Is there an easy way to upgrade from one version of Crafter to another? I was just trying to update from 3.0.1 to 3.0.2 by replacing the repository but it didn't recognize anything. It doesn't seem to like anything done outside Studio. I would like to keep up with latest changes without recreating the whole site.
This is what I normally do: build the version you like using Gradle per https://github.com/craftercms/craftercms/blob/master/README.md
In your bundle folder, backup your bin like this:
mv bin bin.{date}
mv path_to_craftercms_gradle/crafter-authoring/bin bin
You can now start crafter using the new bin folder (new binaries):
bin/crafter.sh start
Heads up: Once you upgrade, the database might get upgraded which means you can't go back. Consider backing things up before. This is how to backup: http://docs.craftercms.org/en/3.0/system-administrators/backup-and-recovery.html
In general, all your data lives in ./data (mariadb, mongodb (if used), repos, solr indexes, etc.)
The reason replacing the repo didn't work because Studio has meta-data in MariaDB and hence simply replacing the repo won't be enough.
Another approach would be to replace the repo, like you tried, but ask Studio to "sync from repo" to rebuild its database based on git. While that's possible, it's involved (you need to create an "Empty" BP site, replace the repo, sync from repo, bulk publish, etc.). This is mostly useful for migrations from 2.5.x to 3.0.x. For your needs, it's simpler to just replace the bin folder.