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Each type has metadata fields which are used to calculate the deploy command.  With the necessary privileges, you can adjust the metadata and re-evaluate the commands.  However, the preferred approach is the to adjust the project properties such that the commands are generated correctly and no manually intervention is required in the majority of cases.  For a deeper understanding of the metadata for each object type, and the role the project properties play in its generation, see EBS Object Types Reference.

For some object types, such as AOLs, you will notice the Build Command.  This is used when you are sourcing the objects from an EBS Development environment rather than an SCM.  In this case, the object will be downloaded from the EBS instance during the build using the build command.  In such cases, you can build the metadata for these objects using FlexDeploy's metadata generator (out of scope for this tutorial).

The project files are only the metadata about our source files.  The actual revision of the file is obtained during build.  Therefore, there is no reason to populate as new revisions are committed for files which are already populated.  You will only need to populate when new files are added to the repository, so that they become available in the catalog.