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Package-based projects have an extra tab called Packages. This tab allows you to define groups of files that will be built and deployed together.
If there are inactive files within the package, they will be ignored during the build process and excluded from the artifacts. However, if a file is deactivated after the package has been built, the inactive file will still be deployed unless the package is rebuilt and a new version is deployed.
The screenshot below shows a Salesforce project with several packages in it.
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