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Number of enabled extenstions.
For each extension check.
- compatibility with Magento version you are upgrading to [CRIT]
- class rewrites
- layout updates
- addition of foreign keys in install scripts
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Custom theme
- if upgrade made from version before 1.4 [CRIT]
- if layout XMLs are overwritten
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app/code/local/Mage [CRIT]
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core modifications [CRIT]