Hooks are not being called when core.hookspath is configured in system or user level git config file

Symptoms

• Pull requests are not being updated when the source or target branch is updated
• Configured repository hooks are not being enforced when updates are pushed to a repository
• Branch permissions are not being enforced when updates are pushed to a repository

The atlassian-bitbucket.log contains this message:

2018-02-08 10:17:33,857 WARN  [http-nio-7990-exec-9] admin @X98WX6x617x66x0 127.0.0.1 "POST /scm/test/test.git/git-receive-pack HTTP/1.1" c.a.s.i.s.g.p.http.HttpReceivePack TEST/test[1]: Git hooks have not been called. Please verify that the hooks are configured correctly - see https://confluence.atlassian.com/display/BITBUCKETSERVERKB/Git+hook+scripts+are+not+executing?utm_campaign=in-app-help&utm_medium=in-app-help&utm_source=stash for details

Summary
The symptoms described above indicate that the repository hooks in Bitbucket's repositories are not being called. This can have a variety of reasons (e.g. hooks being manually overwritten, hooks not being executable). More information about possible causes and ways to resolve them can be found in this Knowledge Base article.

This problem also occurs when the core.hooksPath setting (supported in git 2.9 and higher) is configured in the ~/.gitconfig file of the Bitbucket (service) user, or in the system-wide /etc/gitconfig configuration file, Bitbucket Server's repository hooks are no longer called.

Bitbucket should override the core.hooksPath setting in its shared/config/git/system-config to ensure its own hooks are called.

Workaround
Remove the core.hooksPath setting from the Bitbucket user's ~/.gitconfig and/or the system-wide /etc/gitconfig.