Same here, with the same Jenkins / plugin versions:

Pruning obsolete local branches
FATAL: Command "config --get remote.origin.url" returned status code 1:
stdout:
stderr:
hudson.plugins.git.GitException: Command "config --get remote.origin.url" returned status code 1:
stdout:
stderr:
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:940)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommandIn(CliGitAPIImpl.java:921)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:865)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.launchCommand(CliGitAPIImpl.java:875)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.getRemoteUrl(CliGitAPIImpl.java:603)
at hudson.plugins.git.GitAPI.getRemoteUrl(GitAPI.java:61)
at org.jenkinsci.plugins.gitclient.CliGitAPIImpl.prune(CliGitAPIImpl.java:393)
at hudson.plugins.git.extensions.impl.PruneStaleBranch.beforeCheckout(PruneStaleBranch.java:31)
at hudson.plugins.git.GitSCM.checkout(GitSCM.java:858)
at org.jenkinsci.plugins.multiplescms.MultiSCM.checkout(MultiSCM.java:117)
at hudson.model.AbstractProject.checkout(AbstractProject.java:1376)
at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:655)
at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:560)
at hudson.model.Run.execute(Run.java:1592)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
at hudson.model.ResourceController.execute(ResourceController.java:88)
at hudson.model.Executor.run(Executor.java:237)

Confirm prune option is broken in 2.0

Code changed in jenkins
User: Nicolas De Loof
Path:
src/main/java/org/jenkinsci/plugins/gitclient/CliGitAPIImpl.java
src/main/java/org/jenkinsci/plugins/gitclient/FetchCommand.java
src/main/java/org/jenkinsci/plugins/gitclient/GitClient.java
src/main/java/org/jenkinsci/plugins/gitclient/JGitAPIImpl.java
src/main/java/org/jenkinsci/plugins/gitclient/RemoteGitImpl.java
http://jenkins-ci.org/commit/git-client-plugin/ba2ab8934e62d2cea77ec663a2a07dbfad145e2a
Log:
JENKINS-20258 introduce FetchCommand

Code changed in jenkins
User: Nicolas De Loof
Path:
pom.xml
src/main/java/hudson/plugins/git/GitSCM.java
src/main/java/hudson/plugins/git/extensions/GitSCMExtension.java
src/main/java/hudson/plugins/git/extensions/impl/PruneStaleBranch.java
http://jenkins-ci.org/commit/git-plugin/f6d42c4e7edb102d3330af5ca66a7f5809d1a48e
Log:
JENKINS-20258 prune branches during fetch

Compare: https://github.com/jenkinsci/git-plugin/compare/dc73e2539209...f6d42c4e7edb

We found that we could work around this problem by manually copying the .git folder into the workspace. It's good to know the problem is with prune, because disabling that will be a bit more efficient for us.

This is still an open issue with Git plugin 2.0.

From what I've seen, the problem occurs when the workspace is clean *and* the prune option is enabled. This causes Git plugin to run prune on an empty folder, thus causing the error:

FATAL: Command "config --get remote.origin.url" returned status code 1:

The Git plugin should check if it is on a git repo before attempting to prune it. If it's not on a git repo, ignore it and proceed to the cloning of the repo. Subsequent builds will call prune successfully.

+Henrique I believe it is expected to still be an open issue in Git plugin 2.0 because the change has not been included in a new version of the plugin. Nicolas' change was applied 8 days ago and there has not been a release of the Git plugin since then.

When the latest commit is included in a Git plugin, then that version of the Git plugin (2.0.1 or 2.1 or ...) will have the fix in a user visible version.

I assumed that Nicolas marked this as "Fixed" because the code change is in, and it will be finally resolved when I (or someone else) verifies the fix in a version which has been delivered through the Jenkins Update Center.

Incorrectly reopened, since the fix is on the source code. Can't be fully closed yet, since the fix has not yet been delivered in a release of the Git plugin.

Oh, you are so right, I completely missed those changes. Sorry about the mess.

Git client plugin 1.5.0 was intended to fix this (based on the submission ba2ab8934), but it still fails.

Steps I used to duplicate the problem with Git client plugin 1.5.0:

1. Create a new job (I named mine git-jgit-specific-subdir-prune)
2. Configure git repo URL https://github.com/MarkEWaite/check_git.git
3. Use jgit as the implementation rather than the default
4. Add behavior to checkout to a local subdirectory
5. Add behavior to prune stale remote tracking branches
6. Save the job and run it

Stack trace looks like:

Building on master in workspace /var/lib/jenkins/jobs/git-jgit-specific-subdir-prune-simple/workspace
Pruning obsolete local branches
FATAL: java.net.URISyntaxException: Cannot parse Git URI-ish: The uri was empty or null
hudson.plugins.git.GitException: java.net.URISyntaxException: Cannot parse Git URI-ish: The uri was empty or null
	at org.jenkinsci.plugins.gitclient.JGitAPIImpl.prune(JGitAPIImpl.java:913)
	at hudson.plugins.git.extensions.impl.PruneStaleBranch.beforeCheckout(PruneStaleBranch.java:31)
	at hudson.plugins.git.GitSCM.checkout(GitSCM.java:858)
	at hudson.model.AbstractProject.checkout(AbstractProject.java:1411)
	at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:652)
	at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:557)
	at hudson.model.Run.execute(Run.java:1665)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:46)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:246)
Caused by: java.net.URISyntaxException: Cannot parse Git URI-ish: The uri was empty or null
	at org.eclipse.jgit.transport.URIish.<init>(URIish.java:205)
	at org.jenkinsci.plugins.gitclient.JGitAPIImpl.listRemoteBranches(JGitAPIImpl.java:923)
	at org.jenkinsci.plugins.gitclient.JGitAPIImpl.prune(JGitAPIImpl.java:901)
	... 10 more

This is fixed for the command line implementation in git-client-plugin 1.6.2 and git-plugin 2.0.1.

It is not fixed in the JGit implementation but it now reports a much clearer error message:

JGit don't (yet) support pruning during fetch

Started by user anonymous
Building remotely on jessie64a in workspace /var/lib/jenkins/wheezy64b-slave/workspace/JENKINS-20258-checkout-to-subdir-and-prune-jgit
Cloning the remote Git repository
remote: Counting objects
remote: Compressing objects
Receiving objects
Resolving deltas
Updating references
Pruning obsolete local branches
FATAL: Failed to fetch from git://wheezy64b/git/mwaite/bin.git
hudson.plugins.git.GitException: Failed to fetch from git://wheezy64b/git/mwaite/bin.git
	at hudson.plugins.git.GitSCM.fetchFrom(GitSCM.java:625)
	at hudson.plugins.git.GitSCM.retrieveChanges(GitSCM.java:847)
	at hudson.plugins.git.GitSCM.checkout(GitSCM.java:872)
	at hudson.model.AbstractProject.checkout(AbstractProject.java:1411)
	at hudson.model.AbstractBuild$AbstractBuildExecution.defaultCheckout(AbstractBuild.java:652)
	at jenkins.scm.SCMCheckoutStrategy.checkout(SCMCheckoutStrategy.java:88)
	at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:557)
	at hudson.model.Run.execute(Run.java:1665)
	at hudson.matrix.MatrixBuild.run(MatrixBuild.java:304)
	at hudson.model.ResourceController.execute(ResourceController.java:88)
	at hudson.model.Executor.run(Executor.java:246)
	at hudson.model.OneOffExecutor.run(OneOffExecutor.java:66)
Caused by: hudson.plugins.git.GitException: java.lang.reflect.InvocationTargetException
	at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:156)
	at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:146)
	at hudson.remoting.UserRequest.perform(UserRequest.java:118)
	at hudson.remoting.UserRequest.perform(UserRequest.java:48)
	at hudson.remoting.Request$2.run(Request.java:326)
	at hudson.remoting.InterceptingExecutorService$1.call(InterceptingExecutorService.java:72)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.jenkinsci.plugins.gitclient.RemoteGitImpl$Invocation.replay(RemoteGitImpl.java:101)
	at org.jenkinsci.plugins.gitclient.RemoteGitImpl$CommandInvocationHandler$1.call(RemoteGitImpl.java:151)
	... 9 more
Caused by: java.lang.UnsupportedOperationException: JGit don't (yet) support pruning during fetch
	at org.jenkinsci.plugins.gitclient.JGitAPIImpl$1.prune(JGitAPIImpl.java:375)
	... 15 more

It looks like JGit 3.3 can now do pruning? "Support fetch.prune and remote.<name>.prune to set prune mode when fetching" - https://wiki.eclipse.org/JGit/New_and_Noteworthy/3.3

Should a new ticket be opened to get this fix applied to the JGit implementation?

Code already exists in the JGit implementation to evaluate the prune implementation that was included in JGit 3.3. Unfortunately, the JGit 3.3 prune removes more branches than command line git. Since that would give incompatible behavior between CliGit and JGit, and CliGit is the reference implementation, the JGit prune at fetch can't be enabled.

Refer to this submission which attempted to use JGit prune with JGit 3.5.2 and confirmed that it is still pruning too many branches.

Thanks for the update. Is there an open ticket I can watch for this feature (rather than commenting on this old one)?

Personally I'd be in favor of a "use this feature with JGit at your own risk" message rather than not supporting prune at all, but I understand your logic.

I've been unwilling to accept incompatible behavior between CliGit and JGit. Use at your own risk seems too risky for a plugin used in over 50 000 installations.

You're welcome to open a separate bug report / enhancement request to track it. That seems like it will make it easier to track, and easier to report the problem to the upstream JGit process.

Created and linked JENKINS-26197.