It seems like now you can only have a single Jenkinsfile in a single location in your project when using Multibranch type.
Is there a way to configure so I can place the Jenkinsfile somewhere else than in the root of the project under the name Jenkinsfile. There's hope, as there's an option of Fixed Configuration, maybe this is a feature for the future, but I would much appreciate the option, as in the current situation I do not have the option to run everything as one nicely compiled pipeline due to the size of the repo. I'm thinking of having multiple Jenkins jobs against the same repository.
-- Marcus
Starting with Pipeline: Multibranch plugin version 2.15, you can specify the Jenkinsfile location in your configuration.
See my answer at https://stackoverflow.com/a/45172149/2141666 and the plugin changelog at https://wiki.jenkins.io/display/JENKINS/Pipeline+Multibranch+Plugin. From the changelog:
2.15 (Jun 01, 2017)
JENKINS-34561 Option to select a script name/path other than Jenkinsfile.