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1. Add an index.php in the package from the old package. It is just a file to redirect to the /public folder.
2. Make script where Database ENGINE is InnoDB
3. Copy composer.phar and vendor folder from manual zip.
4. Upgrade guide for 3.2.x to 4.x https://github.com/thebuggenie/thebuggenie/blob/master/UPGRADE.md
5. We are disabling upgrade from 3.2.x because manual upgrade is not working from 3.2 x to 4.1.9. Try to add it in next version.
6. We have disabled script on windows because it creates symlinks to load images and on windows symlinks can not be created.
7. Upgrade Disabled in 4.3.1 because upgrade button disabled on entering password during upgrade.