Since a multibranch project creates all of its subprojects (WorkflowJob), any customizations you may want to make on them must be defined at the multibranch level. So far this has been handled with BranchProperty, but that is undesirable in most cases for several reasons:

1. It defeats the idea of code-as-configuration: you are back to keeping important job configuration in $JENKINS_HOME/jobs/*/config.xml, rather than your own SCM.
2. Adjusting properties on a per-branch basis is awkward. You can use NamedExceptionsBranchPropertyStrategy, but this is extra work to configure if you have a lot of branches, and again cannot be adjusted outside the Jenkins configuration UI, or set right away for newly created branches (unless you follow a strict naming convention).
3. While we can hardcode support for certain aspects of static job configuration, as we do with WorkflowParameterDefinitionBranchProperty, BuildRetentionBranchProperty, and RateLimitBranchProperty¹, this is not extensible to JobProperty implementations defined by other plugins.

kohsuke came up with a novel idea to solve this for workflow-multibranch: add a Step which simply (re-)sets the List<JobProperty> associated with the job it is run on. You need to run one build to get the properties set, but that is usually not onerous since multibranch will always trigger an initial build for every branch anyway, and few properties really need to be set in the short interval between the new project being created and the first build getting as far as this step. Jenkinsfile can feel free to hardcode certain properties, or dynamically include some, or configure some according to branch name, etc. While it may sound weird at first blush to have a dynamic script update static properties, this is actually analogous to how Workflow supports SCM polling and triggers without the need for static SCM configuration.

So then we need to:

1. define the new step
2. delete WorkflowParameterDefinitionBranchProperty (subsumed by the new system)
3. retrofit various fields of WorkflowJob to be configured instead by JobProperty
   1. buildDiscarder (suppress the existing BuildRetentionBranchProperty)
   2. triggers (note that SCMTrigger, GitHubTrigger, etc. would be superfluous in a multibranch project, since SCMSource covers that need, but TimerTrigger and miscellaneous plugin contributions may be wanted)
   3. quietPeriod (if anyone cares)
   4. concurrentBuild
   5. authToken²

TBD whether the literate plugin would want to follow suit, or stick with the existing BranchProperty-driven approach.

Some "closed-class" BranchProperty implementations will still be needed, such as UntrustedBranchProperty or a Workflow equivalent TBD.

¹Probably this should never have been a BranchProperty at all; it has no apparent logical dependency on multibranch. Really it should be a separate plugin with a general-purpose JobProperty.

²Trickier since it is normally a per-Job secret. Fine for it to be the same for all children of a WorkflowMultiBranchProject, but should of course not be hardcoded in the script. Could use StringCredentials, though this will not work well with automatic repository scanning: you would not want to manually create a token for each repository. Nicer would be to keep a HMACConfidentialKey, with the per-project token somehow displayed to anyone with Item.BUILD.