I have resolved this issue by adding the following rule to local_rules.xml.
<rule id="100014" level="0">
<description>Ignoring NodeBB (socket.io).</description>
since node module folder is in gitignore how will custom theme changes be pushed in branch? because when I run git status no file changes are shown but in fact I have modified css and fonts.
You should have the theme in it's own git repository, then pull and link that repository into node_modules when you deploy.