[BUG]: ECJ appears to flush custom JavaFileManager objects repeatedly

Follow up of https://github.com/eclipse-jdt/eclipse.jdt.core/issues/958#issuecomment-2563734737, as requested by @stephan-herrmann.

It appears that when using a custom JavaFileManager implementation, the call to `.flush` at the end of the compilation run is repeated numerous times. It seems to vary depending on what the project is doing but for less than a dozen source files, I have observed it being called more than 20 times in a row.