What actions affect files, DB, or both?

I’m looking into setting up a development -> staging -> production workflow, and the biggest issue so far is figuring out how to sync the databases.

To this end, I’m trying to figure out exactly which actions will affect the filesystem, the database, or both. Here’s how I think it works. Please correct me where I’m wrong, and let me know if my questionable answers are right!

• Registering a new user – database
• Adding a post or comment – database
• Changing to a new theme – database?
• Changing a theme’s settings – database
• Installing or removing a plugin – filesystem
• Activating, or deactivating a plugin – filesystem
• Updating a plugin – filesystem and database? (DB structure may change?)
• Changing a plugin’s settings – database
• Uploading media – filesystem and database?
• Editing custom files not included in a theme or plugin – filesystem
• Upgrading WordPress – filesystem?

• Registering a new user – database
• Adding a post or comment – database
• Changing to a new theme – database(yes)
• Changing a theme’s settings – database
• Installing or removing a plugin – file system,database
• Activating, or deactivating a plugin – file system,database
• Updating a plugin – file system and database (DB structure may change if plugin has custom tables registered and in the new version if it has structure changes)
• Changing a plugin’s settings – database
• Uploading media – file system and database
• Editing custom files not included in a theme or plugin – file system(this depends on the actions you are taking)
• Upgrading WordPress – file system,database