Sonarlint (3.1)/SonarQube(5.6.6) on Eclipse (neon) not checking Java files

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I have a workspace that I want to analyze with my rules configured on the SonarQube server. The code in the workspace is not in any code repository (so far).

So I installed SonarLint(3.1) in Eclipse(neon3 but same issues in edit: neon2), but did not get any reports. In fact when at some point I saw a log, it said for a project with over 50+ Java files, it would check only 8 files.

The java projects are maven projects and the code is stored under src/main/java/com/....some package ... /SomeFile.java

The same result appears whether in unconnected mode, or in connected mode, connected to a server-side project with Java measures ("SonarQube way" selected).

So I can't right now use SonarLint at all with Eclipse!

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