I have upgraded from 4.X to 5.0.1 but made some changes in setenv.sh in 4.x version. where should it go now in 5.0.1 ?
Check the release notes. See "Removal of setenv.sh & setenv.bat".
There is a table with the new locations of the environment variables.
https://confluence.atlassian.com/bitbucketserver/bitbucket-server-5-0-release-notes-889528342.html
Maybe it helps.
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