During upgrade of Jenkins, and when using the "Install without restart" button in pluginManager/available, something removes all executable flags on the "jenkinsdata/plugins" directory (and sometimes plugin subdirectories). For example from 775 to 664.

This makes the plugin installation fail. The same seems to happen during upgrades, i.e. the plugins directory changes and then almost all plugin initializations fail (understandably).

An example stackdump attached.

Note that we have had these problems for a long time, at least since version 1.5xx. We've regularly tried upgrading to new versions but have seen these problems time and again. The only way I could make it repeatable was selecting a plugin (the Active Directory plugin in the example, but I think it could be just about any plugin) and selecting the "Install without restart". Shortly afterwards, the exec flags disappear and then the plugin installation fails.

Unfortunately, the jenkins server is not accessible from the net, so no URL...