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Creating a submodule with --name with git client is problematic to jGit UpdateCommand that ignores the submodule. For example: [submodule "my-name"] path = src/main/webapp/WEB-INF/conf/my-name url = ssh://myrepository is ignored, while [submodule "src/main/webapp/WEB-INF/conf/my-name"] path = src/main/webapp/WEB-INF/conf/my-name url = ssh://myrepository is processed without problems. Due to this, using custom name, Eclipse can't see the submodule.