I am having this issue too. I have created a (tentative) pull request here https://github.com/jenkinsci/workflow-multibranch-plugin/pull/71 to at least leave the choice of the user to use lightweight checkout or not, that might unblock the people who used this unsupported feature until now and which actually worked.
On the comment saying that symlinks to Jenkins file are not supported, well I would say this is not the responsibility of Jenkins in general to decide that, but rather each source plugin. The current git plugin doesn't support it, neither the Bitbucket one, however for example for the Bitbucket plugin we "just" need Atlassian to add some new API in their REST API to allow this kind of things. People working in company having support contracts with Atlassian (this is my case) may have the power to ask Atlassian to do that (we haven't contacted Atlassian yet for that, I still don't know at this point if we will).
Using the above mentionned workaround of specifying a different Jenkinsfile path so that symlink work has two issues:
- all branches have to follow the same naming convention, while with symlink each branch is free to follow any convention, just symlink "Jenkinsfile" at the root
- it doesn't work when you symlink the Jenkinsfile to a submodule (it's my case). Again supporting submodules would be the responsibility of each source plugin, like the git one, or the Bitbucket one.
So please consider the above pull request, that I agree is just a workaround for now, to avoid lightweight checkout in some particular cases, rather than using the big kill switch that would disable it for all builds.