refactor(extension): auto-index on tool call and skip registration when binary missing

- Only register tool if `codexis` binary is in PATH
- Run incremental index via `pi.exec` on each tool call to keep DB fresh
- Remove `findDatabase` helper; derive DB path from git root directly
- Replace `defineTool` with inline `pi.registerTool` call
- Update imports (`@sinclair/typebox`, lazy `execSync`)
- Fix output flag help text in main.go

extension/codexis.ts

@@ -3,11 +3,14 @@
  *
  * Provides a single tool that queries the .codexis/index.db SQLite database
  * containing symbols, files, and line numbers for the codebase.
+ *
+ * - Only registers if `codexis` binary is in PATH
+ * - Auto-indexes on first tool call if DB is missing
+ * - Re-indexes (incremental) on each call to keep index fresh
  */
 
-import { Type } from "@mariozechner/pi-ai";
-import { defineTool, type ExtensionAPI } from "@mariozechner/pi-coding-agent";
-import { execSync } from "node:child_process";
+import { Type } from "@sinclair/typebox";
+import type { ExtensionAPI } from "@mariozechner/pi-coding-agent";
 import { existsSync } from "node:fs";
 import { join } from "node:path";
 import Database from "better-sqlite3";
@@ -56,6 +59,7 @@ Example queries:
 
 function findGitRoot(cwd: string): string | null {
   try {
+    const { execSync } = require("node:child_process");
     return execSync("git rev-parse --show-toplevel", {
       cwd,
       encoding: "utf-8",
@@ -66,16 +70,23 @@ function findGitRoot(cwd: string): string | null {
   }
 }
 
-function findDatabase(cwd: string): string | null {
-  const gitRoot = findGitRoot(cwd);
-  if (!gitRoot) return null;
-  const dbPath = join(gitRoot, ".codexis", "index.db");
-  if (!existsSync(dbPath)) return null;
-  return dbPath;
+function codexisAvailable(): boolean {
+  try {
+    const { execSync } = require("node:child_process");
+    execSync("which codexis", { stdio: ["pipe", "pipe", "pipe"] });
+    return true;
+  } catch {
+    return false;
+  }
 }
 
-const codexisTool = defineTool({
-  name: "codexis",
+export default function (pi: ExtensionAPI) {
+  if (!codexisAvailable()) {
+    return;
+  }
+
+  pi.registerTool({
+    name: "Codexis",
     label: "Codexis",
     description: DESCRIPTION,
     parameters: Type.Object({
@@ -84,11 +95,29 @@ const codexisTool = defineTool({
       }),
     }),
 
-  async execute(_toolCallId, params, _signal, _onUpdate, ctx) {
-    const dbPath = findDatabase(ctx.cwd);
-    if (!dbPath) {
+    async execute(_toolCallId, params, signal, _onUpdate, ctx) {
+      const gitRoot = findGitRoot(ctx.cwd);
+      if (!gitRoot) {
+        throw new Error("Not in a git repository");
+      }
+
+      const dbPath = join(gitRoot, ".codexis", "index.db");
+
+      // Run incremental index to keep DB fresh (fast if nothing changed)
+      const indexResult = await pi.exec("codexis", [gitRoot], {
+        signal,
+        timeout: 120_000,
+      });
+
+      if (indexResult.code !== 0) {
         throw new Error(
-        "No code index found. Run `codexis` in the repo root to generate .codexis/index.db"
+          `codexis indexing failed (exit ${indexResult.code}): ${indexResult.stderr}`,
+        );
+      }
+
+      if (!existsSync(dbPath)) {
+        throw new Error(
+          "codexis ran but no index.db was produced. Check codexis output.",
         );
       }
 
@@ -102,7 +131,9 @@ const codexisTool = defineTool({
           !normalized.startsWith("EXPLAIN") &&
           !normalized.startsWith("PRAGMA")
         ) {
-        throw new Error("Only SELECT, WITH, EXPLAIN, and PRAGMA queries are allowed");
+          throw new Error(
+            "Only SELECT, WITH, EXPLAIN, and PRAGMA queries are allowed",
+          );
         }
 
         const stmt = db.prepare(params.sql);
@@ -123,7 +154,7 @@ const codexisTool = defineTool({
         });
 
         const widths = columns.map((col, i) =>
-        Math.max(col.length, ...data.map((row) => row[i].length))
+          Math.max(col.length, ...data.map((row) => row[i].length)),
         );
 
         const header = columns
@@ -131,9 +162,7 @@ const codexisTool = defineTool({
           .join("  ");
         const separator = widths.map((w) => "-".repeat(w)).join("  ");
         const body = data
-        .map((row) =>
-          row.map((val, i) => val.padEnd(widths[i])).join("  ")
-        )
+          .map((row) => row.map((val, i) => val.padEnd(widths[i])).join("  "))
           .join("\n");
 
         const result = `${header}\n${separator}\n${body}`;
@@ -154,8 +183,5 @@ const codexisTool = defineTool({
         db.close();
       }
     },
-});
-
-export default function (pi: ExtensionAPI) {
-  pi.registerTool(codexisTool);
+  });
 }

main.go

@@ -20,7 +20,7 @@ const dbFileName = "index.db"
 
 func main() {
 	force := flag.Bool("force", false, "Force full re-index (ignore file hashes)")
-	output := flag.String("o", "", "Output database path (default: <root>/.codexis.db)")
+	output := flag.String("o", "", "Output database path (default: <root>/.codexis/index.db)")
 	flag.Parse()
 
 	root := "."