I have .classpath in my gitignore and generate it for each project I work on. This makes autocomplete-java not do anything at all.
I have tracked the issue to this offending line which uses atom.workspace.scan. This doesn't match ignored files. This was introduced in f6947d9.
Taking my .classpath out of .gitignore and everything refreshes as expected.
Is there a reason for using atom.workspace.scan ?