Wrangler D1 Migrations Path Bug (Vite Plugin)

[Karsten-Zhou]

What versions & operating system are you using?

System:
OS: Windows 11 10.0.26200
CPU: (12) x64 12th Gen Intel(R) Core(TM) i5-12400F
Memory: 5.38 GB / 15.85 GB
Binaries:
Node: 24.13.0 - C:\Program Files\nodejs\node.EXE
Yarn: 1.22.19 - C:\Users\wesli\AppData\Roaming\npm\yarn.CMD
npm: 10.4.0 - C:\Program Files\nodejs\npm.CMD
bun: 1.3.7 - C:\Users\wesli.bun\bin\bun.EXE
npmPackages:
@cloudflare/vite-plugin: ^1.54.3 => 1.54.3
wrangler: ^4.128.0 => 4.128.0

Please provide a link to a minimal reproduction

https://github.com/Karsten-Zhou/wrangler-migrations-bug-repro

Describe the Bug

Issue

When using @cloudflare/vite-plugin + wrangler deploy with auto-provisioning, the original wrangler.jsonc gets its migrations_dir path incorrectly rewritten.

Project Layout

project/
├── wrangler.jsonc      # Original config
├── vite.config.ts      # @cloudflare/vite-plugin
├── package.json
├── tsconfig.json
├── migrations/
│   └── 0001_init.sql
└── server/
    └── index.ts

Steps to Reproduce

1. Install dependencies:

   npm install

2. Build the project:

   npx vite build

3. Deploy the first time (the subsequent deployments won't trigger the auto-provisioning):

   npx wrangler deploy

What Happens

1. @cloudflare/vite-plugin generates dist/my-app/wrangler.json with:

   "migrations_dir": "../../migrations"

   This is correct relative to dist/my-app/.

2. Wrangler auto-provisions the D1 database (since database_id is missing).

3. Wrangler writes the database_id back to the config.

4. BUG: It also writes "migrations_dir": "../../migrations" into the original wrangler.jsonc.

5. The original config now has an incorrect path. Subsequent database migrations fail because ../../migrations is wrong relative to the project root.

Root Cause

The bug is in the interaction between two Wrangler behaviors:

1. Vite plugin (output-config.ts) correctly rewrites migrations_dir for the generated dist/<name>/wrangler.json.
2. Wrangler auto-provisioning (experimental_patchConfig) writes the entire binding object (including the rewritten migrations_dir) back to the original config file, instead of only updating the database_id or preserving the original migrations_dir value.

Expected Fix

When experimental_patchConfig patches the original wrangler.jsonc, it should either:

• Only patch the database_id field, leaving migrations_dir untouched
• Rebase migrations_dir back to the original config's directory before writing

Please provide any relevant error logs

No response

[workers-devprod]

Automated triage

Issue assessment

• Actionability: ✅ Actionable.
• Type: Bug (high confidence).
• Reproduction: Automatic attempt requested.
• Labels:
  • package:wrangler (high)
  • package:vite-plugin (high)
  • feature:auto-provisioning (high)
  • product:d1 (medium)
  • product:deploy-config (medium)

Actionability and missing information

Claims wrangler deploy with Vite-plugin output and D1 auto-provisioning rewrites migrations_dir to a dist-relative path in the original wrangler.jsonc, breaking later migrations; root cause attributed to experimental_patchConfig writing the full binding object.

Reproduction reason: A minimal reproduction with install, build, and deploy steps describes a current config-rewrite defect that can be attempted.

Reproduction

• Result: ⚠️ Blocked.
• Summary: Automated reproduction failed before recording a result.

Evidence and attempted steps

Blocker: Automated reproduction failed before recording a result.