SONAR-8623, some files might be indexed and yet they should not be written in the report and published.
Ideally, we should only include them if:
- Sensor explicitly marks the file as source to publish with a new method in the API: sensorContext.markForPublishing(inputFile)
- Sensor saves any data concerning a file (issues, highlighting, ...)
Directories should be included in the report only if they have files to be published under them or if they contain issues.