Manual upgrade is similar than installing the new MyCollab instance, except you re-use the database files and the file assets of the previous version.
Go to https://mycollab.com/on-premise/ and select the appropriate MyCollab distribution for your organization. Delete the folders bin, lib, config, i18 and unzip the downloaded file to the existing MyCollab folder.
Do not delete the entire old MyCollab installation folder before getting everything done! All of file assets are kept in the hidden folder .mycollab. If you delete this folder then all file uploads such as attachments, profile pictures, documents, etc. will be deleted permanently.
Then you follow the instruction Install MyCollab on your server, and re-enter your database information, mail settings, etc. Then it will redirect you to the login page without setting up the application parameters again.