There are many ways to install magento2, deploying from GIT, Downloading from magentocommerce or doing a composer installation.
What i find odd is that those 3 different ways of installing result in 3 different structures. One where the files are in app/code/magento and the other in vendor/magento/
Also one where you can use the upgrade and connect wizard in the backend, and the other where you can do a easy composer update.
What i did a while back since composer kept failing on my dev location, is a git deploy which went smooth but now gives me a hard time updating. Having some dependencies installed from composer, but still stuck on 2.0.0.
Whats the best way to proceed, and whats normally the best-practice way to install, i'd say composer, but not sure what the community thinks. You guys think a fresh install, migration of extensions and theme + adding my DB is the right way to proceed? For now its not running that smooth.
For example what i did now is i made a fresh install via composer, looks the most clean to be honest. Connected it to my existing 2.0.0 db and did
bin/magento setup:upgrade
bin/magento setup:di:compile
but then the next errors pop-up
a:4:{i:0;s:1755:"Please upgrade your database: Run "bin/magento setup:upgrade" from the Magento root directory.
The following modules are outdated:
Magento_Theme schema: current version - 2.0.1, required version - 2.0.0
Magento_Theme data: current version - 2.0.1, required version - 2.0.0
Magento_Customer schema: current version - 2.0.7, required version - 2.0.6
Magento_Customer data: current version - 2.0.7, required version - 2.0.6
Magento_Cms schema: current version - 2.0.1, required version - 2.0.0
Magento_Cms data: current version - 2.0.1, required version - 2.0.0
....