[Bug]: storybook@latest upgrade is not idempotent and misleading

[ianzone]

Describe the bug

When it runs, it

• found a 'viteConfigFile' migration, but there exists a vite.config.ts
• found a 'github-flavored-markdown-mdx' migration, but there is no markdown under src/
• found a 'autodocsTrue' migration, but it's contradicted with the 'autodocs-tags' migration

Reproduction link

https://github.com/ianzone/react-storybook

Reproduction steps

1. clone https://github.com/ianzone/react-storybook
2. bun i
3. bunx storybook@latest upgrade

System

Storybook Environment Info:

  System:
    OS: Linux 5.15 Ubuntu 24.04.1 LTS 24.04.1 LTS (Noble Numbat)
    CPU: (20) x64 13th Gen Intel(R) Core(TM) i7-13800H
    Shell: 5.9 - /home/linuxbrew/.linuxbrew/bin/zsh
  Binaries:
    Node: 22.13.1 - /home/linuxbrew/.linuxbrew/opt/node@22/bin/node
    Yarn: 1.22.22 - /home/linuxbrew/.linuxbrew/bin/yarn
    npm: 10.9.2 - ~/templates/react-storybook/node_modules/.bin/npm
    pnpm: 10.2.0 - /home/linuxbrew/.linuxbrew/bin/pnpm
  npmPackages:
    @storybook/addon-a11y: ^8.5.3 => 8.5.3
    @storybook/addon-coverage: ^1.0.5 => 1.0.5
    @storybook/addon-essentials: ^8.5.3 => 8.5.3
    @storybook/addon-interactions: ^8.5.3 => 8.5.3
    @storybook/addon-links: ^8.5.3 => 8.5.3
    @storybook/blocks: ^8.5.3 => 8.5.3
    @storybook/react: ^8.5.3 => 8.5.3
    @storybook/react-vite: ^8.5.3 => 8.5.3
    @storybook/test: ^8.5.3 => 8.5.3
    @storybook/test-runner: ^0.21.0 => 0.21.0
    chromatic: ^11.25.2 => 11.25.2
    storybook: ^8.5.3 => 8.5.3

Additional context

No response

[greptile-apps]

** Disclaimer** This information might be inaccurate, due to it being generated automatically
This appears to be related to the upgrade command's migration detection logic. The specific issues can be addressed by: 1. For viteConfigFile migration: Add a check in the migration detection to verify if the found config file is actually a Vite config by checking its contents/exports. 2. For github-flavored-markdown-mdx: The migration detection should be updated to only trigger if .md/.mdx files exist in any directory that's included in the Storybook configuration's stories patterns, not just src/. 3. For autodocsTrue and autodocs-tags conflict: These migrations should be made mutually exclusive in the upgrade logic. The autodocs-tags migration should take precedence if both conditions are met. The relevant code would be in the automigrations system, likely under the code/lib/cli/src/automigrate directory.

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