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When Java indexin job is running the whole workbench is less responsible and in some cases it may cause some memory issues (on complete reindex) that could be difficult to track down. However you can only see its progress by enaling showing system jobs in a process view. Please make this job to appear on default process view configuaration to make it more verbose to the user.
Another reason to do this: Java indexing is started when the project is opened - reasonable. However, for large projects it can go on for a long time. The user may well know that no java files have changed since the last time (or may not care that they have). Fortunately you can just stop the process, but you have to have all of the other system tasks visible to do so.
I do not think this must be changed. If user has an easy access to this job, he/she may cancel it and then after complain that his/her search requests do not work! Only advanced user should be able to cancel this job and so we'll keep it as system one.
(In reply to comment #1) > Another reason to do this: Java indexing is started when the project is opened > - reasonable. However, for large projects it can go on for a long time. The > user may well know that no java files have changed since the last time (or may > not care that they have). Fortunately you can just stop the process, but you > have to have all of the other system tasks visible to do so. > As indexing store the results in files, only changed/added files are re-indexed. So, no specific indexing should occur at the startup. If you notice unexpected indexing during the startup sequence, then please open a specific bug.