Pretty simple problem, but can't find a solution. Mostly because most of examples of reading web.config asks to use web application name, which is empty string for central administration. So is there any solution which would help access web.config file from timerjob?

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The owstimer is a separate executable and runs as a separate process. So it does not look at the web.config for any specific web application. You have to add the configuration to the owstimer.exe.config in the 14\BIN directory. This config follows all the same semantics of the web.config so you can add appSettings etc just like you would to your web.config.

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