if (!opts.yes) {
+            const proceed = await confirm("  Are you sure?", false);
+            if (!proceed) {
+                console.log("  Aborted.\n");
+                process.exit(0);
+            }
+        }
+        if (isHard) {
+            // ── Hard reset: tear down Docker entirely ──────────────────
+            const composePath = resolve(dockerDir, "docker-compose.yml");
+            if (!existsSync(composePath)) {
+                console.error("  ERROR: docker-compose.yml not found at " + composePath);
+                console.error("  Run 'codify init' first.\n");
+                process.exit(1);
+            }
+            console.log("\n  [1/3] Stopping Docker and removing volumes...");
+            const down = spawnSync("docker", ["compose", "-f", composePath, "down", "-v"], { stdio: "inherit" });
+            if (down.status !== 0) {
+                console.error("  ERROR: docker compose down -v failed.\n");
+                process.exit(1);
+            }
+            console.log("  Done.");
+            console.log("\n  [2/3] Rebuilding and starting Docker services...");
+            const up = spawnSync("docker", ["compose", "-f", composePath, "up", "-d", "--build"], { stdio: "inherit" });
+            if (up.status !== 0) {
+                console.error("  ERROR: docker compose up failed.\n");
+                process.exit(1);
+            }
+            console.log("  Done.");
+            // Wait for PostgreSQL to be ready
+            console.log("  Waiting for PostgreSQL to accept connections...");
+            const { waitForPostgres } = await import("../lib/docker.js");
+            const pgReady = await waitForPostgres(dockerDir);
+            if (!pgReady) {
+                console.error("  ERROR: PostgreSQL did not become ready within 120s.\n");
+                process.exit(1);
+            }
+            console.log("  PostgreSQL is ready.");
+            console.log("\n  [3/3] Running migrations...");
+            const databaseUrl = process.env.DATABASE_URL ?? "postgresql://codify:codify@localhost:5432/codify";
+            const migrationsDir = getMigrationsDir();
+            const result = await runMigrations(databaseUrl, migrationsDir);
+            console.log(`  ${result.applied.length} migration${result.applied.length === 1 ? "" : "s"} applied.`);
+        }
+        else {
+            // ── Soft reset: truncate tables, re-run migrations ─────────
+            await loadProjectConfig();
+            const { getPool, closePool } = await import("@codify/graph");
+            const pool = getPool();
+            try {
+                await pool.query("SELECT 1");
+            }
+            catch {
+                console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
+                process.exit(1);
+            }
+            console.log("  [1/3] Truncating data tables...");
+            // Order matters: truncate in dependency order with CASCADE
+            const tablesToTruncate = [
+                "collection_plans",
+                "metabolism_audit",
+                "connector_sync_state",
+                "node_versions",
+                "edges",
+                "nodes",
+                "branches",
+            ];
+            for (const table of tablesToTruncate) {
+                try {
+                    await pool.query(`TRUNCATE TABLE ${table} CASCADE`);
+                    console.log(`    Truncated: ${table}`);
+                }
+                catch (err) {
+                    const msg = err instanceof Error ? err.message : String(err);
+                    // Table may not exist if migrations haven't run yet — that's OK
+                    if (msg.includes("does not exist")) {
+                        console.log(`    Skipped: ${table} (does not exist)`);
+                    }
+                    else {
+                        throw err;
+                    }
+                }
+            }
+            console.log("\n  [2/3] Clearing migration tracking...");
+            try {
+                await pool.query("TRUNCATE TABLE _migrations");
+                console.log("    Migration history cleared.");
+            }
+            catch (err) {
+                const msg = err instanceof Error ? err.message : String(err);
+                if (msg.includes("does not exist")) {
+                    console.log("    No migration history to clear.");
+                }
+                else {
+                    throw err;
+                }
+            }
+            await closePool();
+            console.log("\n  [3/3] Re-running migrations...");
+            const databaseUrl = process.env.DATABASE_URL ?? "postgresql://codify:codify@localhost:5432/codify";
+            const migrationsDir = getMigrationsDir();
+            const result = await runMigrations(databaseUrl, migrationsDir);
+            console.log(`    ${result.applied.length} migration${result.applied.length === 1 ? "" : "s"} applied.`);
+        }
+        console.log("\n  Reset complete. Run 'codify bootstrap' to rebuild the graph.\n");
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        if (message.includes("ECONNREFUSED")) {
+            console.error("\n  ERROR: Cannot connect to Codify services.");
+            console.error("  Run 'codify init' to start the infrastructure.\n");
+        }
+        else {
+            console.error(`\n  ERROR: ${message}\n`);
+        }
+        process.exit(1);
+    }
+});
+//# sourceMappingURL=reset.js.map

package/dist/commands/reset.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"reset.js","sourceRoot":"","sources":["../../src/commands/reset.ts"],"names":[],"mappings":"AAAA,uDAAuD;AACvD,EAAE;AACF,8EAA8E;AAC9E,yEAAyE;AAEzE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,SAAS,CAAC;AACrC,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AACrD,OAAO,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AAC3C,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAElD,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,OAAO,CAAC,OAAO,CAAC;KAC7C,WAAW,CAAC,wDAAwD,CAAC;KACrE,MAAM,CAAC,QAAQ,EAAE,kDAAkD,CAAC;KACpE,MAAM,CAAC,OAAO,EAAE,0BAA0B,CAAC;KAC3C,MAAM,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE;IACrB,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,EAAE,CAAC;QAC1B,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC;QAC1C,MAAM,SAAS,GAAG,OAAO,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QAE/C,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC;QAC3B,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC;QAEtC,OAAO,CAAC,GAAG,CAAC,qBAAqB,IAAI,KAAK,CAAC,CAAC;QAE5C,IAAI,MAAM,EAAE,CAAC;YACX,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;YAC5B,OAAO,CAAC,GAAG,CAAC,gCAAgC,CAAC,CAAC;YAC9C,OAAO,CAAC,GAAG,CAAC,gEAAgE,CAAC,CAAC;YAC9E,OAAO,CAAC,GAAG,CAAC,sCAAsC,CAAC,CAAC;YACpD,OAAO,CAAC,GAAG,CAAC,+BAA+B,CAAC,CAAC;QAC/C,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;YAC5B,OAAO,CAAC,GAAG,CAAC,qDAAqD,CAAC,CAAC;YACnE,OAAO,CAAC,GAAG,CAAC,gCAAgC,CAAC,CAAC;YAC9C,OAAO,CAAC,GAAG,CAAC,6BAA6B,CAAC,CAAC;YAC3C,OAAO,CAAC,GAAG,CAAC,wCAAwC,CAAC,CAAC;QACxD,CAAC;QAED,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,iBAAiB,EAAE,KAAK,CAAC,CAAC;YACxD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;gBAC5B,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;QACH,CAAC;QAED,IAAI,MAAM,EAAE,CAAC;YACX,8DAA8D;YAE9D,MAAM,WAAW,GAAG,OAAO,CAAC,SAAS,EAAE,oBAAoB,CAAC,CAAC;YAC7D,IAAI,CAAC,UAAU,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC7B,OAAO,CAAC,KAAK,CAAC,2CAA2C,GAAG,WAAW,CAAC,CAAC;gBACzE,OAAO,CAAC,KAAK,CAAC,8BAA8B,CAAC,CAAC;gBAC9C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YAED,OAAO,CAAC,GAAG,CAAC,mDAAmD,CAAC,CAAC;YACjE,MAAM,IAAI,GAAG,SAAS,CACpB,QAAQ,EACR,CAAC,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,EAC5C,EAAE,KAAK,EAAE,SAAS,EAAE,CACrB,CAAC;YACF,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACtB,OAAO,CAAC,KAAK,CAAC,2CAA2C,CAAC,CAAC;gBAC3D,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YAEvB,OAAO,CAAC,GAAG,CAAC,sDAAsD,CAAC,CAAC;YACpE,MAAM,EAAE,GAAG,SAAS,CAClB,QAAQ,EACR,CAAC,SAAS,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,IAAI,EAAE,SAAS,CAAC,EACrD,EAAE,KAAK,EAAE,SAAS,EAAE,CACrB,CAAC;YACF,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACpB,OAAO,CAAC,KAAK,CAAC,sCAAsC,CAAC,CAAC;gBACtD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;YAEvB,kCAAkC;YAClC,OAAO,CAAC,GAAG,CAAC,mDAAmD,CAAC,CAAC;YACjE,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,MAAM,CAAC,kBAAkB,CAAC,CAAC;YAC7D,MAAM,OAAO,GAAG,MAAM,eAAe,CAAC,SAAS,CAAC,CAAC;YACjD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,OAAO,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;gBACzE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YACD,OAAO,CAAC,GAAG,CAAC,wBAAwB,CAAC,CAAC;YAEtC,OAAO,CAAC,GAAG,CAAC,iCAAiC,CAAC,CAAC;YAC/C,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,IAAI,kDAAkD,CAAC;YACnG,MAAM,aAAa,GAAG,gBAAgB,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC,WAAW,EAAE,aAAa,CAAC,CAAC;YAC/D,OAAO,CAAC,GAAG,CAAC,KAAK,MAAM,CAAC,OAAO,CAAC,MAAM,aAAa,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC;QACxG,CAAC;aAAM,CAAC;YACN,8DAA8D;YAE9D,MAAM,iBAAiB,EAAE,CAAC;YAE1B,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,CAAC;YAC7D,MAAM,IAAI,GAAG,OAAO,EAAE,CAAC;YAEvB,IAAI,CAAC;gBACH,MAAM,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YAC/B,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,CAAC,KAAK,CAAC,mEAAmE,CAAC,CAAC;gBACnF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YAED,OAAO,CAAC,GAAG,CAAC,mCAAmC,CAAC,CAAC;YAEjD,2DAA2D;YAC3D,MAAM,gBAAgB,GAAG;gBACvB,kBAAkB;gBAClB,kBAAkB;gBAClB,sBAAsB;gBACtB,eAAe;gBACf,OAAO;gBACP,OAAO;gBACP,UAAU;aACX,CAAC;YAEF,KAAK,MAAM,KAAK,IAAI,gBAAgB,EAAE,CAAC;gBACrC,IAAI,CAAC;oBACH,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,KAAK,UAAU,CAAC,CAAC;oBACpD,OAAO,CAAC,GAAG,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAC;gBACzC,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;oBAC7D,gEAAgE;oBAChE,IAAI,GAAG,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;wBACnC,OAAO,CAAC,GAAG,CAAC,gBAAgB,KAAK,mBAAmB,CAAC,CAAC;oBACxD,CAAC;yBAAM,CAAC;wBACN,MAAM,GAAG,CAAC;oBACZ,CAAC;gBACH,CAAC;YACH,CAAC;YAED,OAAO,CAAC,GAAG,CAAC,0CAA0C,CAAC,CAAC;YACxD,IAAI,CAAC;gBACH,MAAM,IAAI,CAAC,KAAK,CAAC,4BAA4B,CAAC,CAAC;gBAC/C,OAAO,CAAC,GAAG,CAAC,gCAAgC,CAAC,CAAC;YAChD,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,GAAG,CAAC,QAAQ,CAAC,gBAAgB,CAAC,EAAE,CAAC;oBACnC,OAAO,CAAC,GAAG,CAAC,oCAAoC,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,CAAC;gBACZ,CAAC;YACH,CAAC;YAED,MAAM,SAAS,EAAE,CAAC;YAElB,OAAO,CAAC,GAAG,CAAC,oCAAoC,CAAC,CAAC;YAClD,MAAM,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC,YAAY,IAAI,kDAAkD,CAAC;YACnG,MAAM,aAAa,GAAG,gBAAgB,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,MAAM,aAAa,CAAC,WAAW,EAAE,aAAa,CAAC,CAAC;YAC/D,OAAO,CAAC,GAAG,CAAC,OAAO,MAAM,CAAC,OAAO,CAAC,MAAM,aAAa,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,WAAW,CAAC,CAAC;QAC1G,CAAC;QAED,OAAO,CAAC,GAAG,CAAC,oEAAoE,CAAC,CAAC;IACpF,CAAC;IAAC,OAAO,GAAY,EAAE,CAAC;QACtB,MAAM,OAAO,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAEjE,IAAI,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;YACrC,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;YAC/D,OAAO,CAAC,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACtE,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,cAAc,OAAO,IAAI,CAAC,CAAC;QAC3C,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC,CAAC,CAAC"}

package/dist/commands/search.d.ts

@@ -0,0 +1,3 @@
+import { Command } from "commander";
+export declare const searchCommand: Command;
+//# sourceMappingURL=search.d.ts.map

package/dist/commands/search.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/commands/search.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiDpC,eAAO,MAAM,aAAa,SA4KtB,CAAC"}

package/dist/commands/search.js

@@ -0,0 +1,183 @@
+// codify search — search the context graph from the terminal
+import { Command } from "commander";
+import { loadProjectConfig } from "../lib/config.js";
+// --- Color helpers (ANSI escape codes) ---
+const RESET = "\x1b[0m";
+const BOLD = "\x1b[1m";
+const DIM = "\x1b[2m";
+const CYAN = "\x1b[36m";
+const GREEN = "\x1b[32m";
+const YELLOW = "\x1b[33m";
+const MAGENTA = "\x1b[35m";
+const WHITE = "\x1b[37m";
+function typeColor(type) {
+    const colors = {
+        Decision: "\x1b[33m", // yellow
+        Feature: "\x1b[32m", // green
+        Metric: "\x1b[36m", // cyan
+        CustomerSignal: "\x1b[35m", // magenta
+        CodeArtifact: "\x1b[34m", // blue
+        Discussion: "\x1b[37m", // white
+        Gap: "\x1b[31m", // red
+        Study: "\x1b[36m", // cyan
+        Person: "\x1b[33m", // yellow
+    };
+    return `${colors[type] ?? DIM}${type}${RESET}`;
+}
+function freshnessLabel(freshness) {
+    if (freshness >= 0.8)
+        return `${GREEN}${freshness.toFixed(2)}${RESET}`;
+    if (freshness >= 0.5)
+        return `${YELLOW}${freshness.toFixed(2)}${RESET}`;
+    return `${DIM}${freshness.toFixed(2)}${RESET}`;
+}
+function truncate(str, maxLen) {
+    if (str.length <= maxLen)
+        return str;
+    return str.slice(0, maxLen - 3) + "...";
+}
+// --- Valid node types ---
+const VALID_TYPES = [
+    "Decision", "Feature", "Metric", "CustomerSignal",
+    "CodeArtifact", "Discussion", "Gap", "Study", "Person",
+];
+// --- Command definition ---
+export const searchCommand = new Command("search")
+    .description("Search the context graph by keyword")
+    .argument("<query>", "Search query (keywords)")
+    .option("--type <type>", "Filter by node type: Decision, Feature, Metric, CustomerSignal, CodeArtifact, Discussion, Gap, Study, Person")
+    .option("--limit <n>", "Maximum results to show", "10")
+    .option("--freshness <min>", "Minimum freshness threshold (0.0-1.0)")
+    .option("--json", "Output raw JSON for piping")
+    .action(async (queryStr, opts) => {
+    try {
+        await loadProjectConfig();
+        const { getPool, closePool } = await import("@codify/graph");
+        const pool = getPool();
+        try {
+            await pool.query("SELECT 1");
+        }
+        catch {
+            console.error("  ERROR: Cannot connect to PostgreSQL. Run 'codify init' first.\n");
+            process.exit(1);
+        }
+        // Validate options
+        if (opts.type) {
+            if (!VALID_TYPES.includes(opts.type)) {
+                console.error(`\n  ERROR: Invalid type "${opts.type}". Use: ${VALID_TYPES.join(", ")}\n`);
+                process.exit(1);
+            }
+        }
+        const limit = parseInt(opts.limit, 10);
+        if (isNaN(limit) || limit < 1) {
+            console.error("\n  ERROR: --limit must be a positive integer.\n");
+            process.exit(1);
+        }
+        let minFreshness;
+        if (opts.freshness !== undefined) {
+            minFreshness = parseFloat(opts.freshness);
+            if (isNaN(minFreshness) || minFreshness < 0 || minFreshness > 1) {
+                console.error("\n  ERROR: --freshness must be a number between 0.0 and 1.0.\n");
+                process.exit(1);
+            }
+        }
+        // Build query — split keywords, ILIKE against properties::text and metadata::text
+        const conditions = [
+            "superseded_by IS NULL",
+            "layer = ANY($1)",
+        ];
+        const params = [["permanent", "draft", "hot"]];
+        let paramIdx = 2;
+        // Keyword search: split query into words, match any keyword
+        const keywords = queryStr.split(/\s+/).filter((w) => w.length > 1);
+        if (keywords.length > 0) {
+            const keywordConditions = keywords.map((kw) => {
+                params.push(`%${kw}%`);
+                const idx = paramIdx++;
+                return `(properties::text ILIKE $${idx} OR metadata::text ILIKE $${idx} OR $${idx} = ANY(tags))`;
+            });
+            conditions.push(`(${keywordConditions.join(" OR ")})`);
+        }
+        if (opts.type) {
+            conditions.push(`type = $${paramIdx++}`);
+            params.push(opts.type);
+        }
+        if (minFreshness !== undefined) {
+            conditions.push(`freshness >= $${paramIdx++}`);
+            params.push(minFreshness);
+        }
+        params.push(limit);
+        const sql = `SELECT id, type, properties, metadata, freshness, confidence, tags, layer, created_at, updated_at
+         FROM nodes
+         WHERE ${conditions.join(" AND ")}
+         ORDER BY freshness DESC
+         LIMIT $${paramIdx}`;
+        const result = await pool.query(sql, params);
+        const nodes = result.rows;
+        // JSON output mode
+        if (opts.json) {
+            console.log(JSON.stringify(nodes, null, 2));
+            await closePool();
+            return;
+        }
+        // Pretty output
+        console.log(`\n  ${BOLD}Codify — Search Results${RESET}\n`);
+        if (nodes.length === 0) {
+            const filterDesc = [`query="${queryStr}"`];
+            if (opts.type)
+                filterDesc.push(`type=${opts.type}`);
+            if (minFreshness !== undefined)
+                filterDesc.push(`freshness>=${minFreshness}`);
+            console.log(`  No results found (${filterDesc.join(", ")}).\n`);
+            console.log(`  Try broader keywords, or run 'codify bootstrap' to build the graph.\n`);
+            await closePool();
+            return;
+        }
+        console.log(`  ${nodes.length} result${nodes.length === 1 ? "" : "s"} for "${CYAN}${queryStr}${RESET}"${opts.type ? ` (type: ${opts.type})` : ""}${minFreshness !== undefined ? ` (freshness >= ${minFreshness})` : ""}\n`);
+        for (let i = 0; i < nodes.length; i++) {
+            const node = nodes[i];
+            const props = node.properties ?? {};
+            const meta = node.metadata ?? {};
+            // Extract title
+            const title = props.title ?? meta.title ??
+                props.name ?? meta.name ??
+                node.id.slice(0, 12);
+            // Extract description
+            const description = props.description ?? meta.description ??
+                props.reason ?? props.summary ?? "";
+            // Rank number
+            const rank = `${DIM}#${i + 1}${RESET}`;
+            // Type badge
+            const typeBadge = `[${typeColor(node.type)}]`;
+            // Freshness and confidence
+            const fresh = freshnessLabel(node.freshness ?? 0);
+            const conf = `${DIM}conf:${(node.confidence ?? 0).toFixed(2)}${RESET}`;
+            console.log(`  ${rank}  ${typeBadge}  ${BOLD}${title}${RESET}`);
+            console.log(`      freshness: ${fresh}  ${conf}  ${DIM}${node.layer}${RESET}`);
+            if (description) {
+                console.log(`      ${DIM}${truncate(description, 80)}${RESET}`);
+            }
+            console.log("");
+        }
+        // Footer
+        console.log(`  ${DIM}Flags: --type <Type>  --freshness <0.0-1.0>  --limit <n>  --json${RESET}`);
+        console.log("");
+        await closePool();
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        if (message.includes("ECONNREFUSED")) {
+            console.error("\n  ERROR: Cannot connect to Codify services.");
+            console.error("  Run 'codify init' to start the infrastructure.\n");
+        }
+        else if (message.includes("ANTHROPIC_API_KEY")) {
+            console.error("\n  ERROR: ANTHROPIC_API_KEY not set.");
+            console.error("  Export your API key: export ANTHROPIC_API_KEY=sk-...\n");
+        }
+        else {
+            console.error(`\n  ERROR: ${message}\n`);
+        }
+        process.exit(1);
+    }
+});
+//# sourceMappingURL=search.js.map

package/dist/commands/search.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"search.js","sourceRoot":"","sources":["../../src/commands/search.ts"],"names":[],"mappings":"AAAA,6DAA6D;AAE7D,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAErD,4CAA4C;AAE5C,MAAM,KAAK,GAAG,SAAS,CAAC;AACxB,MAAM,IAAI,GAAG,SAAS,CAAC;AACvB,MAAM,GAAG,GAAG,SAAS,CAAC;AACtB,MAAM,IAAI,GAAG,UAAU,CAAC;AACxB,MAAM,KAAK,GAAG,UAAU,CAAC;AACzB,MAAM,MAAM,GAAG,UAAU,CAAC;AAC1B,MAAM,OAAO,GAAG,UAAU,CAAC;AAC3B,MAAM,KAAK,GAAG,UAAU,CAAC;AAEzB,SAAS,SAAS,CAAC,IAAY;IAC7B,MAAM,MAAM,GAA2B;QACrC,QAAQ,EAAE,UAAU,EAAQ,SAAS;QACrC,OAAO,EAAE,UAAU,EAAS,QAAQ;QACpC,MAAM,EAAE,UAAU,EAAU,OAAO;QACnC,cAAc,EAAE,UAAU,EAAE,UAAU;QACtC,YAAY,EAAE,UAAU,EAAI,OAAO;QACnC,UAAU,EAAE,UAAU,EAAM,QAAQ;QACpC,GAAG,EAAE,UAAU,EAAa,MAAM;QAClC,KAAK,EAAE,UAAU,EAAW,OAAO;QACnC,MAAM,EAAE,UAAU,EAAU,SAAS;KACtC,CAAC;IACF,OAAO,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,GAAG,GAAG,IAAI,GAAG,KAAK,EAAE,CAAC;AACjD,CAAC;AAED,SAAS,cAAc,CAAC,SAAiB;IACvC,IAAI,SAAS,IAAI,GAAG;QAAE,OAAO,GAAG,KAAK,GAAG,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,EAAE,CAAC;IACvE,IAAI,SAAS,IAAI,GAAG;QAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,EAAE,CAAC;IACxE,OAAO,GAAG,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,EAAE,CAAC;AACjD,CAAC;AAED,SAAS,QAAQ,CAAC,GAAW,EAAE,MAAc;IAC3C,IAAI,GAAG,CAAC,MAAM,IAAI,MAAM;QAAE,OAAO,GAAG,CAAC;IACrC,OAAO,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC;AAC1C,CAAC;AAED,2BAA2B;AAE3B,MAAM,WAAW,GAAG;IAClB,UAAU,EAAE,SAAS,EAAE,QAAQ,EAAE,gBAAgB;IACjD,cAAc,EAAE,YAAY,EAAE,KAAK,EAAE,OAAO,EAAE,QAAQ;CACvD,CAAC;AAEF,6BAA6B;AAE7B,MAAM,CAAC,MAAM,aAAa,GAAG,IAAI,OAAO,CAAC,QAAQ,CAAC;KAC/C,WAAW,CAAC,qCAAqC,CAAC;KAClD,QAAQ,CAAC,SAAS,EAAE,yBAAyB,CAAC;KAC9C,MAAM,CAAC,eAAe,EAAE,8GAA8G,CAAC;KACvI,MAAM,CAAC,aAAa,EAAE,yBAAyB,EAAE,IAAI,CAAC;KACtD,MAAM,CAAC,mBAAmB,EAAE,uCAAuC,CAAC;KACpE,MAAM,CAAC,QAAQ,EAAE,4BAA4B,CAAC;KAC9C,MAAM,CAAC,KAAK,EAAE,QAAgB,EAAE,IAAI,EAAE,EAAE;IACvC,IAAI,CAAC;QACH,MAAM,iBAAiB,EAAE,CAAC;QAE1B,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,CAAC;QAE7D,MAAM,IAAI,GAAG,OAAO,EAAE,CAAC;QAEvB,IAAI,CAAC;YACH,MAAM,IAAI,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAC/B,CAAC;QAAC,MAAM,CAAC;YACP,OAAO,CAAC,KAAK,CAAC,mEAAmE,CAAC,CAAC;YACnF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,mBAAmB;QACnB,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,OAAO,CAAC,KAAK,CAAC,4BAA4B,IAAI,CAAC,IAAI,WAAW,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC1F,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;QACH,CAAC;QAED,MAAM,KAAK,GAAG,QAAQ,CAAC,IAAI,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;QACvC,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,KAAK,GAAG,CAAC,EAAE,CAAC;YAC9B,OAAO,CAAC,KAAK,CAAC,kDAAkD,CAAC,CAAC;YAClE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,IAAI,YAAgC,CAAC;QACrC,IAAI,IAAI,CAAC,SAAS,KAAK,SAAS,EAAE,CAAC;YACjC,YAAY,GAAG,UAAU,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;YAC1C,IAAI,KAAK,CAAC,YAAY,CAAC,IAAI,YAAY,GAAG,CAAC,IAAI,YAAY,GAAG,CAAC,EAAE,CAAC;gBAChE,OAAO,CAAC,KAAK,CAAC,gEAAgE,CAAC,CAAC;gBAChF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;QACH,CAAC;QAED,kFAAkF;QAClF,MAAM,UAAU,GAAa;YAC3B,uBAAuB;YACvB,iBAAiB;SAClB,CAAC;QACF,MAAM,MAAM,GAAc,CAAC,CAAC,WAAW,EAAE,OAAO,EAAE,KAAK,CAAC,CAAC,CAAC;QAC1D,IAAI,QAAQ,GAAG,CAAC,CAAC;QAEjB,4DAA4D;QAC5D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;QACnE,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,iBAAiB,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE;gBAC5C,MAAM,CAAC,IAAI,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;gBACvB,MAAM,GAAG,GAAG,QAAQ,EAAE,CAAC;gBACvB,OAAO,4BAA4B,GAAG,6BAA6B,GAAG,QAAQ,GAAG,eAAe,CAAC;YACnG,CAAC,CAAC,CAAC;YACH,UAAU,CAAC,IAAI,CAAC,IAAI,iBAAiB,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACzD,CAAC;QAED,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,UAAU,CAAC,IAAI,CAAC,WAAW,QAAQ,EAAE,EAAE,CAAC,CAAC;YACzC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACzB,CAAC;QAED,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;YAC/B,UAAU,CAAC,IAAI,CAAC,iBAAiB,QAAQ,EAAE,EAAE,CAAC,CAAC;YAC/C,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC;QAC5B,CAAC;QAED,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QAEnB,MAAM,GAAG,GAAG;;iBAED,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC;;kBAEvB,QAAQ,EAAE,CAAC;QAEvB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAW5B,GAAG,EAAE,MAAM,CAAC,CAAC;QAEhB,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC;QAE1B,mBAAmB;QACnB,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC;YAC5C,MAAM,SAAS,EAAE,CAAC;YAClB,OAAO;QACT,CAAC;QAED,gBAAgB;QAChB,OAAO,CAAC,GAAG,CAAC,OAAO,IAAI,0BAA0B,KAAK,IAAI,CAAC,CAAC;QAE5D,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,UAAU,GAAa,CAAC,UAAU,QAAQ,GAAG,CAAC,CAAC;YACrD,IAAI,IAAI,CAAC,IAAI;gBAAE,UAAU,CAAC,IAAI,CAAC,QAAQ,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;YACpD,IAAI,YAAY,KAAK,SAAS;gBAAE,UAAU,CAAC,IAAI,CAAC,cAAc,YAAY,EAAE,CAAC,CAAC;YAC9E,OAAO,CAAC,GAAG,CAAC,uBAAuB,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YAChE,OAAO,CAAC,GAAG,CAAC,yEAAyE,CAAC,CAAC;YACvF,MAAM,SAAS,EAAE,CAAC;YAClB,OAAO;QACT,CAAC;QAED,OAAO,CAAC,GAAG,CAAC,KAAK,KAAK,CAAC,MAAM,UAAU,KAAK,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,SAAS,IAAI,GAAG,QAAQ,GAAG,KAAK,IAAI,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,YAAY,KAAK,SAAS,CAAC,CAAC,CAAC,kBAAkB,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC;QAE5N,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;YACtB,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAC;YACpC,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,IAAI,EAAE,CAAC;YAEjC,gBAAgB;YAChB,MAAM,KAAK,GAAI,KAAK,CAAC,KAAgB,IAAK,IAAI,CAAC,KAAgB;gBAC5D,KAAK,CAAC,IAAe,IAAK,IAAI,CAAC,IAAe;gBAC/C,IAAI,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAEvB,sBAAsB;YACtB,MAAM,WAAW,GAAI,KAAK,CAAC,WAAsB,IAAK,IAAI,CAAC,WAAsB;gBAC9E,KAAK,CAAC,MAAiB,IAAK,KAAK,CAAC,OAAkB,IAAI,EAAE,CAAC;YAE9D,cAAc;YACd,MAAM,IAAI,GAAG,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,EAAE,CAAC;YAEvC,aAAa;YACb,MAAM,SAAS,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;YAE9C,2BAA2B;YAC3B,MAAM,KAAK,GAAG,cAAc,CAAC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC;YAClD,MAAM,IAAI,GAAG,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,KAAK,EAAE,CAAC;YAEvE,OAAO,CAAC,GAAG,CAAC,KAAK,IAAI,KAAK,SAAS,KAAK,IAAI,GAAG,KAAK,GAAG,KAAK,EAAE,CAAC,CAAC;YAChE,OAAO,CAAC,GAAG,CAAC,oBAAoB,KAAK,KAAK,IAAI,KAAK,GAAG,GAAG,IAAI,CAAC,KAAK,GAAG,KAAK,EAAE,CAAC,CAAC;YAE/E,IAAI,WAAW,EAAE,CAAC;gBAChB,OAAO,CAAC,GAAG,CAAC,SAAS,GAAG,GAAG,QAAQ,CAAC,WAAW,EAAE,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,CAAC;YAClE,CAAC;YAED,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAClB,CAAC;QAED,SAAS;QACT,OAAO,CAAC,GAAG,CAAC,KAAK,GAAG,mEAAmE,KAAK,EAAE,CAAC,CAAC;QAChG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAEhB,MAAM,SAAS,EAAE,CAAC;IACpB,CAAC;IAAC,OAAO,GAAY,EAAE,CAAC;QACtB,MAAM,OAAO,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAEjE,IAAI,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;YACrC,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;YAC/D,OAAO,CAAC,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACtE,CAAC;aAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,mBAAmB,CAAC,EAAE,CAAC;YACjD,OAAO,CAAC,KAAK,CAAC,uCAAuC,CAAC,CAAC;YACvD,OAAO,CAAC,KAAK,CAAC,0DAA0D,CAAC,CAAC;QAC5E,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,cAAc,OAAO,IAAI,CAAC,CAAC;QAC3C,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC,CAAC,CAAC"}

package/dist/commands/start.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"start.d.ts","sourceRoot":"","sources":["../../src/commands/start.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,eAAO,MAAM,YAAY,SAmPrB,CAAC"}

package/dist/commands/start.js

@@ -0,0 +1,205 @@
+// codify start — start the Codify MCP server + background services
+import { Command } from "commander";
+import { loadProjectConfig } from "../lib/config.js";
+export const startCommand = new Command("start")
+    .description("Start the Codify MCP server (for Claude Code integration)")
+    .option("--http", "Also start the HTTP API (GraphQL + REST) on port 4000")
+    .action(async (opts) => {
+    try {
+        // Set environment defaults from .codify/config.json if present
+        await loadProjectConfig();
+        // Import app modules dynamically to avoid loading everything at CLI parse time
+        const { getPool, closePool } = await import("@codify/graph");
+        const { createEventBus } = await import("@codify/events");
+        const { startGapEngine, CollectionPlanner } = await import("@codify/agents");
+        const { MetabolismService } = await import("@codify/metabolism");
+        const { GraphServiceAdapter } = await import("@codify/app");
+        // 1. Connect to PostgreSQL
+        const pool = getPool();
+        const { rows } = await pool.query("SELECT 1 AS ok");
+        if (rows[0]?.ok !== 1) {
+            console.error("Failed to connect to PostgreSQL. Run 'codify init' first.");
+            process.exit(1);
+        }
+        console.error("  ✓ PostgreSQL connected");
+        // 2. Set up graph service
+        const graphService = new GraphServiceAdapter();
+        // 3. Connect event bus
+        const eventBus = await createEventBus({
+            servers: process.env.NATS_URL ?? "nats://localhost:4222",
+        });
+        console.error("  ✓ NATS connected");
+        // 4. Start background services
+        const gapEngine = await startGapEngine();
+        const metabolism = new MetabolismService(eventBus);
+        await metabolism.start();
+        // 5. Start collection planner (listens for gap events, creates plans)
+        const collectionPlanner = new CollectionPlanner(eventBus);
+        await collectionPlanner.start();
+        // 5b. Auto-collection subscriber: mine graph for evidence when gaps are detected
+        {
+            const { collectEvidenceForGap } = await import("./collect.js");
+            let lastCollectionTime = 0;
+            let collectionsThisMinute = 0;
+            let minuteStart = Date.now();
+            eventBus.subscriber.subscribe("gap.detected.>", async (event) => {
+                const ev = event;
+                if (!ev.gapNodeId)
+                    return;
+                // Rate limit: max 10 per minute, 5s cooldown
+                const now = Date.now();
+                if (now - minuteStart > 60_000) {
+                    collectionsThisMinute = 0;
+                    minuteStart = now;
+                }
+                if (collectionsThisMinute >= 10)
+                    return;
+                if (now - lastCollectionTime < 5_000)
+                    return;
+                collectionsThisMinute++;
+                lastCollectionTime = now;
+                try {
+                    // Get affected nodes for this gap
+                    const affectedResult = await pool.query(`SELECT n.id, n.type, n.properties, n.metadata
+               FROM nodes n
+               JOIN edges e ON (e.source_id = n.id OR e.target_id = n.id)
+               WHERE (e.source_id = $1 OR e.target_id = $1)
+                 AND n.id != $1
+                 AND n.superseded_by IS NULL
+               GROUP BY n.id, n.type, n.properties, n.metadata`, [ev.gapNodeId]);
+                    const affectedNodes = affectedResult.rows.map((r) => {
+                        const p = r.properties ?? {};
+                        const m = r.metadata ?? {};
+                        return {
+                            id: r.id,
+                            type: r.type,
+                            title: p.title ?? m.title ??
+                                p.name ?? m.name ?? "(untitled)",
+                        };
+                    });
+                    if (affectedNodes.length === 0)
+                        return;
+                    const { evidenceNodes, edgesCreated } = await collectEvidenceForGap(pool, ev.gapNodeId, affectedNodes);
+                    if (evidenceNodes.length > 0) {
+                        // Update gap status to evidence_found
+                        await pool.query(`UPDATE nodes
+                 SET properties = jsonb_set(properties, '{status}', '"evidence_found"'),
+                     updated_at = now()
+                 WHERE id = $1
+                   AND COALESCE(properties->>'status', 'detected') = 'detected'`, [ev.gapNodeId]);
+                        // Get gap title for logging
+                        const gapResult = await pool.query(`SELECT properties FROM nodes WHERE id = $1`, [ev.gapNodeId]);
+                        const gapTitle = gapResult.rows[0]?.properties?.title ??
+                            gapResult.rows[0]?.properties?.description?.slice(0, 50) ?? ev.gapNodeId.slice(0, 12);
+                        console.error(`[collection] Auto-collected ${evidenceNodes.length} evidence node${evidenceNodes.length === 1 ? "" : "s"} for gap: ${gapTitle}`);
+                    }
+                }
+                catch (err) {
+                    // Log and continue — never crash the MCP server
+                    console.error(`[collection] Auto-collection error: ${err instanceof Error ? err.message : String(err)}`);
+                }
+            }, { group: "auto-collector" });
+            console.error("  ✓ Auto-collection subscriber ready");
+        }
+        // 6. Wire up bootstrap and graph stats functions
+        const { createIngestService } = await import("@codify/agents");
+        const bootstrapFn = async (repoPath) => {
+            const ingest = await createIngestService({
+                minerBatchSize: 10,
+                enableDedup: true,
+                autoPromoteThreshold: 0.7,
+            });
+            await ingest.registry.connect("local-git", {
+                type: "local",
+                credentials: { repoPath },
+            });
+            const startTime = Date.now();
+            const result = await ingest.bootstrap.run("local-git");
+            return {
+                connectorId: "local-git",
+                totalArtifacts: result.totalArtifacts,
+                nodesCreated: result.pipeline.created.length,
+                nodesMerged: result.pipeline.merged.length,
+                durationMs: Date.now() - startTime,
+            };
+        };
+        const graphStatsFn = async () => {
+            const { query } = await import("@codify/graph");
+            const [nodeStats, edgeCount, gapCount, freshnessAvg, oldestNewest] = await Promise.all([
+                query("SELECT type, COUNT(*)::int as count FROM nodes WHERE superseded_by IS NULL GROUP BY type"),
+                query("SELECT COUNT(*)::int as count FROM edges"),
+                query("SELECT COUNT(*)::int as count FROM nodes WHERE type = 'Gap' AND superseded_by IS NULL"),
+                query("SELECT COALESCE(AVG(freshness), 0)::float as avg FROM nodes WHERE superseded_by IS NULL"),
+                query("SELECT MIN(created_at) as oldest, MAX(created_at) as newest FROM nodes WHERE superseded_by IS NULL"),
+            ]);
+            const nodesByType = {};
+            let totalNodes = 0;
+            for (const row of nodeStats.rows) {
+                nodesByType[row.type] = row.count;
+                totalNodes += row.count;
+            }
+            const layerStats = await query("SELECT layer, COUNT(*)::int as count FROM nodes WHERE superseded_by IS NULL GROUP BY layer");
+            const nodesByLayer = {};
+            for (const row of layerStats.rows) {
+                nodesByLayer[row.layer] = row.count;
+            }
+            return {
+                totalNodes,
+                totalEdges: edgeCount.rows[0]?.count ?? 0,
+                nodesByType,
+                nodesByLayer,
+                avgFreshness: freshnessAvg.rows[0]?.avg ?? 0,
+                gapCount: gapCount.rows[0]?.count ?? 0,
+                oldestNode: oldestNewest.rows[0]?.oldest?.toISOString() ?? null,
+                newestNode: oldestNewest.rows[0]?.newest?.toISOString() ?? null,
+            };
+        };
+        // 6. Start MCP server on stdio (primary mode for Claude Code)
+        if (opts.http) {
+            const { startServer } = await import("@codify/api");
+            await startServer(graphService, { eventBus });
+        }
+        else {
+            const { startMcpStdio } = await import("@codify/api");
+            await startMcpStdio(graphService, {
+                bootstrapFn,
+                graphStatsFn,
+                collectionPlannerFn: () => collectionPlanner.listPlans(),
+                gapQueueFn: (filters) => gapEngine.gapQueue.listGaps(filters),
+            });
+            console.error("  ✓ MCP server ready on stdio");
+        }
+        // Graceful shutdown
+        const shutdown = async (signal) => {
+            console.error(`[codify] Shutting down (${signal})...`);
+            try {
+                await metabolism.stop();
+                await gapEngine.stop();
+                await eventBus.close();
+                await closePool();
+                process.exit(0);
+            }
+            catch {
+                process.exit(1);
+            }
+        };
+        process.on("SIGINT", () => shutdown("SIGINT"));
+        process.on("SIGTERM", () => shutdown("SIGTERM"));
+    }
+    catch (err) {
+        const message = err instanceof Error ? err.message : String(err);
+        if (message.includes("ECONNREFUSED")) {
+            console.error("\n  ERROR: Cannot connect to Codify services.");
+            console.error("  Run 'codify init' to start the infrastructure.\n");
+        }
+        else if (message.includes("ANTHROPIC_API_KEY")) {
+            console.error("\n  ERROR: ANTHROPIC_API_KEY not set.");
+            console.error("  Export your API key: export ANTHROPIC_API_KEY=sk-...\n");
+        }
+        else {
+            console.error(`\n  ERROR: ${message}\n`);
+        }
+        process.exit(1);
+    }
+});
+//# sourceMappingURL=start.js.map

package/dist/commands/start.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"start.js","sourceRoot":"","sources":["../../src/commands/start.ts"],"names":[],"mappings":"AAAA,mEAAmE;AAEnE,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AACpC,OAAO,EAAE,iBAAiB,EAAE,MAAM,kBAAkB,CAAC;AAErD,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,OAAO,CAAC,OAAO,CAAC;KAC7C,WAAW,CAAC,2DAA2D,CAAC;KACxE,MAAM,CAAC,QAAQ,EAAE,uDAAuD,CAAC;KACzE,MAAM,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE;IACrB,IAAI,CAAC;QACL,+DAA+D;QAC/D,MAAM,iBAAiB,EAAE,CAAC;QAE1B,+EAA+E;QAC/E,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,CAAC;QAC7D,MAAM,EAAE,cAAc,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAC;QAC1D,MAAM,EAAE,cAAc,EAAE,iBAAiB,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAC;QAC7E,MAAM,EAAE,iBAAiB,EAAE,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,CAAC;QACjE,MAAM,EAAE,mBAAmB,EAAE,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC;QAE5D,2BAA2B;QAC3B,MAAM,IAAI,GAAG,OAAO,EAAE,CAAC;QACvB,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC;QACpD,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,CAAC;YACtB,OAAO,CAAC,KAAK,CAAC,2DAA2D,CAAC,CAAC;YAC3E,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QACD,OAAO,CAAC,KAAK,CAAC,0BAA0B,CAAC,CAAC;QAE1C,0BAA0B;QAC1B,MAAM,YAAY,GAAG,IAAI,mBAAmB,EAAE,CAAC;QAE/C,uBAAuB;QACvB,MAAM,QAAQ,GAAG,MAAM,cAAc,CAAC;YACpC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,QAAQ,IAAI,uBAAuB;SACzD,CAAC,CAAC;QACH,OAAO,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC;QAEpC,+BAA+B;QAC/B,MAAM,SAAS,GAAG,MAAM,cAAc,EAAE,CAAC;QACzC,MAAM,UAAU,GAAG,IAAI,iBAAiB,CAAC,QAAQ,CAAC,CAAC;QACnD,MAAM,UAAU,CAAC,KAAK,EAAE,CAAC;QAEzB,sEAAsE;QACtE,MAAM,iBAAiB,GAAG,IAAI,iBAAiB,CAAC,QAAQ,CAAC,CAAC;QAC1D,MAAM,iBAAiB,CAAC,KAAK,EAAE,CAAC;QAEhC,iFAAiF;QACjF,CAAC;YACC,MAAM,EAAE,qBAAqB,EAAE,GAAG,MAAM,MAAM,CAAC,cAAc,CAAC,CAAC;YAC/D,IAAI,kBAAkB,GAAG,CAAC,CAAC;YAC3B,IAAI,qBAAqB,GAAG,CAAC,CAAC;YAC9B,IAAI,WAAW,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAE7B,QAAQ,CAAC,UAAU,CAAC,SAAS,CAC3B,gBAAgB,EAChB,KAAK,EAAE,KAAc,EAAE,EAAE;gBACvB,MAAM,EAAE,GAAG,KAA+B,CAAC;gBAC3C,IAAI,CAAC,EAAE,CAAC,SAAS;oBAAE,OAAO;gBAE1B,6CAA6C;gBAC7C,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;gBACvB,IAAI,GAAG,GAAG,WAAW,GAAG,MAAM,EAAE,CAAC;oBAC/B,qBAAqB,GAAG,CAAC,CAAC;oBAC1B,WAAW,GAAG,GAAG,CAAC;gBACpB,CAAC;gBACD,IAAI,qBAAqB,IAAI,EAAE;oBAAE,OAAO;gBACxC,IAAI,GAAG,GAAG,kBAAkB,GAAG,KAAK;oBAAE,OAAO;gBAE7C,qBAAqB,EAAE,CAAC;gBACxB,kBAAkB,GAAG,GAAG,CAAC;gBAEzB,IAAI,CAAC;oBACH,kCAAkC;oBAClC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,KAAK,CAMrC;;;;;;+DAMiD,EACjD,CAAC,EAAE,CAAC,SAAS,CAAC,CACf,CAAC;oBAEF,MAAM,aAAa,GAAG,cAAc,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;wBAClD,MAAM,CAAC,GAAG,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC;wBAC7B,MAAM,CAAC,GAAG,CAAC,CAAC,QAAQ,IAAI,EAAE,CAAC;wBAC3B,OAAO;4BACL,EAAE,EAAE,CAAC,CAAC,EAAE;4BACR,IAAI,EAAE,CAAC,CAAC,IAAI;4BACZ,KAAK,EAAG,CAAC,CAAC,KAAgB,IAAK,CAAC,CAAC,KAAgB;gCAC9C,CAAC,CAAC,IAAe,IAAK,CAAC,CAAC,IAAe,IAAI,YAAY;yBAC3D,CAAC;oBACJ,CAAC,CAAC,CAAC;oBAEH,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC;wBAAE,OAAO;oBAEvC,MAAM,EAAE,aAAa,EAAE,YAAY,EAAE,GAAG,MAAM,qBAAqB,CACjE,IAAI,EACJ,EAAE,CAAC,SAAS,EACZ,aAAa,CACd,CAAC;oBAEF,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;wBAC7B,sCAAsC;wBACtC,MAAM,IAAI,CAAC,KAAK,CACd;;;;gFAIgE,EAChE,CAAC,EAAE,CAAC,SAAS,CAAC,CACf,CAAC;wBAEF,4BAA4B;wBAC5B,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAChC,4CAA4C,EAC5C,CAAC,EAAE,CAAC,SAAS,CAAC,CACf,CAAC;wBACF,MAAM,QAAQ,GAAI,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,KAAgB;4BAC9D,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,WAAsB,EAAE,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAEpG,OAAO,CAAC,KAAK,CAAC,+BAA+B,aAAa,CAAC,MAAM,iBAAiB,aAAa,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,aAAa,QAAQ,EAAE,CAAC,CAAC;oBAClJ,CAAC;gBACH,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,gDAAgD;oBAChD,OAAO,CAAC,KAAK,CAAC,uCAAuC,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;gBAC3G,CAAC;YACH,CAAC,EACD,EAAE,KAAK,EAAE,gBAAgB,EAAE,CAC5B,CAAC;YACF,OAAO,CAAC,KAAK,CAAC,sCAAsC,CAAC,CAAC;QACxD,CAAC;QAED,iDAAiD;QACjD,MAAM,EAAE,mBAAmB,EAAE,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,CAAC;QAE/D,MAAM,WAAW,GAAG,KAAK,EAAE,QAAgB,EAAE,EAAE;YAC7C,MAAM,MAAM,GAAG,MAAM,mBAAmB,CAAC;gBACvC,cAAc,EAAE,EAAE;gBAClB,WAAW,EAAE,IAAI;gBACjB,oBAAoB,EAAE,GAAG;aAC1B,CAAC,CAAC;YAEH,MAAM,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,WAAW,EAAE;gBACzC,IAAI,EAAE,OAAO;gBACb,WAAW,EAAE,EAAE,QAAQ,EAAE;aAC1B,CAAC,CAAC;YAEH,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAC7B,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC;YAEvD,OAAO;gBACL,WAAW,EAAE,WAAW;gBACxB,cAAc,EAAE,MAAM,CAAC,cAAc;gBACrC,YAAY,EAAE,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,MAAM;gBAC5C,WAAW,EAAE,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM;gBAC1C,UAAU,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS;aACnC,CAAC;QACJ,CAAC,CAAC;QAEF,MAAM,YAAY,GAAG,KAAK,IAAI,EAAE;YAC9B,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,CAAC;YAEhD,MAAM,CAAC,SAAS,EAAE,SAAS,EAAE,QAAQ,EAAE,YAAY,EAAE,YAAY,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;gBACrF,KAAK,CAAC,0FAA0F,CAAC;gBACjG,KAAK,CAAC,0CAA0C,CAAC;gBACjD,KAAK,CAAC,uFAAuF,CAAC;gBAC9F,KAAK,CAAC,yFAAyF,CAAC;gBAChG,KAAK,CAAC,oGAAoG,CAAC;aAC5G,CAAC,CAAC;YAEH,MAAM,WAAW,GAA2B,EAAE,CAAC;YAC/C,IAAI,UAAU,GAAG,CAAC,CAAC;YACnB,KAAK,MAAM,GAAG,IAAI,SAAS,CAAC,IAAI,EAAE,CAAC;gBACjC,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC;gBAClC,UAAU,IAAI,GAAG,CAAC,KAAK,CAAC;YAC1B,CAAC;YAED,MAAM,UAAU,GAAG,MAAM,KAAK,CAAC,4FAA4F,CAAC,CAAC;YAC7H,MAAM,YAAY,GAA2B,EAAE,CAAC;YAChD,KAAK,MAAM,GAAG,IAAI,UAAU,CAAC,IAAI,EAAE,CAAC;gBAClC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,KAAK,CAAC;YACtC,CAAC;YAED,OAAO;gBACL,UAAU;gBACV,UAAU,EAAE,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC;gBACzC,WAAW;gBACX,YAAY;gBACZ,YAAY,EAAE,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,CAAC;gBAC5C,QAAQ,EAAE,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,KAAK,IAAI,CAAC;gBACtC,UAAU,EAAE,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,IAAI,IAAI;gBAC/D,UAAU,EAAE,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,WAAW,EAAE,IAAI,IAAI;aAChE,CAAC;QACJ,CAAC,CAAC;QAEF,8DAA8D;QAC9D,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YACd,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC;YACpD,MAAM,WAAW,CAAC,YAAY,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAC;QAChD,CAAC;aAAM,CAAC;YACN,MAAM,EAAE,aAAa,EAAE,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC;YACtD,MAAM,aAAa,CAAC,YAAY,EAAE;gBAChC,WAAW;gBACX,YAAY;gBACZ,mBAAmB,EAAE,GAAG,EAAE,CAAC,iBAAiB,CAAC,SAAS,EAAE;gBACxD,UAAU,EAAE,CAAC,OAAO,EAAE,EAAE,CAAC,SAAS,CAAC,QAAQ,CAAC,QAAQ,CAAC,OAAO,CAAC;aAC9D,CAAC,CAAC;YACH,OAAO,CAAC,KAAK,CAAC,+BAA+B,CAAC,CAAC;QACjD,CAAC;QAED,oBAAoB;QACpB,MAAM,QAAQ,GAAG,KAAK,EAAE,MAAc,EAAE,EAAE;YACxC,OAAO,CAAC,KAAK,CAAC,2BAA2B,MAAM,MAAM,CAAC,CAAC;YACvD,IAAI,CAAC;gBACH,MAAM,UAAU,CAAC,IAAI,EAAE,CAAC;gBACxB,MAAM,SAAS,CAAC,IAAI,EAAE,CAAC;gBACvB,MAAM,QAAQ,CAAC,KAAK,EAAE,CAAC;gBACvB,MAAM,SAAS,EAAE,CAAC;gBAClB,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;QACH,CAAC,CAAC;QAEF,OAAO,CAAC,EAAE,CAAC,QAAQ,EAAE,GAAG,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAC;QAC/C,OAAO,CAAC,EAAE,CAAC,SAAS,EAAE,GAAG,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC;IACjD,CAAC;IAAC,OAAO,GAAY,EAAE,CAAC;QACtB,MAAM,OAAO,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QAEjE,IAAI,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAC,EAAE,CAAC;YACrC,OAAO,CAAC,KAAK,CAAC,+CAA+C,CAAC,CAAC;YAC/D,OAAO,CAAC,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACtE,CAAC;aAAM,IAAI,OAAO,CAAC,QAAQ,CAAC,mBAAmB,CAAC,EAAE,CAAC;YACjD,OAAO,CAAC,KAAK,CAAC,uCAAuC,CAAC,CAAC;YACvD,OAAO,CAAC,KAAK,CAAC,0DAA0D,CAAC,CAAC;QAC5E,CAAC;aAAM,CAAC;YACN,OAAO,CAAC,KAAK,CAAC,cAAc,OAAO,IAAI,CAAC,CAAC;QAC3C,CAAC;QACD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;AACH,CAAC,CAAC,CAAC"}

package/dist/commands/status.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"status.d.ts","sourceRoot":"","sources":["../../src/commands/status.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAGpC,eAAO,MAAM,aAAa,SAiStB,CAAC"}