So i have multiple folders inside a empty IDEA project and each folder has a pom.xml.
I need to deploy each folder separately but gitlab ci only recognize the main folder which is the empty project.
If I understand your achitecture well, you should have a separate git repository for each of your folders in the parent IDEA project.
It would look like that :
/rootProject
|- gitRepo1
|- .gitlab-ci.yml
|- gitRepo2
|- .gitlab-ci.yml
|- gitRepo3
|- .gitlab-ci.yml
This way you can have separate CI pipelines and deployments for each subfolder.
There is an open issue considering the possibility to change the default location of the .gitlab-ci.yml file, but it is not yet available : https://gitlab.com/gitlab-org/gitlab-ce/issues/15041
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