Pull request diffs fail for repositories with submodules in directories other than the root

2017-08-30 12:12:12,121 INFO  [http-nio-7990-exec-1] user @3J8EQFx370x444444x4 2zzzzz2 1.1.1.1 "GET /rest/api/latest/projects/KEY/repos/slug/pull-requests/1/merge HTTP/1.1" c.a.s.i.s.g.p.DefaultPullRequestAutoMergeStrategy KEY/slug[1]: Pull request 1@1 failed automatic merging
com.atlassian.bitbucket.scm.MergeException: The merge could not be completed automatically. Please clone 'KEY/slug', checkout 'master' and merge 'submodule-branch' (or commit '3b0b26edc4b62877663ab1fe5d04069d00319771') manually, resolving any conflicts, and push the result.
	at com.atlassian.stash.internal.scm.git.merge.MergeCommand.newMergeException(MergeCommand.java:172)
	at com.atlassian.stash.internal.scm.git.merge.MergeCommand.doWithWorkTree(MergeCommand.java:166)
	at com.atlassian.stash.internal.scm.git.merge.MergeCommand.call(MergeCommand.java:68)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestAutoMergeStrategy.doMerge(DefaultPullRequestAutoMergeStrategy.java:104)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestAutoMergeStrategy.merge(DefaultPullRequestAutoMergeStrategy.java:72)
	at com.atlassian.stash.internal.scm.git.pull.CompositePullRequestAutoMergeStrategy.merge(CompositePullRequestAutoMergeStrategy.java:22)
	at com.atlassian.stash.internal.scm.git.pull.CachingPullRequestAutoMergeStrategy.merge(CachingPullRequestAutoMergeStrategy.java:49)
	at com.atlassian.stash.internal.scm.git.pull.CompositePullRequestAutoMergeStrategy.merge(CompositePullRequestAutoMergeStrategy.java:22)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper.resolveNewEffectiveDiff(DefaultPullRequestRefHelper.java:425)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper.access$500(DefaultPullRequestRefHelper.java:53)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper$EffectiveDiffOperation.perform(DefaultPullRequestRefHelper.java:545)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper$EffectiveDiffOperation.perform(DefaultPullRequestRefHelper.java:510)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper$AbstractOperation.perform(DefaultPullRequestRefHelper.java:476)
	at com.atlassian.stash.internal.concurrent.ClusterMappedLock.withLock(ClusterMappedLock.java:49)
	at com.atlassian.stash.internal.concurrent.ClusterPullRequestLock.withLock(ClusterPullRequestLock.java:25)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper.withLock(DefaultPullRequestRefHelper.java:458)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper.access$300(DefaultPullRequestRefHelper.java:53)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper$EffectiveDiffOperation.call(DefaultPullRequestRefHelper.java:522)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper$EffectiveDiffOperation.call(DefaultPullRequestRefHelper.java:510)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at com.atlassian.util.concurrent.ConcurrentOperationMapImpl$CallerRunsFuture.get(ConcurrentOperationMapImpl.java:63)
	at com.atlassian.util.concurrent.ConcurrentOperationMapImpl.runOperation(ConcurrentOperationMapImpl.java:51)
	at com.atlassian.stash.internal.scm.git.pull.DefaultPullRequestRefHelper.resolveEffectiveDiff(DefaultPullRequestRefHelper.java:132)
	at com.atlassian.stash.internal.scm.git.DefaultGitPullRequestCommandFactory$2.call(DefaultGitPullRequestCommandFactory.java:181)
	at com.atlassian.stash.internal.scm.git.DefaultGitPullRequestCommandFactory$2.call(DefaultGitPullRequestCommandFactory.java:177)
	at com.atlassian.stash.internal.pull.DefaultMergeRequestCheckService.tryMerge(DefaultMergeRequestCheckService.java:70)
	at com.atlassian.stash.internal.pull.DefaultMergeRequestCheckService.checkMergeability(DefaultMergeRequestCheckService.java:47)
	at com.atlassian.stash.internal.pull.DefaultPullRequestService.canMerge(DefaultPullRequestService.java:246)
	at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26)
	at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:56)
	at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:60)
	at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:70)
	at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:53)
	at org.eclipse.gemini.blueprint.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:57)
	at com.atlassian.stash.internal.rest.pull.PullRequestResource.canMerge(PullRequestResource.java:480)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:24)
	at com.atlassian.analytics.client.filter.UniversalAnalyticsFilter.doFilter(UniversalAnalyticsFilter.java:92)
	at com.atlassian.analytics.client.filter.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:39)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.plugin.connect.plugin.auth.scope.ApiScopingFilter.doFilter(ApiScopingFilter.java:81)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.spring.security.StashAuthenticationFilter.doFilter(StashAuthenticationFilter.java:88)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doInsideSpringSecurityChain(BeforeLoginPluginAuthenticationFilter.java:112)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doFilter(BeforeLoginPluginAuthenticationFilter.java:75)
	at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:94)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:67)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.plugin.connect.plugin.auth.user.ThreeLeggedAuthFilter.doFilter(ThreeLeggedAuthFilter.java:109)
	at com.atlassian.jwt.internal.servlet.JwtAuthFilter.doFilter(JwtAuthFilter.java:32)
	at com.atlassian.analytics.client.filter.DefaultAnalyticsFilter.doFilter(DefaultAnalyticsFilter.java:38)
	at com.atlassian.analytics.client.filter.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:39)
	at com.atlassian.stash.internal.spring.lifecycle.LifecycleJohnsonServletFilterModuleContainerFilter.doFilter(LifecycleJohnsonServletFilterModuleContainerFilter.java:42)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doBeforeBeforeLoginFilters(BeforeLoginPluginAuthenticationFilter.java:90)
	at com.atlassian.stash.internal.web.auth.BeforeLoginPluginAuthenticationFilter.doFilter(BeforeLoginPluginAuthenticationFilter.java:73)
	at com.atlassian.stash.internal.request.DefaultRequestManager.doAsRequest(DefaultRequestManager.java:89)
	at com.atlassian.stash.internal.hazelcast.ConfigurableWebFilter.doFilter(ConfigurableWebFilter.java:38)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.lang.Thread.run(Thread.java:745)
	... 307 frames trimmed
Caused by: java.lang.IllegalStateException: Could not create conflict file for submodule in path: path/to/submodule
	at com.atlassian.stash.internal.scm.git.pull.MergeConflictHandler.visit(MergeConflictHandler.java:219)
	at com.atlassian.bitbucket.scm.git.command.merge.conflict.SubmoduleGitMergeConflict.accept(SubmoduleGitMergeConflict.java:19)
	at com.atlassian.stash.internal.scm.git.pull.PullRequestAutoMergeCommand.handleConflicts(PullRequestAutoMergeCommand.java:190)
	at com.atlassian.stash.internal.scm.git.pull.PullRequestAutoMergeCommand.commitConflicts(PullRequestAutoMergeCommand.java:128)
	at com.atlassian.stash.internal.scm.git.pull.PullRequestAutoMergeCommand.doMerge(PullRequestAutoMergeCommand.java:106)
	at com.atlassian.stash.internal.scm.git.merge.MergeCommand.doWithWorkTree(MergeCommand.java:126)
	... 61 common frames omitted