Branch Indexing fails with "Empty path not permitted" error

Issue

A Multibranch Pipeline is configured with Git SCM and a Custom Marker file but the Branch Indexing fails with:

ERROR: [Mon Sep 18 09:40:40 AEST 2017] Could not fetch branches from source xxxxx-xxxxx-xxxx-xxxx-xxxxx
java.lang.IllegalArgumentException: Empty path not permitted.
	at org.eclipse.jgit.treewalk.filter.PathFilter.create(PathFilter.java:80)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:205)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:249)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:281)
	at jenkins.plugins.git.AbstractGitSCMSource$2$1.stat(AbstractGitSCMSource.java:304)
	at jenkins.scm.api.SCMProbe.exists(SCMProbe.java:51)
	at com.cloudbees.workflow.multibranch.CustomBranchProjectFactory$1.isHead(CustomBranchProjectFactory.java:57)
	[...]

Environment

CloudBees Jenkins Enterprise - Managed controller (CJEMM)
CloudBees Jenkins Platform - Client controller (CJPCM)
CloudBees Jenkins Team (CJT)
Jenkins LTS
Git plugin
Pipeline: Multibranch Plugin
CloudBees Pipeline: Templates Plugin

Resolution

The CloudBees Pipeline Templates plugin offers the possibility to define Custom Pipeline as Code Scripts for your pipeline branches. It consists of:

the path to a marker file
the Pipeline script to run

So even for that mode, a Marker File is required. If the Marker File field is left empty, then Branch Indexing fails with the stacktrace

ERROR: [Mon Sep 18 09:40:40 AEST 2017] Could not fetch branches from source <sourceId>
java.lang.IllegalArgumentException: Empty path not permitted.
	at org.eclipse.jgit.treewalk.filter.PathFilter.create(PathFilter.java:80)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:205)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:249)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:281)
	at jenkins.plugins.git.AbstractGitSCMSource$2$1.stat(AbstractGitSCMSource.java:304)
	at jenkins.scm.api.SCMProbe.exists(SCMProbe.java:51)
	at com.cloudbees.workflow.multibranch.CustomBranchProjectFactory$1.isHead(CustomBranchProjectFactory.java:57)
	at jenkins.plugins.git.AbstractGitSCMSource$2.run(AbstractGitSCMSource.java:328)
	at jenkins.plugins.git.AbstractGitSCMSource$2.run(AbstractGitSCMSource.java:256)
	at jenkins.plugins.git.AbstractGitSCMSource.doRetrieve(AbstractGitSCMSource.java:225)
	at jenkins.plugins.git.AbstractGitSCMSource.retrieve(AbstractGitSCMSource.java:256)
	at jenkins.scm.api.SCMSource._retrieve(SCMSource.java:300)
	at jenkins.scm.api.SCMSource.fetch(SCMSource.java:210)
	at jenkins.branch.MultiBranchProject.computeChildren(MultiBranchProject.java:630)
	at com.cloudbees.hudson.plugins.folder.computed.ComputedFolder.updateChildren(ComputedFolder.java:266)
	at com.cloudbees.hudson.plugins.folder.computed.FolderComputation.run(FolderComputation.java:162)
	at jenkins.branch.MultiBranchProject$BranchIndexing.run(MultiBranchProject.java:969)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:405)
[Mon Sep 18 09:40:40 AEST 2017] Finished branch indexing. Indexing took 7.3 sec
FATAL: Failed to recompute children of <multibranchProjectName>
java.lang.IllegalArgumentException: Empty path not permitted.
	at org.eclipse.jgit.treewalk.filter.PathFilter.create(PathFilter.java:80)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:205)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:249)
	at org.eclipse.jgit.treewalk.TreeWalk.forPath(TreeWalk.java:281)
	at jenkins.plugins.git.AbstractGitSCMSource$2$1.stat(AbstractGitSCMSource.java:304)
	at jenkins.scm.api.SCMProbe.exists(SCMProbe.java:51)
	at com.cloudbees.workflow.multibranch.CustomBranchProjectFactory$1.isHead(CustomBranchProjectFactory.java:57)
	at jenkins.plugins.git.AbstractGitSCMSource$2.run(AbstractGitSCMSource.java:328)
	at jenkins.plugins.git.AbstractGitSCMSource$2.run(AbstractGitSCMSource.java:256)
	at jenkins.plugins.git.AbstractGitSCMSource.doRetrieve(AbstractGitSCMSource.java:225)
	at jenkins.plugins.git.AbstractGitSCMSource.retrieve(AbstractGitSCMSource.java:256)
	at jenkins.scm.api.SCMSource._retrieve(SCMSource.java:300)
	at jenkins.scm.api.SCMSource.fetch(SCMSource.java:210)
	at jenkins.branch.MultiBranchProject.computeChildren(MultiBranchProject.java:630)
	at com.cloudbees.hudson.plugins.folder.computed.ComputedFolder.updateChildren(ComputedFolder.java:266)
	at com.cloudbees.hudson.plugins.folder.computed.FolderComputation.run(FolderComputation.java:162)
	at jenkins.branch.MultiBranchProject$BranchIndexing.run(MultiBranchProject.java:969)
	at hudson.model.ResourceController.execute(ResourceController.java:97)
	at hudson.model.Executor.run(Executor.java:405)