I'm having the same issue, for now I've worked around it (somewhat) with the following Vite config (using vite-plugin-restart):

import { defineConfig } from "vite";
import tailwindcss from "@tailwindcss/vite";
import react from "@vitejs/plugin-react";
import tsconfigPaths from "vite-tsconfig-paths";
import ViteRestart from "vite-plugin-restart";
import { TanStackRouterVite } from "@tanstack/router-plugin/vite";

export default defineConfig({
  root: "src/frontend",
  build: {
    outDir: "../../dist",
  },
  plugins: [
    // remove once https://github.com/TanStack/router/issues/3624 is fixed
    ViteRestart({
      restart: ["routes/**/*.ts(x)?"],
    }),
    tsconfigPaths(),
    TanStackRouterVite({
      target: "react",
      autoCodeSplitting: true,
      routesDirectory: "src/frontend/routes",
      generatedRouteTree: "src/frontend/routeTree.gen.ts",
    }),
    tailwindcss(),
    react(),
  ],
});

This restarts the vite process completely when any .ts(x)? file changes in the routes directory, which is definitely not ideal, but gets the job done until this gets sorted.

Found a workaround, since there seems to be bug related to the Vite root config option.
Making sure the routesDirectory option is an absolute path should fix it.

Here's an example of my vite.config.ts

import path from "path"
import tailwindcss from '@tailwindcss/vite'
import react from '@vitejs/plugin-react'
import { defineConfig } from 'vite'
import { TanStackRouterVite } from '@tanstack/router-plugin/vite'

// https://vite.dev/config/
export default defineConfig({
  plugins: [
    TanStackRouterVite({
      routesDirectory: path.resolve(process.cwd(), 'app/client/routes'),
      generatedRouteTree: 'app/client/routeTree.gen.ts',
    }),
    react(),
    tailwindcss()
  ],
  root: 'app/client',
  envDir: "../../",
  publicDir: 'public',
  resolve: {
    alias: {
      "@": path.resolve(__dirname, "./app"),
    },
  },
  server: {
    host: '127.0.0.1',
  }
})

I am also facing this. Some additional debugging:

Vite root is set as app/client

With the plugin configured as:

{
      routesDirectory: "app/client/routes",
      generatedRouteTree: "app/client/routeTree.gen.ts",
}

In https://github.com/TanStack/router/blob/main/packages/router-plugin/src/core/router-generator-plugin.ts#L66 I can observe:

• `filePath = "/app/client/routes/books/$bookId/preview.tsx"
• routesDirectoryPath = "<prefix>/app/client/app/client/routes"
  You can notice that routesDirectoryPath adds routesDirectory after the Vite root path. Also the route tree is generated at the expected location (<prefix>/app/client/routeTree.gen.ts) without prepending the Vite root path.

Initial generation works when Vite starts, but then when files are updated the generator is not ran.

If I change the plugin settings to:

{
      routesDirectory: "routes",
      generatedRouteTree: "app/client/routeTree.gen.ts",
}

Then Vite crashes at startup with

Error: ENOENT: no such file or directory, scandir '/<prefix>/routes'
    at async Module.readdir (node:internal/fs/promises:949:18)
    at async recurse (file:///<prefix>/node_modules/@tanstack/router-generator/dist/esm/filesystem/physical/getRouteNodes.js:15:19)
    at async getRouteNodes (file:///<prefix>/node_modules/@tanstack/router-generator/dist/esm/filesystem/physical/getRouteNodes.js:127:3)
    at async generator (file:///<prefix>/node_modules/@tanstack/router-generator/dist/esm/generator.js:46:27)
    at async generate (file:///<prefix>/node_modules/@tanstack/router-plugin/dist/esm/core/router-generator-plugin.js:22:7)
    at async run (file:///<prefix>/node_modules/@tanstack/router-plugin/dist/esm/core/router-generator-plugin.js:47:7)
    at async configResolved (file:///<prefix>/node_modules/@tanstack/router-plugin/dist/esm/core/router-generator-plugin.js:61:9)
    …

So the issue seems to stem from the routes path not being computed the same way between the router start and a file update. In the first case the Vite root path is not appended, but it is in the 2nd case. It also seems to never be prepended to generatedRouteTree.

A fix would probably involve unifying the behaviour here, and I would recommend always appending Vite's root path to the routes directory path and the generated route tree path for consistency.

The docs state that the routesDirectory is relative to the CWD, while it seems to be relative to root on start-up.

Based on this, expected behaviour with root of ./src and routesDirectory of ./src/routes would be that it looks for routes in {cwd}/src/routes, not ./src/src/routes as witnessed.

The issue seems to be that the plugin uses the Vite root, rather than the process.cwd(), here.

This can be removed, and it'll give the documented behaviour.