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See also bugtraq bug 4463066. After Autoupdate, the updated restarts the IDE. New modules are installed and the IDE updates the installedmodules.xml file. The modules may also update the IDE Global Options, they may for example add new loaders and specify order of these loaders relative to other loaders. However, this information is not saved until the IDE is closed. So when the IDE is closed forcibly, this information is 'out of sync' with the installedmodules.xml. When the IDE starts the next time, the order of loaders may not respect the relative constraints provided by module.
Moving to projects.
Anybody solving this, please see issue #8958 as well.
We are going to reimplement Data Loaders subsystem to be more extensible and declarative, new storage should fulfill requirement from this issue. Please, see the progress of issue #16389. *** This issue has been marked as a duplicate of 16389 ***
This is no duplicate, though it may be blocked by another issue.
In fact such problems should be fixed by now (at least for 4.0, possibly for 3.4 too). All loaders are stored to loaders.ser and relative constraints in the loader pool are always checked at startup. Reopen if you have any reason to believe otherwise. Note that loader storage is done entirely by core at the moment; projects module is not involved.
Verified.