Hi Mark,
There are several things going on here.
First, your final log line holds a key clue: forced language 'java'
You have apparently included in your analysis configuration: sonar.language=java. Doing so disables multi-language analysis and thus forces the analysis to ignore files that don't correspond to the selected language.
But even if you hadn't forced a language, it appears that your project has been explicitly configured to exclude certain patterns, e.g. **/*.pdf. That's typically done via the UI by a project administrator.
But even if exclusions hadn't been configured, those files would probably still be ignored, because as far as I know, there aren't analyzers than handle .pdf, .png, and .sh files. File extensions that aren't "claimed" by a language analyzer are ignored by default, altho I don't believe that would show up in the log.
HTH,
Ann