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I use git and composer in my project. My flow: 1 Each module has its own git repository. 2 I use composer and install and update modules to my project

update composer.json
composer update <module name>
composer install
./bin/magento setup:upgrade
./bin/magento cache:flush
git commit ...

In Primary repository i store composer.lock and composer.json

When i checkout to other branch and call composer install some modules are deleted. But EAV attributes remain in the database and my Magento 2 store crashes.

How I can correct uninstall modules and his EAV attributes in my flow?

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Sometimes module are not deleted correctly so you can manually remove them with the following steps

1-remove the folder app/code/<Vendor>/<Module>

2-drop module tables from database

3-remove the config settings.

DELETE FROM core_config_data WHERE path LIKE 'vendor_module/%'

4-remove the module <Vendor>_<Module> from app/etc/config.php

5-remove the module <Vendor>_<Module> from table setup_module

DELETE FROM setup_module WHERE module='<Vendor>_<Module>'

You can check here for more info https://nwdthemes.com/2016/07/12/magento-2-uninstall-module/

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