I have many modules in intellij (checked out from SCM) and intellij is slow on many actions (indexing,make etc'...) I got a suggestion to ignore the maven project by right click pom.xml and then clicking that:
.
What is it going to do? what is the difference between ignore and remove?
Since I have many modules I want to do it from command line. Are these settings stored in files?
Take a look at the IntelliJ docs, particularly the Maven Projects Tool Window.
Ignore Project / Unignore Project - Choose the Ignore Projects command to ignore project in build, or, on the contrary, include in build the previously ignored project. Ignored projects are not imported into IntelliJ IDEA.
Remove Project - Choose this command to delete the selected Maven modules from the Maven structure. So doing you can opt to delete the corresponding Maven module from the IntelliJ IDEA project as well.
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