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Scaffold directory exists but looks incomplete. Run: bash .mex/setup.sh #24

Description

@zloeber

Describe the bug
When running npx mex check immediately after initial setup I get Scaffold directory exists but looks incomplete. Run: bash .mex/setup.sh. This file does not exist after setup. Note that I did run the agent configuration as prompted and it did update all relevant ./.mex/* templates.

To Reproduce
Follow all directions as posted in your docs for installing and configuring mex.

Expected behavior
Not this.

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